Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 12:45:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/04_2023/8fhr_29100_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/04_2023/8fhr_29100.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/04_2023/8fhr_29100_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/04_2023/8fhr_29100_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/04_2023/8fhr_29100_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/04_2023/8fhr_29100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/04_2023/8fhr_29100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/04_2023/8fhr_29100_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/04_2023/8fhr_29100_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.063 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: 7 Type Number sf(0) Gaussians S 48 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 4836 2.51 5 N 1144 2.21 5 O 1268 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ASP 366": "OD1" <-> "OD2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7306 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3627 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain: "B" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3627 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' NA': 1, 'XZF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' NA': 1, 'XZF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.25, per 1000 atoms: 0.58 Number of scatterers: 7306 At special positions: 0 Unit cell: (89.44, 104.06, 95.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 48 16.00 Na 2 11.00 F 6 9.00 O 1268 8.00 N 1144 7.00 C 4836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.0 seconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 0 sheets defined 66.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 154 through 157 No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 167 through 195 removed outlier: 3.731A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 removed outlier: 4.278A pdb=" N LEU A 206 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 210 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 211 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 249 removed outlier: 3.540A pdb=" N GLY A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 277 removed outlier: 3.759A pdb=" N GLY A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 removed outlier: 3.848A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 340 through 351 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 367 through 393 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 454 through 483 removed outlier: 4.333A pdb=" N LEU A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 477 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 479 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 480 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN A 481 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 522 removed outlier: 4.080A pdb=" N LEU A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 552 removed outlier: 3.586A pdb=" N PHE A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.657A pdb=" N VAL A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 167 through 195 removed outlier: 3.730A pdb=" N THR B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 removed outlier: 4.277A pdb=" N LEU B 206 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 210 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 249 removed outlier: 3.539A pdb=" N GLY B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 277 removed outlier: 3.984A pdb=" N ARG B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 305 removed outlier: 3.848A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 340 through 351 Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 367 through 393 Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 454 through 484 removed outlier: 4.332A pdb=" N LEU B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER B 467 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 476 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 477 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 478 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 479 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 480 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN B 481 " --> pdb=" O LYS B 478 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS B 484 " --> pdb=" O GLN B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 522 removed outlier: 4.079A pdb=" N LEU B 511 " --> pdb=" O ARG B 507 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 552 removed outlier: 3.587A pdb=" N PHE B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 539 " --> pdb=" O PHE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 584 removed outlier: 3.656A pdb=" N VAL B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 604 406 hydrogen bonds defined for protein. 1080 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: 1.83 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1099 1.31 - 1.44: 2157 1.44 - 1.56: 4172 1.56 - 1.69: 4 1.69 - 1.81: 72 Bond restraints: 7504 Sorted by residual: bond pdb=" C ASN A 149 " pdb=" O ASN A 149 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.29e-02 6.01e+03 1.41e+01 bond pdb=" C ASN B 149 " pdb=" O ASN B 149 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.29e-02 6.01e+03 1.39e+01 bond pdb=" CA ASN B 149 " pdb=" C ASN B 149 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.37e-02 5.33e+03 1.33e+01 bond pdb=" CA ASN A 149 " pdb=" C ASN A 149 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.37e-02 5.33e+03 8.65e+00 bond pdb=" C16 XZF B1101 " pdb=" C17 XZF B1101 " ideal model delta sigma weight residual 1.368 1.315 0.053 2.00e-02 2.50e+03 6.99e+00 ... (remaining 7499 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.79: 137 105.79 - 113.03: 4075 113.03 - 120.27: 3046 120.27 - 127.52: 2913 127.52 - 134.76: 85 Bond angle restraints: 10256 Sorted by residual: angle pdb=" C ASP A 255 " pdb=" N PRO A 256 " pdb=" CA PRO A 256 " ideal model delta sigma weight residual 119.82 116.16 3.66 9.80e-01 1.04e+00 1.39e+01 angle pdb=" C ALA B 251 " pdb=" N PRO B 252 " pdb=" CA PRO B 252 " ideal model delta sigma weight residual 119.84 115.19 4.65 1.25e+00 6.40e-01 1.39e+01 angle pdb=" O LEU A 148 " pdb=" C LEU A 148 " pdb=" N ASN A 149 " ideal model delta sigma weight residual 122.27 117.88 4.39 1.23e+00 6.61e-01 1.27e+01 angle pdb=" C ILE B 257 " pdb=" CA ILE B 257 " pdb=" CB ILE B 257 " ideal model delta sigma weight residual 111.88 107.59 4.29 1.28e+00 6.10e-01 1.12e+01 angle pdb=" CA LEU A 148 " pdb=" C LEU A 148 " pdb=" N ASN A 149 " ideal model delta sigma weight residual 117.72 122.08 -4.36 1.31e+00 5.83e-01 1.11e+01 ... (remaining 10251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 3868 16.41 - 32.83: 308 32.83 - 49.24: 66 49.24 - 65.65: 14 65.65 - 82.06: 8 Dihedral angle restraints: 4264 sinusoidal: 1554 harmonic: 2710 Sorted by residual: dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sinusoidal sigma weight residual -86.00 -168.06 82.06 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 421 " pdb=" CB CYS B 421 " ideal model delta sinusoidal sigma weight residual -86.00 -168.05 82.05 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS B 430 " pdb=" SG CYS B 430 " pdb=" SG CYS B 436 " pdb=" CB CYS B 436 " ideal model delta sinusoidal sigma weight residual 93.00 130.56 -37.56 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 4261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 694 0.041 - 0.081: 379 0.081 - 0.122: 103 0.122 - 0.163: 13 0.163 - 0.204: 3 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA ASN A 149 " pdb=" N ASN A 149 " pdb=" C ASN A 149 " pdb=" CB ASN A 149 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ARG A 399 " pdb=" N ARG A 399 " pdb=" C ARG A 399 " pdb=" CB ARG A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA ARG B 399 " pdb=" N ARG B 399 " pdb=" C ARG B 399 " pdb=" CB ARG B 399 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1189 not shown) Planarity restraints: 1246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 148 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C LEU A 148 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 148 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 149 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 330 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO B 331 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 330 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO A 331 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " -0.026 5.00e-02 4.00e+02 ... (remaining 1243 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2141 2.81 - 3.33: 6978 3.33 - 3.86: 11761 3.86 - 4.38: 14041 4.38 - 4.90: 24275 Nonbonded interactions: 59196 Sorted by model distance: nonbonded pdb=" O LEU B 148 " pdb="NA NA B1102 " model vdw 2.289 2.470 nonbonded pdb=" O LEU A 148 " pdb="NA NA A1102 " model vdw 2.289 2.470 nonbonded pdb=" OG SER B 468 " pdb="NA NA B1102 " model vdw 2.304 2.470 nonbonded pdb=" O ALA A 464 " pdb="NA NA A1102 " model vdw 2.304 2.470 nonbonded pdb=" OG SER A 468 " pdb="NA NA A1102 " model vdw 2.304 2.470 ... (remaining 59191 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' 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 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.300 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.530 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.009 0.053 7504 Z= 0.553 Angle : 0.819 9.762 10256 Z= 0.439 Chirality : 0.049 0.204 1192 Planarity : 0.005 0.047 1246 Dihedral : 13.014 76.398 2528 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.25), residues: 946 helix: -0.34 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.57 (0.30), residues: 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.733 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 95 average time/residue: 0.8620 time to fit residues: 88.4032 Evaluate side-chains 77 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.9920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.0670 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 359 ASN A 481 GLN A 526 ASN B 359 ASN B 481 GLN B 526 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 7504 Z= 0.155 Angle : 0.502 7.339 10256 Z= 0.259 Chirality : 0.038 0.133 1192 Planarity : 0.004 0.041 1246 Dihedral : 4.748 32.418 1020 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.27), residues: 946 helix: 0.74 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.721 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 96 average time/residue: 0.8794 time to fit residues: 91.2450 Evaluate side-chains 76 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.1649 time to fit residues: 3.5962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN B 299 ASN B 526 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 7504 Z= 0.186 Angle : 0.500 6.124 10256 Z= 0.253 Chirality : 0.039 0.132 1192 Planarity : 0.004 0.037 1246 Dihedral : 4.469 32.430 1020 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.27), residues: 946 helix: 0.86 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -2.05 (0.32), residues: 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.836 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 82 average time/residue: 0.9127 time to fit residues: 81.5691 Evaluate side-chains 76 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.3702 time to fit residues: 3.9793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 526 ASN B 526 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 7504 Z= 0.233 Angle : 0.520 5.962 10256 Z= 0.262 Chirality : 0.040 0.130 1192 Planarity : 0.004 0.036 1246 Dihedral : 4.500 33.826 1020 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 2.35 % 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: -0.08 (0.27), residues: 946 helix: 0.90 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.02 (0.31), residues: 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.714 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 78 average time/residue: 0.8905 time to fit residues: 75.1458 Evaluate side-chains 77 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.0653 time to fit residues: 1.3459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7504 Z= 0.203 Angle : 0.494 5.350 10256 Z= 0.249 Chirality : 0.039 0.132 1192 Planarity : 0.004 0.034 1246 Dihedral : 4.352 33.261 1020 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 946 helix: 1.03 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.93 (0.31), residues: 318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.893 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 77 average time/residue: 0.9170 time to fit residues: 76.5409 Evaluate side-chains 74 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0678 time to fit residues: 1.2578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 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 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 7504 Z= 0.277 Angle : 0.537 5.623 10256 Z= 0.270 Chirality : 0.041 0.130 1192 Planarity : 0.004 0.034 1246 Dihedral : 4.521 34.556 1020 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 2.22 % 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: -0.00 (0.27), residues: 946 helix: 0.93 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.91 (0.31), residues: 318 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.790 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.9733 time to fit residues: 84.8245 Evaluate side-chains 80 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.0967 time to fit residues: 1.5608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 7504 Z= 0.145 Angle : 0.452 5.192 10256 Z= 0.230 Chirality : 0.037 0.134 1192 Planarity : 0.003 0.034 1246 Dihedral : 4.113 31.261 1020 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 1.44 % 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: 0.41 (0.27), residues: 946 helix: 1.30 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.86 (0.31), residues: 318 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.728 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.8538 time to fit residues: 68.6135 Evaluate side-chains 74 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.5421 time to fit residues: 2.2174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 526 ASN B 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 7504 Z= 0.170 Angle : 0.466 5.247 10256 Z= 0.236 Chirality : 0.038 0.131 1192 Planarity : 0.003 0.034 1246 Dihedral : 4.086 30.896 1020 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.17 % 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: 0.53 (0.27), residues: 946 helix: 1.33 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -1.72 (0.32), residues: 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.810 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 76 average time/residue: 0.8830 time to fit residues: 73.1445 Evaluate side-chains 77 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.6541 time to fit residues: 2.5045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 66 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 7504 Z= 0.137 Angle : 0.436 5.231 10256 Z= 0.221 Chirality : 0.037 0.136 1192 Planarity : 0.003 0.033 1246 Dihedral : 3.879 28.873 1020 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.17 % 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: 0.74 (0.28), residues: 946 helix: 1.48 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -1.62 (0.32), residues: 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.841 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 80 average time/residue: 0.8723 time to fit residues: 75.6439 Evaluate side-chains 80 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.2168 time to fit residues: 1.3905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 526 ASN B 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 7504 Z= 0.161 Angle : 0.453 5.259 10256 Z= 0.229 Chirality : 0.038 0.133 1192 Planarity : 0.003 0.032 1246 Dihedral : 3.896 28.651 1020 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.91 % 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: 0.82 (0.28), residues: 946 helix: 1.54 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -1.59 (0.32), residues: 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.860 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 79 average time/residue: 0.8787 time to fit residues: 75.4804 Evaluate side-chains 79 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.0556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.0770 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.145307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.104112 restraints weight = 7890.869| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.96 r_work: 0.2922 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 7504 Z= 0.147 Angle : 0.441 5.250 10256 Z= 0.224 Chirality : 0.038 0.135 1192 Planarity : 0.003 0.032 1246 Dihedral : 3.842 28.057 1020 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.17 % 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: 0.92 (0.28), residues: 946 helix: 1.61 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -1.53 (0.32), residues: 312 =============================================================================== Job complete usr+sys time: 2249.44 seconds wall clock time: 40 minutes 55.91 seconds (2455.91 seconds total)