Starting phenix.real_space_refine on Fri Nov 15 10:18:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flq_29283/11_2024/8flq_29283.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flq_29283/11_2024/8flq_29283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flq_29283/11_2024/8flq_29283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flq_29283/11_2024/8flq_29283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flq_29283/11_2024/8flq_29283.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flq_29283/11_2024/8flq_29283.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.070 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 58 5.16 5 C 5709 2.51 5 N 1569 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8992 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1906 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2568 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 424 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 269 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2858 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 3 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 5.74, per 1000 atoms: 0.64 Number of scatterers: 8992 At special positions: 0 Unit cell: (72.8, 96.2, 173.55, 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 58 16.00 O 1656 8.00 N 1569 7.00 C 5709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 43.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.567A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.504A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.592A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.257A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.120A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.851A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.517A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 25 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 53 Processing helix chain 'R' and resid 167 through 172 removed outlier: 4.053A pdb=" N LYS R 172 " --> pdb=" O GLU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 4.482A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 246 removed outlier: 3.588A pdb=" N SER R 246 " --> pdb=" O ALA R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.529A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.538A pdb=" N TYR R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.516A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 359 Processing helix chain 'R' and resid 360 through 392 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.385A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 479 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.345A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.549A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.292A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.235A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.551A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.093A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.562A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.674A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.619A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.664A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 494 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.67 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: 2941 1.34 - 1.46: 2250 1.46 - 1.58: 3904 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9177 Sorted by residual: bond pdb=" N VAL B 187 " pdb=" CA VAL B 187 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.17e-02 7.31e+03 7.88e+00 bond pdb=" N SER B 160 " pdb=" CA SER B 160 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.91e+00 bond pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.89e+00 bond pdb=" N THR B 165 " pdb=" CA THR B 165 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.29e-02 6.01e+03 6.62e+00 bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.531 1.491 0.040 1.56e-02 4.11e+03 6.62e+00 ... (remaining 9172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 12017 1.37 - 2.75: 349 2.75 - 4.12: 65 4.12 - 5.49: 12 5.49 - 6.87: 4 Bond angle restraints: 12447 Sorted by residual: angle pdb=" N GLY B 162 " pdb=" CA GLY B 162 " pdb=" C GLY B 162 " ideal model delta sigma weight residual 114.67 109.69 4.98 1.10e+00 8.26e-01 2.05e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 113.19 108.03 5.16 1.19e+00 7.06e-01 1.88e+01 angle pdb=" C ILE R 190 " pdb=" N TYR R 191 " pdb=" CA TYR R 191 " ideal model delta sigma weight residual 121.14 114.27 6.87 1.75e+00 3.27e-01 1.54e+01 angle pdb=" N TYR B 59 " pdb=" CA TYR B 59 " pdb=" C TYR B 59 " ideal model delta sigma weight residual 113.41 109.21 4.20 1.22e+00 6.72e-01 1.19e+01 angle pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 113.90 120.00 -6.10 1.80e+00 3.09e-01 1.15e+01 ... (remaining 12442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4907 17.66 - 35.32: 415 35.32 - 52.98: 64 52.98 - 70.63: 16 70.63 - 88.29: 9 Dihedral angle restraints: 5411 sinusoidal: 2081 harmonic: 3330 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 143.52 -50.52 1 1.00e+01 1.00e-02 3.50e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 970 0.039 - 0.077: 308 0.077 - 0.116: 87 0.116 - 0.155: 18 0.155 - 0.193: 3 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CB ILE R 190 " pdb=" CA ILE R 190 " pdb=" CG1 ILE R 190 " pdb=" CG2 ILE R 190 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA VAL B 187 " pdb=" N VAL B 187 " pdb=" C VAL B 187 " pdb=" CB VAL B 187 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.96e-01 ... (remaining 1383 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 376 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C ILE R 376 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE R 376 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU R 377 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 378 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C PHE R 378 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE R 378 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE R 379 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 377 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C LEU R 377 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU R 377 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE R 378 " -0.010 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 926 2.75 - 3.29: 9083 3.29 - 3.82: 16195 3.82 - 4.36: 19609 4.36 - 4.90: 32721 Nonbonded interactions: 78534 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.254 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.259 3.040 nonbonded pdb=" OE1 GLU R 302 " pdb=" O HOH R 701 " model vdw 2.265 3.040 ... (remaining 78529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9177 Z= 0.215 Angle : 0.569 6.865 12447 Z= 0.352 Chirality : 0.042 0.193 1386 Planarity : 0.004 0.036 1588 Dihedral : 13.874 88.292 3241 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.21 % Allowed : 0.53 % Favored : 99.25 % 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: 1.35 (0.25), residues: 1124 helix: 2.39 (0.24), residues: 443 sheet: -0.26 (0.33), residues: 214 loop : 0.08 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.021 0.001 PHE R 335 TYR 0.013 0.001 TYR A 358 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.990 Fit side-chains REVERT: R 32 MET cc_start: 0.4510 (ptt) cc_final: 0.4234 (tpp) outliers start: 2 outliers final: 2 residues processed: 128 average time/residue: 1.3220 time to fit residues: 180.5088 Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 101 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN N 84 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9177 Z= 0.157 Angle : 0.486 5.915 12447 Z= 0.272 Chirality : 0.041 0.175 1386 Planarity : 0.004 0.035 1588 Dihedral : 4.388 23.868 1250 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.75 % Allowed : 7.46 % Favored : 91.79 % 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: 1.69 (0.26), residues: 1124 helix: 2.90 (0.24), residues: 438 sheet: -0.34 (0.31), residues: 231 loop : 0.22 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.010 0.001 HIS A 357 PHE 0.022 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 1.022 Fit side-chains REVERT: A 296 LEU cc_start: 0.6791 (tp) cc_final: 0.6580 (tt) REVERT: R 32 MET cc_start: 0.4479 (ptt) cc_final: 0.4241 (tpp) outliers start: 7 outliers final: 5 residues processed: 120 average time/residue: 1.1950 time to fit residues: 154.0758 Evaluate side-chains 116 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 100 optimal weight: 0.9980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9177 Z= 0.278 Angle : 0.546 6.427 12447 Z= 0.301 Chirality : 0.043 0.189 1386 Planarity : 0.004 0.039 1588 Dihedral : 4.744 24.099 1249 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 10.34 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1124 helix: 2.66 (0.24), residues: 444 sheet: -0.48 (0.31), residues: 238 loop : 0.17 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.014 0.001 HIS A 357 PHE 0.022 0.002 PHE R 335 TYR 0.021 0.002 TYR R 191 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.070 Fit side-chains REVERT: B 215 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6023 (tp30) outliers start: 13 outliers final: 6 residues processed: 121 average time/residue: 1.1707 time to fit residues: 152.5023 Evaluate side-chains 117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 29 optimal weight: 0.0670 chunk 90 optimal weight: 3.9990 overall best weight: 1.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 380 ASN R 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9177 Z= 0.215 Angle : 0.509 6.392 12447 Z= 0.282 Chirality : 0.042 0.201 1386 Planarity : 0.004 0.037 1588 Dihedral : 4.593 23.312 1247 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.39 % Allowed : 11.30 % Favored : 87.31 % 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: 1.47 (0.26), residues: 1124 helix: 2.69 (0.24), residues: 443 sheet: -0.53 (0.31), residues: 239 loop : 0.15 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.010 0.001 HIS A 357 PHE 0.021 0.001 PHE R 335 TYR 0.023 0.002 TYR R 191 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 1.048 Fit side-chains REVERT: B 215 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5982 (tp30) outliers start: 13 outliers final: 6 residues processed: 116 average time/residue: 1.1769 time to fit residues: 146.7420 Evaluate side-chains 114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 471 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9177 Z= 0.286 Angle : 0.546 6.473 12447 Z= 0.301 Chirality : 0.043 0.206 1386 Planarity : 0.004 0.043 1588 Dihedral : 4.773 24.198 1247 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.60 % Allowed : 12.26 % Favored : 86.14 % 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: 1.37 (0.25), residues: 1124 helix: 2.59 (0.24), residues: 443 sheet: -0.55 (0.31), residues: 238 loop : 0.11 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.011 0.001 HIS A 357 PHE 0.023 0.002 PHE R 335 TYR 0.021 0.002 TYR R 191 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.987 Fit side-chains REVERT: B 215 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6023 (tp30) REVERT: B 263 THR cc_start: 0.7255 (m) cc_final: 0.6854 (m) outliers start: 15 outliers final: 7 residues processed: 122 average time/residue: 1.1178 time to fit residues: 146.9699 Evaluate side-chains 119 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.0070 chunk 56 optimal weight: 0.4980 chunk 104 optimal weight: 5.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 380 ASN R 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9177 Z= 0.141 Angle : 0.472 6.837 12447 Z= 0.261 Chirality : 0.040 0.221 1386 Planarity : 0.003 0.037 1588 Dihedral : 4.342 23.221 1247 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.96 % Allowed : 13.65 % Favored : 85.39 % 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: 1.62 (0.26), residues: 1124 helix: 2.91 (0.24), residues: 437 sheet: -0.49 (0.30), residues: 236 loop : 0.19 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.020 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.932 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 116 average time/residue: 1.2068 time to fit residues: 151.7438 Evaluate side-chains 107 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 65 optimal weight: 0.0770 chunk 49 optimal weight: 0.0040 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9177 Z= 0.198 Angle : 0.495 6.668 12447 Z= 0.272 Chirality : 0.041 0.232 1386 Planarity : 0.004 0.039 1588 Dihedral : 4.427 23.154 1247 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.17 % Allowed : 14.07 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1124 helix: 2.83 (0.24), residues: 443 sheet: -0.57 (0.30), residues: 240 loop : 0.20 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.001 PHE R 335 TYR 0.022 0.002 TYR R 191 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.976 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 110 average time/residue: 1.2065 time to fit residues: 142.7254 Evaluate side-chains 107 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 84 optimal weight: 30.0000 chunk 98 optimal weight: 0.0270 chunk 103 optimal weight: 5.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9177 Z= 0.151 Angle : 0.476 6.272 12447 Z= 0.261 Chirality : 0.040 0.235 1386 Planarity : 0.003 0.039 1588 Dihedral : 4.286 22.812 1247 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.64 % Allowed : 14.71 % Favored : 84.65 % 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: 1.68 (0.26), residues: 1124 helix: 2.96 (0.24), residues: 437 sheet: -0.43 (0.31), residues: 237 loop : 0.21 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.009 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 1.167 Fit side-chains REVERT: A 296 LEU cc_start: 0.6714 (tp) cc_final: 0.6452 (tt) outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 1.1125 time to fit residues: 134.7705 Evaluate side-chains 107 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 0.0030 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9177 Z= 0.139 Angle : 0.462 6.239 12447 Z= 0.254 Chirality : 0.040 0.239 1386 Planarity : 0.003 0.042 1588 Dihedral : 4.154 22.200 1247 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.96 % Allowed : 14.50 % Favored : 84.54 % 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: 1.76 (0.26), residues: 1124 helix: 3.03 (0.24), residues: 437 sheet: -0.36 (0.31), residues: 232 loop : 0.22 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.001 Fit side-chains REVERT: A 296 LEU cc_start: 0.6731 (tp) cc_final: 0.6480 (tt) REVERT: B 59 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8280 (t80) REVERT: N 39 GLN cc_start: 0.6889 (tt0) cc_final: 0.6661 (tp40) outliers start: 9 outliers final: 4 residues processed: 118 average time/residue: 1.0719 time to fit residues: 136.6495 Evaluate side-chains 111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9177 Z= 0.185 Angle : 0.493 6.260 12447 Z= 0.270 Chirality : 0.041 0.246 1386 Planarity : 0.004 0.040 1588 Dihedral : 4.332 22.291 1247 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.96 % Allowed : 14.71 % Favored : 84.33 % 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: 1.62 (0.26), residues: 1124 helix: 2.87 (0.24), residues: 444 sheet: -0.50 (0.31), residues: 240 loop : 0.22 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.001 PHE R 335 TYR 0.022 0.002 TYR R 191 ARG 0.010 0.000 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.069 Fit side-chains REVERT: A 296 LEU cc_start: 0.6734 (tp) cc_final: 0.6472 (tt) REVERT: N 39 GLN cc_start: 0.6888 (tt0) cc_final: 0.6662 (tp40) outliers start: 9 outliers final: 5 residues processed: 110 average time/residue: 1.0940 time to fit residues: 130.0250 Evaluate side-chains 108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.188456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140295 restraints weight = 9876.484| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.43 r_work: 0.3496 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9177 Z= 0.335 Angle : 0.584 7.614 12447 Z= 0.318 Chirality : 0.045 0.234 1386 Planarity : 0.004 0.043 1588 Dihedral : 4.844 24.414 1247 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.85 % Allowed : 14.82 % Favored : 84.33 % 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: 1.36 (0.25), residues: 1124 helix: 2.56 (0.24), residues: 444 sheet: -0.57 (0.30), residues: 245 loop : 0.15 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.012 0.002 HIS A 357 PHE 0.022 0.002 PHE R 335 TYR 0.021 0.002 TYR A 358 ARG 0.007 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3353.76 seconds wall clock time: 60 minutes 53.66 seconds (3653.66 seconds total)