Starting phenix.real_space_refine (version: dev) on Mon Dec 12 10:16:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/12_2022/5a63_3061_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/12_2022/5a63_3061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/12_2022/5a63_3061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/12_2022/5a63_3061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/12_2022/5a63_3061_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/12_2022/5a63_3061_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.015 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10003 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 37, 'TRANS': 627} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1702 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 2 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 850 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 6.31, per 1000 atoms: 0.63 Number of scatterers: 10003 At special positions: 0 Unit cell: (91, 147, 95.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 2 15.00 O 1841 8.00 N 1589 7.00 C 6536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.54 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=1.86 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=1.12 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 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A1705 " - " ASN A 387 " " NAG A1712 " - " ASN A 464 " " NAG A1713 " - " ASN A 506 " " NAG A1714 " - " ASN A 264 " " NAG A1715 " - " ASN A 187 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 5.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 5 sheets defined 54.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.579A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 299 through 314 removed outlier: 4.047A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 388 through 407 removed outlier: 3.665A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 removed outlier: 4.147A pdb=" N ALA A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 463 No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 482 through 502 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 542 through 545 Processing helix chain 'A' and resid 562 through 575 removed outlier: 3.515A pdb=" N VAL A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 633 through 636 No H-bonds generated for 'chain 'A' and resid 633 through 636' Processing helix chain 'A' and resid 666 through 692 Processing helix chain 'A' and resid 694 through 697 No H-bonds generated for 'chain 'A' and resid 694 through 697' Processing helix chain 'B' and resid 79 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 168 through 189 removed outlier: 4.219A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 219 through 240 Processing helix chain 'B' and resid 243 through 259 removed outlier: 3.544A pdb=" N ALA B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 405 through 427 Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'C' and resid 3 through 23 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 29 through 60 Processing helix chain 'C' and resid 65 through 102 Processing helix chain 'C' and resid 114 through 142 removed outlier: 3.553A pdb=" N TYR C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 184 removed outlier: 3.500A pdb=" N THR C 172 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 206 removed outlier: 3.631A pdb=" N LEU C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 231 removed outlier: 4.074A pdb=" N LEU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 236 through 243 removed outlier: 3.651A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 5 No H-bonds generated for 'chain 'D' and resid 3 through 5' Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.602A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 43 removed outlier: 4.031A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 84 removed outlier: 3.597A pdb=" N TRP D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 87 through 92 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 removed outlier: 4.633A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 13.686A pdb=" N VAL A 75 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 49 removed outlier: 6.270A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 248 through 250 Processing sheet with id= D, first strand: chain 'A' and resid 627 through 630 removed outlier: 3.802A pdb=" N ASP A 253 " --> pdb=" O ALA A 630 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLY A 366 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.091A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 5.41 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: 1535 1.31 - 1.44: 2969 1.44 - 1.56: 5683 1.56 - 1.69: 15 1.69 - 1.81: 53 Bond restraints: 10255 Sorted by residual: bond pdb=" C21 PC1 C1245 " pdb=" O21 PC1 C1245 " ideal model delta sigma weight residual 1.331 1.462 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C LEU A 422 " pdb=" N PRO A 423 " ideal model delta sigma weight residual 1.329 1.406 -0.077 1.18e-02 7.18e+03 4.20e+01 bond pdb=" C31 PC1 C1245 " pdb=" O31 PC1 C1245 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C21 PC1 B1468 " pdb=" O21 PC1 B1468 " ideal model delta sigma weight residual 1.331 1.459 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C31 PC1 B1468 " pdb=" O31 PC1 B1468 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.93e+01 ... (remaining 10250 not shown) Histogram of bond angle deviations from ideal: 98.55 - 107.29: 446 107.29 - 116.03: 6727 116.03 - 124.77: 6309 124.77 - 133.51: 442 133.51 - 142.25: 42 Bond angle restraints: 13966 Sorted by residual: angle pdb=" N THR A 372 " pdb=" CA THR A 372 " pdb=" C THR A 372 " ideal model delta sigma weight residual 111.14 122.90 -11.76 1.08e+00 8.57e-01 1.18e+02 angle pdb=" N LEU A 370 " pdb=" CA LEU A 370 " pdb=" C LEU A 370 " ideal model delta sigma weight residual 111.14 122.32 -11.18 1.08e+00 8.57e-01 1.07e+02 angle pdb=" N GLU A 161 " pdb=" CA GLU A 161 " pdb=" C GLU A 161 " ideal model delta sigma weight residual 111.14 122.01 -10.87 1.08e+00 8.57e-01 1.01e+02 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 119.78 -9.08 1.22e+00 6.72e-01 5.54e+01 angle pdb=" N GLU A 644 " pdb=" CA GLU A 644 " pdb=" C GLU A 644 " ideal model delta sigma weight residual 112.88 122.45 -9.57 1.29e+00 6.01e-01 5.50e+01 ... (remaining 13961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.65: 5207 20.65 - 41.30: 520 41.30 - 61.95: 205 61.95 - 82.60: 21 82.60 - 103.25: 11 Dihedral angle restraints: 5964 sinusoidal: 2400 harmonic: 3564 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -176.03 90.03 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 180.00 142.45 37.55 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -148.02 62.02 1 1.00e+01 1.00e-02 5.10e+01 ... (remaining 5961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 1610 0.261 - 0.522: 43 0.522 - 0.783: 1 0.783 - 1.044: 0 1.044 - 1.305: 3 Chirality restraints: 1657 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.20e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 435 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.26e+01 chirality pdb=" C1 NAG A1712 " pdb=" ND2 ASN A 464 " pdb=" C2 NAG A1712 " pdb=" O5 NAG A1712 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.05e+01 ... (remaining 1654 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 187 " 0.193 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" CG ASN A 187 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN A 187 " -0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 187 " -0.295 2.00e-02 2.50e+03 pdb=" C1 NAG A1715 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 387 " -0.132 2.00e-02 2.50e+03 1.30e-01 2.11e+02 pdb=" CG ASN A 387 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 387 " 0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 387 " 0.189 2.00e-02 2.50e+03 pdb=" C1 NAG A1705 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 435 " -0.116 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" CG ASN A 435 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 435 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 435 " 0.177 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.134 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 239 2.64 - 3.21: 10007 3.21 - 3.77: 16744 3.77 - 4.34: 21874 4.34 - 4.90: 35662 Nonbonded interactions: 84526 Sorted by model distance: nonbonded pdb=" O GLY A 504 " pdb=" OG1 THR A 505 " model vdw 2.079 2.440 nonbonded pdb=" OD1 ASN A 324 " pdb=" N VAL A 325 " model vdw 2.123 2.520 nonbonded pdb=" OE1 GLU A 186 " pdb=" OG1 THR A 189 " model vdw 2.209 2.440 nonbonded pdb=" O TYR A 645 " pdb=" OG SER A 646 " model vdw 2.228 2.440 nonbonded pdb=" O HIS A 222 " pdb=" OG SER A 651 " model vdw 2.234 2.440 ... (remaining 84521 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 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 35 5.16 5 C 6536 2.51 5 N 1589 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 2.410 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.090 Process input model: 31.500 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3972 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 : 0.010 0.131 10255 Z= 0.646 Angle : 1.681 17.252 13966 Z= 1.205 Chirality : 0.109 1.305 1657 Planarity : 0.008 0.106 1705 Dihedral : 19.250 103.255 3651 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 39.51 Ramachandran Plot: Outliers : 2.15 % Allowed : 6.36 % Favored : 91.49 % Rotamer Outliers : 13.74 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.17 % 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: -0.17 (0.22), residues: 1211 helix: 1.34 (0.17), residues: 672 sheet: -1.51 (0.48), residues: 113 loop : -2.13 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 299 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 53 residues processed: 395 average time/residue: 0.2257 time to fit residues: 122.4982 Evaluate side-chains 257 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 204 time to evaluate : 1.166 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 53 outliers final: 1 residues processed: 53 average time/residue: 0.1419 time to fit residues: 13.3777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 142 ASN A 150 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 367 GLN A 418 GLN A 428 GLN A 449 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 606 GLN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 79 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4028 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 10255 Z= 0.299 Angle : 0.794 11.491 13966 Z= 0.415 Chirality : 0.061 1.278 1657 Planarity : 0.006 0.064 1705 Dihedral : 10.551 103.121 1506 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.79 % Favored : 94.63 % Rotamer Outliers : 5.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.09 % 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 (0.25), residues: 1211 helix: 2.41 (0.20), residues: 681 sheet: -1.42 (0.44), residues: 123 loop : -2.38 (0.28), residues: 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 242 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 28 residues processed: 278 average time/residue: 0.1916 time to fit residues: 76.7028 Evaluate side-chains 220 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.0941 time to fit residues: 6.5216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 chunk 88 optimal weight: 0.8980 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN C 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4048 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 10255 Z= 0.299 Angle : 0.711 10.494 13966 Z= 0.365 Chirality : 0.051 0.780 1657 Planarity : 0.005 0.047 1705 Dihedral : 10.060 102.019 1506 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.45 % Favored : 94.14 % Rotamer Outliers : 5.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.47 (0.25), residues: 1211 helix: 2.10 (0.20), residues: 674 sheet: -1.63 (0.44), residues: 123 loop : -2.22 (0.28), residues: 414 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 219 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 27 residues processed: 260 average time/residue: 0.1997 time to fit residues: 75.2023 Evaluate side-chains 228 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0961 time to fit residues: 6.2694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 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 58 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4060 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 10255 Z= 0.244 Angle : 0.676 10.179 13966 Z= 0.343 Chirality : 0.045 0.296 1657 Planarity : 0.004 0.043 1705 Dihedral : 9.827 102.390 1506 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.20 % Favored : 94.38 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.35 (0.25), residues: 1211 helix: 1.93 (0.20), residues: 665 sheet: -1.52 (0.43), residues: 123 loop : -2.08 (0.29), residues: 423 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 232 average time/residue: 0.2042 time to fit residues: 68.5242 Evaluate side-chains 210 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0954 time to fit residues: 4.5344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4061 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10255 Z= 0.253 Angle : 0.646 7.709 13966 Z= 0.331 Chirality : 0.043 0.269 1657 Planarity : 0.004 0.043 1705 Dihedral : 9.679 102.467 1506 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.28 % Favored : 94.30 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.22 (0.24), residues: 1211 helix: 1.72 (0.19), residues: 672 sheet: -1.64 (0.43), residues: 121 loop : -1.98 (0.29), residues: 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 213 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 236 average time/residue: 0.2010 time to fit residues: 68.9732 Evaluate side-chains 214 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1182 time to fit residues: 6.0922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 38 optimal weight: 0.0060 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN D 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4067 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10255 Z= 0.259 Angle : 0.648 12.956 13966 Z= 0.331 Chirality : 0.045 0.401 1657 Planarity : 0.004 0.041 1705 Dihedral : 9.585 102.593 1506 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.70 % Favored : 93.97 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.17 (0.24), residues: 1211 helix: 1.64 (0.19), residues: 673 sheet: -1.45 (0.44), residues: 119 loop : -1.99 (0.29), residues: 419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 210 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 231 average time/residue: 0.2041 time to fit residues: 68.0088 Evaluate side-chains 215 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1110 time to fit residues: 5.6867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN D 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4072 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 10255 Z= 0.325 Angle : 0.671 11.403 13966 Z= 0.343 Chirality : 0.046 0.341 1657 Planarity : 0.004 0.041 1705 Dihedral : 9.569 102.633 1506 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.45 % Favored : 94.22 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.04 (0.24), residues: 1211 helix: 1.50 (0.19), residues: 673 sheet: -1.36 (0.44), residues: 122 loop : -2.05 (0.29), residues: 416 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 221 average time/residue: 0.2127 time to fit residues: 68.0841 Evaluate side-chains 212 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1027 time to fit residues: 4.4064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 0.0570 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 199 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4067 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 10255 Z= 0.237 Angle : 0.653 13.590 13966 Z= 0.329 Chirality : 0.044 0.375 1657 Planarity : 0.004 0.058 1705 Dihedral : 9.441 102.602 1506 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.78 % Favored : 93.89 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 (0.24), residues: 1211 helix: 1.54 (0.20), residues: 668 sheet: -1.49 (0.45), residues: 107 loop : -1.92 (0.29), residues: 436 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 222 average time/residue: 0.1961 time to fit residues: 63.7134 Evaluate side-chains 209 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 205 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0995 time to fit residues: 2.2336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 102 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4072 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 10255 Z= 0.306 Angle : 0.672 13.151 13966 Z= 0.341 Chirality : 0.045 0.389 1657 Planarity : 0.004 0.042 1705 Dihedral : 9.382 102.928 1506 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.37 % Favored : 94.30 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.03 (0.24), residues: 1211 helix: 1.47 (0.20), residues: 668 sheet: -1.43 (0.44), residues: 126 loop : -1.93 (0.30), residues: 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 204 average time/residue: 0.2010 time to fit residues: 60.2617 Evaluate side-chains 206 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0978 time to fit residues: 4.1286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.0050 chunk 120 optimal weight: 0.0670 chunk 110 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.5534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4071 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 10255 Z= 0.210 Angle : 0.649 14.871 13966 Z= 0.326 Chirality : 0.044 0.464 1657 Planarity : 0.004 0.039 1705 Dihedral : 9.258 102.899 1506 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.53 % Favored : 94.14 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.12 (0.24), residues: 1211 helix: 1.52 (0.20), residues: 668 sheet: -1.60 (0.47), residues: 111 loop : -1.78 (0.29), residues: 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 219 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 221 average time/residue: 0.2006 time to fit residues: 64.6194 Evaluate side-chains 201 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0919 time to fit residues: 1.9636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 17 optimal weight: 0.0870 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 69 optimal weight: 6.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114478 restraints weight = 15149.335| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.43 r_work: 0.3183 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 10255 Z= 0.202 Angle : 0.646 14.491 13966 Z= 0.324 Chirality : 0.044 0.444 1657 Planarity : 0.004 0.043 1705 Dihedral : 9.171 103.353 1506 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.95 % Favored : 94.63 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.18 (0.24), residues: 1211 helix: 1.57 (0.20), residues: 666 sheet: -1.47 (0.47), residues: 113 loop : -1.78 (0.29), residues: 432 =============================================================================== Job complete usr+sys time: 2247.59 seconds wall clock time: 41 minutes 37.13 seconds (2497.13 seconds total)