Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 15:13:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/08_2023/5a63_3061_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/08_2023/5a63_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_3061/08_2023/5a63_3061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/08_2023/5a63_3061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/08_2023/5a63_3061_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/08_2023/5a63_3061_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 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. 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-1.21rc1-5044/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 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: 5.63, per 1000 atoms: 0.56 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: 4.43 Conformation dependent library (CDL) restraints added in 1.3 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: 1.55 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: 2.91 Time building geometry restraints manager: 4.74 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 - 18.01: 4968 18.01 - 36.01: 559 36.01 - 54.02: 229 54.02 - 72.02: 58 72.02 - 90.03: 18 Dihedral angle restraints: 5832 sinusoidal: 2268 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 5829 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 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: 0.360 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: 2.270 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.120 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4049 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 : 1.689 17.252 13966 Z= 1.178 Chirality : 0.109 1.305 1657 Planarity : 0.008 0.106 1705 Dihedral : 19.070 86.887 3519 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 : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 53 residues processed: 395 average time/residue: 0.2332 time to fit residues: 126.1069 Evaluate side-chains 257 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 204 time to evaluate : 1.145 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 53 outliers final: 1 residues processed: 53 average time/residue: 0.1401 time to fit residues: 13.2082 ------------------------------------------------------------------------------- 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 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.4102 moved from start: 0.3018 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= 0.269 Angle : 0.813 10.346 13966 Z= 0.405 Chirality : 0.051 0.367 1657 Planarity : 0.006 0.067 1705 Dihedral : 8.482 71.702 1374 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.79 % Favored : 94.63 % Rotamer Outliers : 5.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.09 % 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: 0.78 (0.25), residues: 1211 helix: 2.44 (0.20), residues: 681 sheet: -1.41 (0.44), residues: 123 loop : -2.36 (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 297 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 240 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 27 residues processed: 276 average time/residue: 0.2001 time to fit residues: 79.2748 Evaluate side-chains 218 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0976 time to fit residues: 6.4795 ------------------------------------------------------------------------------- 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: 6.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4129 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 10255 Z= 0.392 Angle : 0.781 9.613 13966 Z= 0.383 Chirality : 0.048 0.326 1657 Planarity : 0.005 0.047 1705 Dihedral : 8.014 67.227 1374 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.20 % Favored : 94.38 % Rotamer Outliers : 5.73 % 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: 0.32 (0.24), residues: 1211 helix: 1.95 (0.20), residues: 674 sheet: -1.49 (0.44), residues: 122 loop : -2.29 (0.28), residues: 415 *********************** 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 266 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 206 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 29 residues processed: 247 average time/residue: 0.1976 time to fit residues: 70.7114 Evaluate side-chains 222 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.0984 time to fit residues: 6.7153 ------------------------------------------------------------------------------- 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: 2.9990 chunk 82 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 B 464 GLN D 8 ASN D 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4130 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 10255 Z= 0.366 Angle : 0.744 11.635 13966 Z= 0.363 Chirality : 0.048 0.318 1657 Planarity : 0.005 0.044 1705 Dihedral : 7.773 64.567 1374 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.12 % Favored : 94.47 % Rotamer Outliers : 3.34 % 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: 0.07 (0.24), residues: 1211 helix: 1.61 (0.19), residues: 676 sheet: -1.44 (0.43), residues: 122 loop : -2.22 (0.29), residues: 413 *********************** 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 238 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 224 average time/residue: 0.2029 time to fit residues: 65.9526 Evaluate side-chains 200 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1432 time to fit residues: 6.3754 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN B 463 HIS D 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4130 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10255 Z= 0.219 Angle : 0.667 12.549 13966 Z= 0.326 Chirality : 0.044 0.340 1657 Planarity : 0.004 0.042 1705 Dihedral : 7.341 61.908 1374 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.04 % Favored : 94.47 % Rotamer Outliers : 3.72 % 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: 1.70 (0.20), residues: 672 sheet: -1.39 (0.43), residues: 126 loop : -2.12 (0.29), residues: 413 *********************** 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 262 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 223 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 15 residues processed: 245 average time/residue: 0.2036 time to fit residues: 72.2311 Evaluate side-chains 218 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 203 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1166 time to fit residues: 4.5020 ------------------------------------------------------------------------------- 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: 0.7980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 199 HIS A 243 ASN A 462 ASN A 587 GLN B 463 HIS D 8 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4139 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 10255 Z= 0.293 Angle : 0.703 10.833 13966 Z= 0.342 Chirality : 0.046 0.342 1657 Planarity : 0.004 0.039 1705 Dihedral : 7.194 59.042 1374 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.53 % Favored : 94.14 % Rotamer Outliers : 3.44 % 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: 0.04 (0.24), residues: 1211 helix: 1.49 (0.20), residues: 672 sheet: -1.24 (0.44), residues: 122 loop : -2.06 (0.29), residues: 417 *********************** 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: 36 poor density : 206 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 226 average time/residue: 0.1992 time to fit residues: 65.9805 Evaluate side-chains 227 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 202 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0959 time to fit residues: 5.8817 ------------------------------------------------------------------------------- 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: 5.9990 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 587 GLN B 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4146 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.092 10255 Z= 0.342 Angle : 0.717 12.799 13966 Z= 0.350 Chirality : 0.046 0.336 1657 Planarity : 0.004 0.042 1705 Dihedral : 7.129 56.689 1374 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.62 % Favored : 94.05 % Rotamer Outliers : 2.39 % 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: -0.07 (0.24), residues: 1211 helix: 1.45 (0.20), residues: 664 sheet: -1.33 (0.43), residues: 122 loop : -2.11 (0.29), residues: 425 *********************** 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 227 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 202 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 217 average time/residue: 0.2058 time to fit residues: 64.5306 Evaluate side-chains 199 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 189 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1176 time to fit residues: 3.7998 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 0.0050 chunk 101 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4139 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 10255 Z= 0.200 Angle : 0.661 13.536 13966 Z= 0.320 Chirality : 0.043 0.351 1657 Planarity : 0.004 0.040 1705 Dihedral : 6.849 54.488 1374 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.62 % Favored : 94.05 % Rotamer Outliers : 1.53 % 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: 0.14 (0.24), residues: 1211 helix: 1.57 (0.20), residues: 668 sheet: -1.20 (0.44), residues: 128 loop : -1.99 (0.29), residues: 415 *********************** 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 230 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 222 average time/residue: 0.2078 time to fit residues: 66.6450 Evaluate side-chains 215 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 204 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1021 time to fit residues: 3.5048 ------------------------------------------------------------------------------- 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: 6.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 587 GLN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4143 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 10255 Z= 0.262 Angle : 0.682 12.315 13966 Z= 0.332 Chirality : 0.044 0.383 1657 Planarity : 0.004 0.043 1705 Dihedral : 6.867 52.290 1374 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.78 % Favored : 93.89 % Rotamer Outliers : 1.05 % 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: 0.03 (0.24), residues: 1211 helix: 1.44 (0.20), residues: 668 sheet: -1.18 (0.45), residues: 128 loop : -1.98 (0.30), residues: 415 *********************** 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 208 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 200 average time/residue: 0.2047 time to fit residues: 59.2939 Evaluate side-chains 196 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0982 time to fit residues: 2.8895 ------------------------------------------------------------------------------- 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: 6.9990 chunk 120 optimal weight: 0.0170 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS B 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4144 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 10255 Z= 0.213 Angle : 0.673 12.626 13966 Z= 0.324 Chirality : 0.044 0.429 1657 Planarity : 0.004 0.040 1705 Dihedral : 6.764 50.655 1374 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.78 % Favored : 93.89 % Rotamer Outliers : 0.86 % 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: 1.44 (0.20), residues: 666 sheet: -1.37 (0.45), residues: 120 loop : -1.88 (0.30), residues: 425 ********************** 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 227 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 221 average time/residue: 0.2166 time to fit residues: 68.7926 Evaluate side-chains 207 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 203 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1169 time to fit residues: 2.3592 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 17 optimal weight: 6.9990 chunk 84 optimal weight: 0.0010 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.5746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115585 restraints weight = 15045.319| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.30 r_work: 0.3131 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 10255 Z= 0.208 Angle : 0.671 12.167 13966 Z= 0.325 Chirality : 0.044 0.439 1657 Planarity : 0.004 0.042 1705 Dihedral : 6.702 50.875 1374 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.53 % Favored : 94.14 % Rotamer Outliers : 0.86 % 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: 0.06 (0.24), residues: 1211 helix: 1.42 (0.20), residues: 667 sheet: -1.20 (0.46), residues: 127 loop : -1.87 (0.30), residues: 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2292.43 seconds wall clock time: 42 minutes 31.47 seconds (2551.47 seconds total)