Starting phenix.real_space_refine on Sun Aug 4 12:06:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp8_37711/08_2024/8wp8_37711.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp8_37711/08_2024/8wp8_37711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp8_37711/08_2024/8wp8_37711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp8_37711/08_2024/8wp8_37711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp8_37711/08_2024/8wp8_37711.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp8_37711/08_2024/8wp8_37711.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4869 atoms to isotropic. 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 Zn 1 6.06 5 S 36 5.16 5 C 4185 2.51 5 N 1068 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6539 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1493 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 11, 'TRANS': 172} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.29, per 1000 atoms: 1.11 Number of scatterers: 6539 At special positions: 0 Unit cell: (77.97, 87.63, 117.99, 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) Zn 1 29.99 S 36 16.00 O 1249 8.00 N 1068 7.00 C 4185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 432 " " NAG B 601 " - " ASN B 354 " " NAG B 602 " - " ASN B 343 " " NAG C 1 " - " ASN A 90 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 103 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1474 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 55.0% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.147A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.565A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.776A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 173 removed outlier: 3.780A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.632A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.956A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.912A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.560A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.649A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.613A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.653A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.817A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.588A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.639A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.245A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.701A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.609A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.227A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 268 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1185 1.33 - 1.45: 1904 1.45 - 1.57: 3581 1.57 - 1.69: 0 1.69 - 1.82: 57 Bond restraints: 6727 Sorted by residual: bond pdb=" C PRO B 491 " pdb=" O PRO B 491 " ideal model delta sigma weight residual 1.239 1.205 0.034 1.27e-02 6.20e+03 7.14e+00 bond pdb=" N PHE B 490 " pdb=" CA PHE B 490 " ideal model delta sigma weight residual 1.452 1.490 -0.037 1.41e-02 5.03e+03 7.05e+00 bond pdb=" N LEU B 492 " pdb=" CA LEU B 492 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.23e-02 6.61e+03 5.97e+00 bond pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 1.469 1.445 0.024 1.25e-02 6.40e+03 3.73e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 6722 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 216 106.57 - 113.43: 3546 113.43 - 120.30: 2510 120.30 - 127.16: 2769 127.16 - 134.03: 101 Bond angle restraints: 9142 Sorted by residual: angle pdb=" N PHE B 338 " pdb=" CA PHE B 338 " pdb=" C PHE B 338 " ideal model delta sigma weight residual 114.31 108.01 6.30 1.29e+00 6.01e-01 2.38e+01 angle pdb=" CA PHE B 490 " pdb=" C PHE B 490 " pdb=" N PRO B 491 " ideal model delta sigma weight residual 117.67 121.79 -4.12 1.01e+00 9.80e-01 1.66e+01 angle pdb=" N CYS B 361 " pdb=" CA CYS B 361 " pdb=" C CYS B 361 " ideal model delta sigma weight residual 107.88 112.87 -4.99 1.41e+00 5.03e-01 1.25e+01 angle pdb=" C GLU A 171 " pdb=" N VAL A 172 " pdb=" CA VAL A 172 " ideal model delta sigma weight residual 122.63 118.69 3.94 1.19e+00 7.06e-01 1.10e+01 angle pdb=" C LEU B 492 " pdb=" N GLN B 493 " pdb=" CA GLN B 493 " ideal model delta sigma weight residual 121.94 127.24 -5.30 1.76e+00 3.23e-01 9.06e+00 ... (remaining 9137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 3840 21.98 - 43.96: 235 43.96 - 65.94: 22 65.94 - 87.92: 23 87.92 - 109.90: 8 Dihedral angle restraints: 4128 sinusoidal: 1831 harmonic: 2297 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -9.72 -76.28 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 164.97 -71.97 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -119.82 33.82 1 1.00e+01 1.00e-02 1.62e+01 ... (remaining 4125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 964 0.106 - 0.212: 17 0.212 - 0.317: 3 0.317 - 0.423: 0 0.423 - 0.529: 2 Chirality restraints: 986 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 983 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.303 2.00e-02 2.50e+03 2.55e-01 8.12e+02 pdb=" C7 NAG B 602 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.437 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " 0.044 2.00e-02 2.50e+03 3.66e-02 1.67e+01 pdb=" C7 NAG B 601 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 354 " 0.014 2.00e-02 2.50e+03 1.69e-02 3.56e+00 pdb=" CG ASN B 354 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN B 354 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 354 " -0.028 2.00e-02 2.50e+03 pdb=" C1 NAG B 601 " 0.020 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 73 2.66 - 3.22: 5961 3.22 - 3.78: 9514 3.78 - 4.34: 12755 4.34 - 4.90: 21373 Nonbonded interactions: 49676 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.100 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.118 2.230 nonbonded pdb=" OG SER B 469 " pdb=" OE1 GLU B 471 " model vdw 2.246 3.040 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.283 3.040 nonbonded pdb=" O MET A 152 " pdb=" NH2 ARG A 161 " model vdw 2.315 3.120 ... (remaining 49671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.960 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6727 Z= 0.207 Angle : 0.584 6.999 9142 Z= 0.302 Chirality : 0.049 0.529 986 Planarity : 0.008 0.255 1164 Dihedral : 15.475 109.902 2636 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.31), residues: 777 helix: 1.72 (0.29), residues: 362 sheet: -1.07 (0.89), residues: 32 loop : -1.32 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 203 HIS 0.008 0.001 HIS A 374 PHE 0.019 0.001 PHE B 515 TYR 0.013 0.001 TYR B 489 ARG 0.002 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7688 (tp) cc_final: 0.7455 (tt) REVERT: A 190 MET cc_start: 0.7344 (tmm) cc_final: 0.7135 (tmt) REVERT: A 218 SER cc_start: 0.8610 (t) cc_final: 0.8227 (p) REVERT: A 227 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6925 (mm-30) REVERT: A 368 ASP cc_start: 0.6784 (m-30) cc_final: 0.6567 (m-30) REVERT: A 471 ASP cc_start: 0.7591 (p0) cc_final: 0.7355 (p0) REVERT: A 536 GLU cc_start: 0.6453 (tm-30) cc_final: 0.6221 (tm-30) REVERT: A 544 ILE cc_start: 0.8361 (pt) cc_final: 0.8003 (mp) REVERT: A 547 SER cc_start: 0.7799 (t) cc_final: 0.7148 (p) REVERT: B 420 ASP cc_start: 0.7445 (m-30) cc_final: 0.7239 (m-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 1.1078 time to fit residues: 227.0466 Evaluate side-chains 169 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 401 HIS A 535 HIS A 572 ASN B 339 HIS B 409 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6727 Z= 0.246 Angle : 0.611 10.285 9142 Z= 0.309 Chirality : 0.049 0.586 986 Planarity : 0.005 0.039 1164 Dihedral : 8.778 66.934 1118 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.77 % Allowed : 11.21 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.31), residues: 777 helix: 1.54 (0.29), residues: 366 sheet: -0.68 (0.86), residues: 34 loop : -1.26 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 203 HIS 0.005 0.001 HIS A 401 PHE 0.016 0.002 PHE B 515 TYR 0.015 0.002 TYR A 385 ARG 0.003 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: A 88 ILE cc_start: 0.8097 (pt) cc_final: 0.7581 (pp) REVERT: A 126 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8078 (tt) REVERT: A 149 ASN cc_start: 0.7707 (m-40) cc_final: 0.7395 (m-40) REVERT: A 192 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7703 (mtt-85) REVERT: A 227 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6997 (mm-30) REVERT: A 297 MET cc_start: 0.7903 (mmm) cc_final: 0.7584 (mtp) REVERT: A 471 ASP cc_start: 0.7721 (p0) cc_final: 0.7468 (p0) REVERT: A 489 GLU cc_start: 0.7917 (pm20) cc_final: 0.7496 (pm20) REVERT: A 536 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6246 (tm-30) REVERT: A 544 ILE cc_start: 0.8426 (pt) cc_final: 0.8185 (mp) REVERT: B 405 ASN cc_start: 0.8292 (p0) cc_final: 0.7856 (p0) REVERT: B 420 ASP cc_start: 0.7453 (m-30) cc_final: 0.7169 (m-30) outliers start: 19 outliers final: 7 residues processed: 179 average time/residue: 1.0149 time to fit residues: 191.9996 Evaluate side-chains 172 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.0470 chunk 47 optimal weight: 0.0030 chunk 19 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 overall best weight: 0.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 210 ASN B 339 HIS B 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6727 Z= 0.145 Angle : 0.545 11.129 9142 Z= 0.272 Chirality : 0.045 0.490 986 Planarity : 0.004 0.037 1164 Dihedral : 6.091 52.565 1118 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.77 % Allowed : 15.87 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.31), residues: 777 helix: 1.64 (0.28), residues: 367 sheet: -0.79 (1.07), residues: 22 loop : -1.15 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS A 401 PHE 0.016 0.001 PHE B 515 TYR 0.018 0.001 TYR A 202 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ILE cc_start: 0.8178 (tt) cc_final: 0.7959 (tt) REVERT: A 192 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7688 (mtt-85) REVERT: A 227 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6997 (mm-30) REVERT: A 249 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5677 (ttm) REVERT: A 297 MET cc_start: 0.7878 (mmm) cc_final: 0.7632 (mtp) REVERT: A 408 MET cc_start: 0.6673 (mmt) cc_final: 0.6161 (mmt) REVERT: A 471 ASP cc_start: 0.7722 (p0) cc_final: 0.7467 (p0) REVERT: A 485 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7627 (t) REVERT: A 527 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: A 536 GLU cc_start: 0.6445 (tm-30) cc_final: 0.6203 (tm-30) REVERT: A 544 ILE cc_start: 0.8390 (pt) cc_final: 0.8149 (mp) REVERT: B 405 ASN cc_start: 0.8325 (p0) cc_final: 0.7879 (p0) REVERT: B 420 ASP cc_start: 0.7401 (m-30) cc_final: 0.7115 (m-30) outliers start: 19 outliers final: 3 residues processed: 167 average time/residue: 1.0508 time to fit residues: 184.9988 Evaluate side-chains 151 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 527 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 70 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 210 ASN A 572 ASN B 437 ASN B 439 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6727 Z= 0.187 Angle : 0.542 10.335 9142 Z= 0.274 Chirality : 0.045 0.497 986 Planarity : 0.004 0.034 1164 Dihedral : 5.082 52.460 1118 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.20 % Allowed : 16.30 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 777 helix: 1.66 (0.28), residues: 368 sheet: -0.77 (0.94), residues: 32 loop : -1.11 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS A 265 PHE 0.015 0.001 PHE B 515 TYR 0.017 0.001 TYR A 202 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7718 (ttm) REVERT: A 126 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.8008 (tt) REVERT: A 149 ASN cc_start: 0.7745 (m-40) cc_final: 0.7492 (m-40) REVERT: A 150 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7175 (tm-30) REVERT: A 169 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6890 (mtt-85) REVERT: A 192 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7713 (mtt-85) REVERT: A 227 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6921 (mm-30) REVERT: A 249 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5681 (ttm) REVERT: A 297 MET cc_start: 0.7881 (mmm) cc_final: 0.7611 (mtp) REVERT: A 313 LYS cc_start: 0.7932 (ttpp) cc_final: 0.7721 (ttpp) REVERT: A 471 ASP cc_start: 0.7733 (p0) cc_final: 0.7473 (p0) REVERT: A 527 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7092 (tp30) REVERT: A 536 GLU cc_start: 0.6458 (tm-30) cc_final: 0.6225 (tm-30) REVERT: A 544 ILE cc_start: 0.8451 (pt) cc_final: 0.8162 (mp) REVERT: B 405 ASN cc_start: 0.8369 (p0) cc_final: 0.7903 (p0) REVERT: B 420 ASP cc_start: 0.7398 (m-30) cc_final: 0.7098 (m-30) REVERT: B 468 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8141 (mp) outliers start: 22 outliers final: 6 residues processed: 155 average time/residue: 1.1127 time to fit residues: 181.7727 Evaluate side-chains 156 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 63 optimal weight: 0.0470 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 210 ASN B 437 ASN B 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6727 Z= 0.193 Angle : 0.533 10.154 9142 Z= 0.271 Chirality : 0.045 0.470 986 Planarity : 0.004 0.037 1164 Dihedral : 4.878 52.393 1118 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.49 % Allowed : 16.45 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.31), residues: 777 helix: 1.69 (0.28), residues: 365 sheet: -1.36 (0.75), residues: 44 loop : -1.04 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.009 0.001 HIS A 265 PHE 0.015 0.001 PHE A 308 TYR 0.019 0.002 TYR A 202 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7699 (ttm) REVERT: A 123 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7504 (mtt) REVERT: A 126 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8039 (tt) REVERT: A 149 ASN cc_start: 0.7735 (m-40) cc_final: 0.7493 (m-40) REVERT: A 150 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7197 (tm-30) REVERT: A 192 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7710 (mtt-85) REVERT: A 227 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6904 (mm-30) REVERT: A 249 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5675 (ttm) REVERT: A 252 TYR cc_start: 0.7871 (m-80) cc_final: 0.7570 (m-80) REVERT: A 297 MET cc_start: 0.7849 (mmm) cc_final: 0.7589 (mtp) REVERT: A 460 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7442 (mtm180) REVERT: A 471 ASP cc_start: 0.7738 (p0) cc_final: 0.7481 (p0) REVERT: A 527 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: A 536 GLU cc_start: 0.6448 (tm-30) cc_final: 0.6225 (tm-30) REVERT: B 405 ASN cc_start: 0.8400 (p0) cc_final: 0.7923 (p0) REVERT: B 420 ASP cc_start: 0.7381 (m-30) cc_final: 0.7087 (m-30) REVERT: B 468 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8138 (mp) outliers start: 24 outliers final: 7 residues processed: 160 average time/residue: 1.1364 time to fit residues: 191.3319 Evaluate side-chains 161 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.0030 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.3726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN B 437 ASN B 439 ASN B 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6727 Z= 0.163 Angle : 0.538 11.529 9142 Z= 0.272 Chirality : 0.044 0.455 986 Planarity : 0.004 0.038 1164 Dihedral : 4.785 52.645 1118 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.93 % Allowed : 16.89 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.32), residues: 777 helix: 1.71 (0.28), residues: 367 sheet: -1.42 (0.77), residues: 42 loop : -1.00 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.009 0.001 HIS A 265 PHE 0.014 0.001 PHE A 308 TYR 0.019 0.001 TYR A 202 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7680 (ttm) REVERT: A 123 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7488 (mtt) REVERT: A 126 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8033 (tt) REVERT: A 149 ASN cc_start: 0.7724 (m-40) cc_final: 0.7477 (m-40) REVERT: A 150 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 192 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7730 (mtt-85) REVERT: A 227 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6912 (mm-30) REVERT: A 249 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.5665 (ttm) REVERT: A 252 TYR cc_start: 0.7770 (m-80) cc_final: 0.7457 (m-80) REVERT: A 376 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7485 (mtt) REVERT: A 471 ASP cc_start: 0.7736 (p0) cc_final: 0.7480 (p0) REVERT: A 527 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: A 536 GLU cc_start: 0.6434 (tm-30) cc_final: 0.6212 (tm-30) REVERT: A 544 ILE cc_start: 0.8376 (pt) cc_final: 0.8128 (mt) REVERT: B 405 ASN cc_start: 0.8409 (p0) cc_final: 0.7944 (p0) REVERT: B 420 ASP cc_start: 0.7356 (m-30) cc_final: 0.7053 (m-30) REVERT: B 441 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6794 (mp) REVERT: B 468 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8139 (mp) outliers start: 27 outliers final: 10 residues processed: 166 average time/residue: 1.0762 time to fit residues: 188.1437 Evaluate side-chains 160 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN B 437 ASN B 439 ASN B 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6727 Z= 0.243 Angle : 0.566 10.453 9142 Z= 0.292 Chirality : 0.046 0.457 986 Planarity : 0.004 0.039 1164 Dihedral : 4.782 52.385 1118 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.93 % Allowed : 17.61 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.31), residues: 777 helix: 1.67 (0.28), residues: 365 sheet: -1.19 (0.77), residues: 44 loop : -1.07 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 203 HIS 0.009 0.001 HIS A 265 PHE 0.018 0.002 PHE A 308 TYR 0.022 0.002 TYR B 489 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8090 (tt) REVERT: A 149 ASN cc_start: 0.7746 (m-40) cc_final: 0.7534 (m-40) REVERT: A 150 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7227 (tm-30) REVERT: A 169 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7185 (mtt-85) REVERT: A 174 LYS cc_start: 0.8586 (mttm) cc_final: 0.8223 (mttp) REVERT: A 227 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6873 (mm-30) REVERT: A 249 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5680 (ttm) REVERT: A 252 TYR cc_start: 0.7817 (m-80) cc_final: 0.7540 (m-80) REVERT: A 297 MET cc_start: 0.7866 (mmm) cc_final: 0.7568 (mtp) REVERT: A 527 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7122 (tp30) REVERT: A 536 GLU cc_start: 0.6449 (tm-30) cc_final: 0.6231 (tm-30) REVERT: A 544 ILE cc_start: 0.8390 (pt) cc_final: 0.8154 (mt) REVERT: B 405 ASN cc_start: 0.8443 (p0) cc_final: 0.7952 (p0) REVERT: B 420 ASP cc_start: 0.7414 (m-30) cc_final: 0.7114 (m-30) REVERT: B 468 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8146 (mp) REVERT: B 481 LYS cc_start: 0.8340 (mtmm) cc_final: 0.8085 (mtmm) outliers start: 27 outliers final: 10 residues processed: 166 average time/residue: 1.1474 time to fit residues: 200.1724 Evaluate side-chains 157 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 58 optimal weight: 0.0470 chunk 67 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.0070 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 ASN B 439 ASN B 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6727 Z= 0.151 Angle : 0.554 11.693 9142 Z= 0.279 Chirality : 0.045 0.434 986 Planarity : 0.004 0.038 1164 Dihedral : 4.727 52.580 1118 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.62 % Allowed : 19.21 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.32), residues: 777 helix: 1.74 (0.28), residues: 367 sheet: -1.31 (0.78), residues: 42 loop : -0.98 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 610 HIS 0.007 0.001 HIS A 265 PHE 0.012 0.001 PHE A 308 TYR 0.021 0.001 TYR B 489 ARG 0.007 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7058 (tp30) cc_final: 0.6669 (tp30) REVERT: A 123 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7487 (mtt) REVERT: A 126 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8059 (tt) REVERT: A 149 ASN cc_start: 0.7731 (m-40) cc_final: 0.7529 (m-40) REVERT: A 150 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 249 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5706 (ttm) REVERT: A 297 MET cc_start: 0.7823 (mmm) cc_final: 0.7327 (mtp) REVERT: A 313 LYS cc_start: 0.7838 (ttpp) cc_final: 0.7620 (ttpp) REVERT: A 471 ASP cc_start: 0.7731 (p0) cc_final: 0.7486 (p0) REVERT: A 527 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7103 (tp30) REVERT: A 536 GLU cc_start: 0.6418 (tm-30) cc_final: 0.6201 (tm-30) REVERT: A 544 ILE cc_start: 0.8405 (pt) cc_final: 0.8165 (mt) REVERT: B 405 ASN cc_start: 0.8437 (p0) cc_final: 0.7959 (p0) REVERT: B 420 ASP cc_start: 0.7338 (m-30) cc_final: 0.7038 (m-30) REVERT: B 468 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8136 (mp) outliers start: 18 outliers final: 8 residues processed: 154 average time/residue: 1.1580 time to fit residues: 187.6153 Evaluate side-chains 153 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 0.0670 chunk 45 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN B 437 ASN B 439 ASN B 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6727 Z= 0.203 Angle : 0.567 10.903 9142 Z= 0.288 Chirality : 0.045 0.428 986 Planarity : 0.004 0.041 1164 Dihedral : 4.789 52.542 1118 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.62 % Allowed : 19.65 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.31), residues: 777 helix: 1.62 (0.28), residues: 373 sheet: -1.20 (0.76), residues: 44 loop : -1.11 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 203 HIS 0.006 0.001 HIS A 265 PHE 0.016 0.001 PHE A 308 TYR 0.018 0.001 TYR B 423 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7066 (tp30) cc_final: 0.6613 (tp30) REVERT: A 123 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7508 (mtt) REVERT: A 126 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8077 (tt) REVERT: A 149 ASN cc_start: 0.7725 (m-40) cc_final: 0.7511 (m-40) REVERT: A 150 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 249 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5691 (ttm) REVERT: A 313 LYS cc_start: 0.7833 (ttpp) cc_final: 0.7614 (ttpp) REVERT: A 471 ASP cc_start: 0.7745 (p0) cc_final: 0.7511 (p0) REVERT: A 527 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7098 (tp30) REVERT: A 536 GLU cc_start: 0.6424 (tm-30) cc_final: 0.6208 (tm-30) REVERT: A 544 ILE cc_start: 0.8385 (pt) cc_final: 0.8139 (mt) REVERT: B 405 ASN cc_start: 0.8443 (p0) cc_final: 0.7922 (p0) REVERT: B 420 ASP cc_start: 0.7380 (m-30) cc_final: 0.7083 (m-30) REVERT: B 468 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8142 (mp) REVERT: B 481 LYS cc_start: 0.8336 (mtmm) cc_final: 0.8078 (mtmm) outliers start: 18 outliers final: 8 residues processed: 147 average time/residue: 1.0721 time to fit residues: 166.4731 Evaluate side-chains 152 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 61 optimal weight: 0.0870 chunk 6 optimal weight: 0.0370 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN B 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6727 Z= 0.167 Angle : 0.573 13.186 9142 Z= 0.284 Chirality : 0.044 0.412 986 Planarity : 0.004 0.040 1164 Dihedral : 4.752 52.625 1118 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.89 % Allowed : 20.82 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.31), residues: 777 helix: 1.62 (0.28), residues: 374 sheet: -1.22 (0.79), residues: 42 loop : -1.09 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 203 HIS 0.005 0.001 HIS A 265 PHE 0.014 0.001 PHE A 308 TYR 0.025 0.001 TYR B 489 ARG 0.010 0.001 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7069 (tp30) cc_final: 0.6660 (tp30) REVERT: A 123 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7500 (mtt) REVERT: A 126 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 149 ASN cc_start: 0.7696 (m-40) cc_final: 0.7495 (m-40) REVERT: A 150 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 249 MET cc_start: 0.5880 (OUTLIER) cc_final: 0.5678 (ttm) REVERT: A 313 LYS cc_start: 0.7817 (ttpp) cc_final: 0.7599 (ttpp) REVERT: A 471 ASP cc_start: 0.7725 (p0) cc_final: 0.7482 (p0) REVERT: A 536 GLU cc_start: 0.6382 (tm-30) cc_final: 0.6174 (tm-30) REVERT: A 544 ILE cc_start: 0.8385 (pt) cc_final: 0.8111 (mt) REVERT: B 405 ASN cc_start: 0.8431 (p0) cc_final: 0.7960 (p0) REVERT: B 420 ASP cc_start: 0.7341 (m-30) cc_final: 0.7083 (m-30) REVERT: B 481 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8066 (mtmm) outliers start: 13 outliers final: 8 residues processed: 155 average time/residue: 1.0409 time to fit residues: 171.0263 Evaluate side-chains 155 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 409 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 61 optimal weight: 0.3980 chunk 25 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 0.0000 chunk 11 optimal weight: 0.3980 chunk 53 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 210 ASN B 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126331 restraints weight = 17342.020| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.41 r_work: 0.3481 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6727 Z= 0.153 Angle : 0.569 12.340 9142 Z= 0.280 Chirality : 0.043 0.403 986 Planarity : 0.004 0.040 1164 Dihedral : 4.670 52.658 1118 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.60 % Allowed : 21.11 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.31), residues: 777 helix: 1.54 (0.28), residues: 380 sheet: -1.24 (0.79), residues: 42 loop : -1.03 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.007 0.001 HIS A 265 PHE 0.012 0.001 PHE A 308 TYR 0.017 0.001 TYR A 50 ARG 0.009 0.001 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.10 seconds wall clock time: 63 minutes 15.03 seconds (3795.03 seconds total)