Starting phenix.real_space_refine on Sat Nov 16 03:46:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/11_2024/8ils_35545.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/11_2024/8ils_35545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/11_2024/8ils_35545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/11_2024/8ils_35545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/11_2024/8ils_35545.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/11_2024/8ils_35545.cif" } resolution = 3.1 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= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 6602 2.51 5 N 1792 2.21 5 O 1907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10374 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7980 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 977, 7980 Classifications: {'peptide': 977} Link IDs: {'PTRANS': 47, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2346 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 48 Unusual residues: {'7U5': 1} Classifications: {'undetermined': 1, 'water': 8} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N BGLU A 950 " occ=0.46 ... (7 atoms not shown) pdb=" OE2BGLU A 950 " occ=0.46 residue: pdb=" N BARG A 951 " occ=0.46 ... (9 atoms not shown) pdb=" NH2BARG A 951 " occ=0.46 residue: pdb=" N BVAL A 952 " occ=0.46 ... (4 atoms not shown) pdb=" CG2BVAL A 952 " occ=0.46 residue: pdb=" N BPRO A 953 " occ=0.46 ... (5 atoms not shown) pdb=" CD BPRO A 953 " occ=0.46 residue: pdb=" N BVAL A 955 " occ=0.46 ... (5 atoms not shown) pdb=" CG2BVAL A 955 " occ=0.46 residue: pdb=" N BLEU A 956 " occ=0.50 ... (6 atoms not shown) pdb=" CD2BLEU A 956 " occ=0.50 Time building chain proxies: 6.32, per 1000 atoms: 0.61 Number of scatterers: 10374 At special positions: 0 Unit cell: (85.696, 131.456, 109.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1907 8.00 N 1792 7.00 C 6602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.6 seconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2398 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 12 sheets defined 51.7% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.557A pdb=" N LEU A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 removed outlier: 4.106A pdb=" N ARG A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.549A pdb=" N VAL A 131 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.526A pdb=" N ARG A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.611A pdb=" N CYS A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 removed outlier: 3.787A pdb=" N ARG A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 199 through 202 Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.569A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.535A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 528 through 536 removed outlier: 3.502A pdb=" N THR A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 3.562A pdb=" N SER A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.645A pdb=" N THR A 560 " --> pdb=" O TYR A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 571 removed outlier: 3.650A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 removed outlier: 3.606A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.607A pdb=" N LYS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.680A pdb=" N GLN A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 660 through 673 removed outlier: 3.504A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.016A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 741 through 748 Processing helix chain 'A' and resid 765 through 769 Processing helix chain 'A' and resid 787 through 791 removed outlier: 4.543A pdb=" N GLU A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.546A pdb=" N LEU A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 815 " --> pdb=" O MET A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 889 through 912 Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.659A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 994 removed outlier: 3.695A pdb=" N HIS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.686A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A1002 " --> pdb=" O PHE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1009 removed outlier: 4.102A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1026 removed outlier: 3.683A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1047 removed outlier: 3.583A pdb=" N HIS A1047 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 400 through 409 Processing helix chain 'B' and resid 433 through 437 removed outlier: 3.791A pdb=" N VAL B 436 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 433 through 437' Processing helix chain 'B' and resid 441 through 505 removed outlier: 3.554A pdb=" N VAL B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 502 " --> pdb=" O CYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 515 removed outlier: 3.738A pdb=" N LYS B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 587 removed outlier: 3.541A pdb=" N ILE B 521 " --> pdb=" O ASN B 517 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) Proline residue: B 568 - end of helix removed outlier: 3.778A pdb=" N THR B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 removed outlier: 4.066A pdb=" N LEU B 594 " --> pdb=" O ARG B 590 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 596 " --> pdb=" O LYS B 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.542A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU A 99 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU A 23 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 212 removed outlier: 8.329A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TRP A 195 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 392 removed outlier: 9.884A pdb=" N GLU A 385 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N CYS A 340 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU A 387 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE A 338 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR A 389 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE A 336 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 391 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.910A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.634A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AA9, first strand: chain 'A' and resid 779 through 782 Processing sheet with id=AB1, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB2, first strand: chain 'B' and resid 377 through 381 removed outlier: 3.895A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 384 through 385 480 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2212 1.33 - 1.45: 2311 1.45 - 1.57: 5950 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 10587 Sorted by residual: bond pdb=" CA SER A 773 " pdb=" C SER A 773 " ideal model delta sigma weight residual 1.522 1.470 0.052 1.40e-02 5.10e+03 1.37e+01 bond pdb=" N LYS A 776 " pdb=" CA LYS A 776 " ideal model delta sigma weight residual 1.457 1.418 0.039 1.10e-02 8.26e+03 1.28e+01 bond pdb=" CA SER A 774 " pdb=" C SER A 774 " ideal model delta sigma weight residual 1.523 1.487 0.037 1.34e-02 5.57e+03 7.46e+00 bond pdb=" C LEU A 755 " pdb=" N ASN A 756 " ideal model delta sigma weight residual 1.332 1.311 0.020 7.50e-03 1.78e+04 7.26e+00 bond pdb=" C14 7U5 A1101 " pdb=" N13 7U5 A1101 " ideal model delta sigma weight residual 1.309 1.359 -0.050 2.00e-02 2.50e+03 6.34e+00 ... (remaining 10582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 14136 2.14 - 4.28: 139 4.28 - 6.42: 4 6.42 - 8.55: 0 8.55 - 10.69: 1 Bond angle restraints: 14280 Sorted by residual: angle pdb=" N ALA A 775 " pdb=" CA ALA A 775 " pdb=" C ALA A 775 " ideal model delta sigma weight residual 110.80 121.49 -10.69 2.13e+00 2.20e-01 2.52e+01 angle pdb=" C TRP A 383 " pdb=" N ASN A 384 " pdb=" CA ASN A 384 " ideal model delta sigma weight residual 122.05 118.05 4.00 1.48e+00 4.57e-01 7.32e+00 angle pdb=" C ALA A 775 " pdb=" N LYS A 776 " pdb=" CA LYS A 776 " ideal model delta sigma weight residual 122.83 118.84 3.99 1.54e+00 4.22e-01 6.71e+00 angle pdb=" O MET A 772 " pdb=" C MET A 772 " pdb=" N SER A 773 " ideal model delta sigma weight residual 122.81 119.66 3.15 1.23e+00 6.61e-01 6.56e+00 angle pdb=" CA LYS A 776 " pdb=" C LYS A 776 " pdb=" O LYS A 776 " ideal model delta sigma weight residual 120.15 116.86 3.29 1.29e+00 6.01e-01 6.50e+00 ... (remaining 14275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5716 17.98 - 35.97: 638 35.97 - 53.95: 81 53.95 - 71.94: 22 71.94 - 89.92: 11 Dihedral angle restraints: 6468 sinusoidal: 2773 harmonic: 3695 Sorted by residual: dihedral pdb=" CA LYS A 111 " pdb=" C LYS A 111 " pdb=" N ILE A 112 " pdb=" CA ILE A 112 " ideal model delta harmonic sigma weight residual 180.00 149.95 30.05 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA SER A 158 " pdb=" C SER A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLY A 828 " pdb=" C GLY A 828 " pdb=" N LEU A 829 " pdb=" CA LEU A 829 " ideal model delta harmonic sigma weight residual 180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1306 0.057 - 0.114: 211 0.114 - 0.170: 19 0.170 - 0.227: 0 0.227 - 0.284: 1 Chirality restraints: 1537 Sorted by residual: chirality pdb=" CA ALA A 775 " pdb=" N ALA A 775 " pdb=" C ALA A 775 " pdb=" CB ALA A 775 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ILE A 561 " pdb=" N ILE A 561 " pdb=" C ILE A 561 " pdb=" CB ILE A 561 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA LYS A 111 " pdb=" N LYS A 111 " pdb=" C LYS A 111 " pdb=" CB LYS A 111 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1534 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 7U5 A1101 " -0.095 2.00e-02 2.50e+03 4.77e-02 6.81e+01 pdb=" C30 7U5 A1101 " -0.017 2.00e-02 2.50e+03 pdb=" C31 7U5 A1101 " 0.039 2.00e-02 2.50e+03 pdb=" C32 7U5 A1101 " 0.024 2.00e-02 2.50e+03 pdb=" C33 7U5 A1101 " 0.019 2.00e-02 2.50e+03 pdb=" C34 7U5 A1101 " 0.073 2.00e-02 2.50e+03 pdb=" C35 7U5 A1101 " 0.048 2.00e-02 2.50e+03 pdb=" C36 7U5 A1101 " 0.018 2.00e-02 2.50e+03 pdb=" C38 7U5 A1101 " -0.065 2.00e-02 2.50e+03 pdb=" C39 7U5 A1101 " -0.040 2.00e-02 2.50e+03 pdb=" N37 7U5 A1101 " -0.031 2.00e-02 2.50e+03 pdb=" N40 7U5 A1101 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 7U5 A1101 " 0.107 2.00e-02 2.50e+03 5.00e-02 5.63e+01 pdb=" C23 7U5 A1101 " -0.018 2.00e-02 2.50e+03 pdb=" C24 7U5 A1101 " -0.039 2.00e-02 2.50e+03 pdb=" C25 7U5 A1101 " -0.034 2.00e-02 2.50e+03 pdb=" C26 7U5 A1101 " -0.039 2.00e-02 2.50e+03 pdb=" C27 7U5 A1101 " -0.040 2.00e-02 2.50e+03 pdb=" C28 7U5 A1101 " -0.022 2.00e-02 2.50e+03 pdb=" C29 7U5 A1101 " 0.022 2.00e-02 2.50e+03 pdb=" C30 7U5 A1101 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 7U5 A1101 " 0.042 2.00e-02 2.50e+03 3.01e-02 2.94e+01 pdb=" C09 7U5 A1101 " 0.028 2.00e-02 2.50e+03 pdb=" C10 7U5 A1101 " -0.005 2.00e-02 2.50e+03 pdb=" C11 7U5 A1101 " -0.050 2.00e-02 2.50e+03 pdb=" C12 7U5 A1101 " -0.028 2.00e-02 2.50e+03 pdb=" C14 7U5 A1101 " 0.012 2.00e-02 2.50e+03 pdb=" C15 7U5 A1101 " 0.067 2.00e-02 2.50e+03 pdb=" C16 7U5 A1101 " -0.010 2.00e-02 2.50e+03 pdb=" C17 7U5 A1101 " -0.014 2.00e-02 2.50e+03 pdb=" C19 7U5 A1101 " -0.019 2.00e-02 2.50e+03 pdb=" C20 7U5 A1101 " 0.006 2.00e-02 2.50e+03 pdb=" N13 7U5 A1101 " -0.004 2.00e-02 2.50e+03 pdb=" N18 7U5 A1101 " -0.024 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 82 2.57 - 3.16: 8935 3.16 - 3.74: 15191 3.74 - 4.32: 22927 4.32 - 4.90: 37713 Nonbonded interactions: 84848 Sorted by model distance: nonbonded pdb=" OD1 ASN A 428 " pdb=" NE2 GLN A 643 " model vdw 1.993 3.120 nonbonded pdb=" OE2 GLU A 642 " pdb=" O HOH A1201 " model vdw 2.027 3.040 nonbonded pdb=" O ASP A 138 " pdb=" ND2 ASN A 142 " model vdw 2.110 3.120 nonbonded pdb=" N SER B 399 " pdb=" OE2 GLU B 403 " model vdw 2.124 3.120 nonbonded pdb=" O ALA B 331 " pdb=" NZ LYS B 430 " model vdw 2.150 3.120 ... (remaining 84843 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.006 0.052 10587 Z= 0.377 Angle : 0.549 10.692 14280 Z= 0.298 Chirality : 0.042 0.284 1537 Planarity : 0.004 0.050 1835 Dihedral : 14.928 89.920 4070 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 25.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.57 % Favored : 93.34 % Rotamer: Outliers : 0.17 % Allowed : 0.52 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.24), residues: 1239 helix: -0.26 (0.22), residues: 550 sheet: -1.56 (0.40), residues: 168 loop : -0.96 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 597 HIS 0.003 0.001 HIS A 917 PHE 0.016 0.002 PHE A 430 TYR 0.011 0.001 TYR A 432 ARG 0.003 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 286 MET cc_start: 0.7614 (ttp) cc_final: 0.7346 (ttp) REVERT: A 488 ASP cc_start: 0.7504 (p0) cc_final: 0.7054 (p0) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.2593 time to fit residues: 64.5720 Evaluate side-chains 154 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.0870 chunk 112 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN A 682 GLN A 749 GLN ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10587 Z= 0.184 Angle : 0.566 6.944 14280 Z= 0.295 Chirality : 0.042 0.175 1537 Planarity : 0.004 0.058 1835 Dihedral : 4.264 31.560 1388 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 0.78 % Allowed : 7.30 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.24), residues: 1239 helix: 0.82 (0.21), residues: 568 sheet: -1.27 (0.40), residues: 159 loop : -0.99 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 597 HIS 0.004 0.001 HIS A 59 PHE 0.021 0.002 PHE A 70 TYR 0.015 0.001 TYR A 904 ARG 0.005 0.000 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.6273 (mmp) cc_final: 0.5892 (mmm) REVERT: A 100 LYS cc_start: 0.7252 (tttt) cc_final: 0.6946 (tttt) REVERT: A 162 ARG cc_start: 0.8388 (tpp80) cc_final: 0.7582 (mtm180) REVERT: A 352 ASP cc_start: 0.7416 (m-30) cc_final: 0.7045 (m-30) REVERT: A 488 ASP cc_start: 0.7345 (p0) cc_final: 0.6913 (p0) REVERT: A 733 LYS cc_start: 0.8587 (ptpt) cc_final: 0.8113 (ptmm) REVERT: A 976 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7204 (mm-30) REVERT: B 525 MET cc_start: 0.8229 (mmp) cc_final: 0.8000 (mmp) outliers start: 9 outliers final: 8 residues processed: 169 average time/residue: 0.2497 time to fit residues: 59.1622 Evaluate side-chains 147 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN A 809 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10587 Z= 0.312 Angle : 0.573 6.510 14280 Z= 0.296 Chirality : 0.044 0.158 1537 Planarity : 0.004 0.065 1835 Dihedral : 4.353 28.739 1388 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 1.13 % Allowed : 10.17 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1239 helix: 0.99 (0.21), residues: 572 sheet: -1.19 (0.39), residues: 159 loop : -1.17 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 479 HIS 0.005 0.001 HIS A1047 PHE 0.019 0.002 PHE A 70 TYR 0.013 0.001 TYR B 470 ARG 0.004 0.000 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.6195 (mmp) cc_final: 0.5812 (mmm) REVERT: A 58 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5982 (mp) REVERT: A 162 ARG cc_start: 0.8430 (tpp80) cc_final: 0.7589 (mtm180) REVERT: A 352 ASP cc_start: 0.7451 (m-30) cc_final: 0.7026 (m-30) REVERT: A 488 ASP cc_start: 0.7236 (p0) cc_final: 0.6831 (p0) REVERT: A 733 LYS cc_start: 0.8596 (ptpt) cc_final: 0.8088 (ptmm) REVERT: A 976 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7196 (mm-30) REVERT: B 525 MET cc_start: 0.8263 (mmp) cc_final: 0.7898 (mmp) outliers start: 13 outliers final: 9 residues processed: 161 average time/residue: 0.3038 time to fit residues: 67.9357 Evaluate side-chains 153 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10587 Z= 0.211 Angle : 0.522 6.466 14280 Z= 0.269 Chirality : 0.042 0.145 1537 Planarity : 0.004 0.065 1835 Dihedral : 4.226 28.276 1388 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 1.22 % Allowed : 11.13 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1239 helix: 1.24 (0.22), residues: 572 sheet: -1.16 (0.38), residues: 159 loop : -1.13 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.003 0.001 HIS A 665 PHE 0.019 0.002 PHE A 70 TYR 0.013 0.001 TYR B 470 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6255 (mmp) cc_final: 0.5768 (mmm) REVERT: A 162 ARG cc_start: 0.8471 (tpp80) cc_final: 0.7592 (mtm180) REVERT: A 352 ASP cc_start: 0.7429 (m-30) cc_final: 0.6972 (m-30) REVERT: A 476 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: A 488 ASP cc_start: 0.7219 (p0) cc_final: 0.6836 (p0) REVERT: A 976 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7077 (mm-30) REVERT: B 525 MET cc_start: 0.8203 (mmp) cc_final: 0.7189 (tpp) outliers start: 14 outliers final: 11 residues processed: 162 average time/residue: 0.2571 time to fit residues: 57.7495 Evaluate side-chains 154 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0570 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN A 803 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10587 Z= 0.285 Angle : 0.545 7.180 14280 Z= 0.280 Chirality : 0.043 0.153 1537 Planarity : 0.004 0.066 1835 Dihedral : 4.263 27.652 1388 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 1.83 % Allowed : 11.74 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1239 helix: 1.19 (0.21), residues: 574 sheet: -1.12 (0.38), residues: 161 loop : -1.25 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 479 HIS 0.004 0.001 HIS A 665 PHE 0.024 0.002 PHE A 98 TYR 0.014 0.001 TYR B 470 ARG 0.004 0.000 ARG A 777 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8507 (tpp80) cc_final: 0.7660 (mtm180) REVERT: A 352 ASP cc_start: 0.7442 (m-30) cc_final: 0.6963 (m-30) REVERT: A 476 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: A 488 ASP cc_start: 0.7200 (p0) cc_final: 0.6821 (p0) REVERT: B 403 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6551 (mm-30) REVERT: B 525 MET cc_start: 0.8075 (mmp) cc_final: 0.7076 (tpp) outliers start: 21 outliers final: 15 residues processed: 166 average time/residue: 0.2628 time to fit residues: 59.9807 Evaluate side-chains 164 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10587 Z= 0.154 Angle : 0.491 6.446 14280 Z= 0.255 Chirality : 0.040 0.147 1537 Planarity : 0.004 0.067 1835 Dihedral : 4.042 25.351 1388 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 1.48 % Allowed : 12.52 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1239 helix: 1.36 (0.22), residues: 579 sheet: -1.03 (0.38), residues: 161 loop : -1.23 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 479 HIS 0.003 0.000 HIS A 59 PHE 0.023 0.001 PHE A 98 TYR 0.014 0.001 TYR B 470 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7828 (m-80) cc_final: 0.7507 (m-80) REVERT: A 291 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7397 (mm-30) REVERT: A 352 ASP cc_start: 0.7430 (m-30) cc_final: 0.6980 (m-30) REVERT: A 476 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: A 488 ASP cc_start: 0.7116 (p0) cc_final: 0.6776 (p0) REVERT: A 599 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8547 (mtp) REVERT: B 403 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6535 (mm-30) REVERT: B 525 MET cc_start: 0.7987 (mmp) cc_final: 0.6651 (tpt) REVERT: B 584 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6411 (tt) outliers start: 17 outliers final: 11 residues processed: 167 average time/residue: 0.2631 time to fit residues: 63.4063 Evaluate side-chains 165 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN A 749 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10587 Z= 0.248 Angle : 0.530 7.252 14280 Z= 0.271 Chirality : 0.042 0.148 1537 Planarity : 0.004 0.068 1835 Dihedral : 4.100 25.619 1388 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 1.91 % Allowed : 13.04 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1239 helix: 1.34 (0.21), residues: 580 sheet: -1.00 (0.38), residues: 159 loop : -1.22 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.004 0.001 HIS A 665 PHE 0.020 0.002 PHE A 98 TYR 0.015 0.001 TYR B 470 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7873 (m-80) cc_final: 0.7470 (m-80) REVERT: A 162 ARG cc_start: 0.8464 (tpp80) cc_final: 0.7937 (mtm180) REVERT: A 291 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 352 ASP cc_start: 0.7442 (m-30) cc_final: 0.7016 (m-30) REVERT: A 476 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: A 488 ASP cc_start: 0.7160 (p0) cc_final: 0.6804 (p0) REVERT: A 739 MET cc_start: 0.9113 (mtm) cc_final: 0.8864 (mtm) REVERT: A 970 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6741 (tm-30) REVERT: B 403 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6544 (mm-30) REVERT: B 525 MET cc_start: 0.7924 (mmp) cc_final: 0.7423 (mmp) outliers start: 22 outliers final: 16 residues processed: 165 average time/residue: 0.2661 time to fit residues: 60.3673 Evaluate side-chains 166 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10587 Z= 0.181 Angle : 0.505 6.515 14280 Z= 0.260 Chirality : 0.041 0.146 1537 Planarity : 0.004 0.066 1835 Dihedral : 4.022 24.717 1388 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 1.74 % Allowed : 13.22 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1239 helix: 1.43 (0.21), residues: 579 sheet: -0.83 (0.40), residues: 147 loop : -1.18 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 479 HIS 0.003 0.001 HIS A 59 PHE 0.018 0.001 PHE A 98 TYR 0.014 0.001 TYR B 470 ARG 0.004 0.000 ARG A 777 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7871 (m-80) cc_final: 0.7416 (m-80) REVERT: A 352 ASP cc_start: 0.7434 (m-30) cc_final: 0.7007 (m-30) REVERT: A 476 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: A 488 ASP cc_start: 0.7137 (p0) cc_final: 0.6789 (p0) REVERT: A 599 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8574 (mtp) REVERT: A 739 MET cc_start: 0.9102 (mtm) cc_final: 0.8826 (mtm) REVERT: A 970 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 403 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6543 (mm-30) REVERT: B 525 MET cc_start: 0.7971 (mmp) cc_final: 0.7487 (mmp) outliers start: 20 outliers final: 13 residues processed: 161 average time/residue: 0.2558 time to fit residues: 56.9265 Evaluate side-chains 161 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.0970 chunk 34 optimal weight: 0.0170 chunk 100 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10587 Z= 0.268 Angle : 0.540 7.130 14280 Z= 0.277 Chirality : 0.042 0.153 1537 Planarity : 0.004 0.067 1835 Dihedral : 4.113 25.243 1388 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % Rotamer: Outliers : 1.65 % Allowed : 13.65 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1239 helix: 1.36 (0.21), residues: 580 sheet: -0.81 (0.40), residues: 147 loop : -1.20 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.004 0.001 HIS A 665 PHE 0.017 0.002 PHE A 98 TYR 0.015 0.001 TYR B 470 ARG 0.004 0.000 ARG A 777 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7869 (m-80) cc_final: 0.7368 (m-80) REVERT: A 162 ARG cc_start: 0.8479 (tpp80) cc_final: 0.7652 (mtm180) REVERT: A 352 ASP cc_start: 0.7446 (m-30) cc_final: 0.7009 (m-30) REVERT: A 476 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: A 488 ASP cc_start: 0.7133 (p0) cc_final: 0.6789 (p0) REVERT: A 970 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6653 (tm-30) REVERT: B 403 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6544 (mm-30) REVERT: B 525 MET cc_start: 0.7943 (mmp) cc_final: 0.7434 (mmp) outliers start: 19 outliers final: 16 residues processed: 158 average time/residue: 0.2586 time to fit residues: 56.8711 Evaluate side-chains 161 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 20.0000 chunk 71 optimal weight: 0.0980 chunk 55 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10587 Z= 0.192 Angle : 0.520 7.402 14280 Z= 0.267 Chirality : 0.041 0.148 1537 Planarity : 0.004 0.066 1835 Dihedral : 4.041 24.532 1388 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.74 % Allowed : 13.91 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1239 helix: 1.42 (0.21), residues: 581 sheet: -0.74 (0.41), residues: 147 loop : -1.15 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 479 HIS 0.003 0.001 HIS A 665 PHE 0.017 0.002 PHE A 98 TYR 0.014 0.001 TYR B 470 ARG 0.004 0.000 ARG A 777 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7847 (m-80) cc_final: 0.7363 (m-80) REVERT: A 162 ARG cc_start: 0.8462 (tpp80) cc_final: 0.7930 (mtm180) REVERT: A 352 ASP cc_start: 0.7437 (m-30) cc_final: 0.7003 (m-30) REVERT: A 476 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: A 488 ASP cc_start: 0.7111 (p0) cc_final: 0.6781 (p0) REVERT: A 599 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8536 (mtp) REVERT: A 970 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6569 (tm-30) REVERT: B 403 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6539 (mm-30) REVERT: B 525 MET cc_start: 0.7871 (mmp) cc_final: 0.7367 (mmp) REVERT: B 584 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6466 (tt) outliers start: 20 outliers final: 15 residues processed: 160 average time/residue: 0.2823 time to fit residues: 62.1525 Evaluate side-chains 161 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.171950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112106 restraints weight = 11562.526| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.29 r_work: 0.2932 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10587 Z= 0.311 Angle : 0.564 7.241 14280 Z= 0.289 Chirality : 0.043 0.173 1537 Planarity : 0.004 0.068 1835 Dihedral : 4.188 25.406 1388 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.65 % Allowed : 14.61 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1239 helix: 1.28 (0.21), residues: 580 sheet: -0.78 (0.41), residues: 147 loop : -1.21 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 479 HIS 0.004 0.001 HIS A 665 PHE 0.028 0.002 PHE A 98 TYR 0.015 0.001 TYR B 470 ARG 0.004 0.000 ARG A 777 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2603.96 seconds wall clock time: 48 minutes 21.48 seconds (2901.48 seconds total)