Starting phenix.real_space_refine on Sun Dec 29 22:18:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t56_25696/12_2024/7t56_25696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t56_25696/12_2024/7t56_25696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t56_25696/12_2024/7t56_25696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t56_25696/12_2024/7t56_25696.map" model { file = "/net/cci-nas-00/data/ceres_data/7t56_25696/12_2024/7t56_25696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t56_25696/12_2024/7t56_25696.cif" } resolution = 3.7 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= 0.033 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 7382 2.51 5 N 1870 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.73, per 1000 atoms: 0.67 Number of scatterers: 11460 At special positions: 0 Unit cell: (109.18, 107.12, 138.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 6 15.00 Mg 2 11.99 O 2140 8.00 N 1870 7.00 C 7382 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 8 sheets defined 61.3% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 165 through 186 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 205 through 253 removed outlier: 4.228A pdb=" N PHE A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.919A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 removed outlier: 3.551A pdb=" N ILE A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 281 through 305 removed outlier: 3.599A pdb=" N LEU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 354 removed outlier: 3.654A pdb=" N ILE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 4.079A pdb=" N GLN A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 417 Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 435 through 460 removed outlier: 3.605A pdb=" N VAL A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Proline residue: A 447 - end of helix removed outlier: 3.720A pdb=" N ARG A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 525 through 533 removed outlier: 4.043A pdb=" N ALA A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.991A pdb=" N ILE A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 624 through 639 removed outlier: 4.239A pdb=" N ARG A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 667 Processing helix chain 'A' and resid 707 through 711 Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.634A pdb=" N GLU A 722 " --> pdb=" O TRP A 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 removed outlier: 3.556A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 124 through 132 Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.644A pdb=" N LYS B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 165 through 186 Processing helix chain 'B' and resid 188 through 196 Processing helix chain 'B' and resid 205 through 253 removed outlier: 4.248A pdb=" N PHE B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.902A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.549A pdb=" N ILE B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 281 through 305 removed outlier: 3.748A pdb=" N LEU B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 354 removed outlier: 3.670A pdb=" N ILE B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 4.049A pdb=" N GLN B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 363 through 417 removed outlier: 3.712A pdb=" N GLU B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 435 through 460 removed outlier: 3.561A pdb=" N VAL B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.612A pdb=" N ARG B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 524 through 533 removed outlier: 3.846A pdb=" N ALA B 529 " --> pdb=" O LYS B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 575 through 581 removed outlier: 3.565A pdb=" N CYS B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 600 removed outlier: 3.737A pdb=" N ILE B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.586A pdb=" N ILE B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 624 through 639 removed outlier: 3.638A pdb=" N ARG B 630 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 669 removed outlier: 4.030A pdb=" N GLU B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 685 removed outlier: 3.536A pdb=" N ILE B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 710 Processing helix chain 'B' and resid 713 through 722 removed outlier: 3.821A pdb=" N MET B 717 " --> pdb=" O CYS B 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 removed outlier: 3.609A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 93 removed outlier: 4.027A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 103 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 114 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 105 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 removed outlier: 4.072A pdb=" N LEU A 507 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE A 488 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 544 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN A 490 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP A 542 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 540 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 562 through 564 removed outlier: 6.696A pdb=" N LEU A 644 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE A 677 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 646 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N HIS A 679 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 515 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 519 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR A 514 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR A 691 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA A 516 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 693 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 518 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 700 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 72 removed outlier: 4.035A pdb=" N LEU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 102 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 506 through 509 removed outlier: 3.965A pdb=" N VAL B 491 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS B 540 " --> pdb=" O VAL B 491 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 562 through 564 removed outlier: 6.732A pdb=" N VAL B 515 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 690 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER B 701 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 692 " --> pdb=" O VAL B 699 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1962 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: 4.14 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3576 1.34 - 1.46: 1485 1.46 - 1.57: 6460 1.57 - 1.69: 11 1.69 - 1.81: 104 Bond restraints: 11636 Sorted by residual: bond pdb=" N MET A 533 " pdb=" CA MET A 533 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.26e-02 6.30e+03 9.59e+00 bond pdb=" N VAL A 672 " pdb=" CA VAL A 672 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.19e-02 7.06e+03 8.51e+00 bond pdb=" N VAL A 501 " pdb=" CA VAL A 501 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.59e+00 bond pdb=" N LEU A 502 " pdb=" CA LEU A 502 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.22e-02 6.72e+03 7.43e+00 bond pdb=" N ILE A 505 " pdb=" CA ILE A 505 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.19e+00 ... (remaining 11631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 15333 1.90 - 3.80: 312 3.80 - 5.70: 36 5.70 - 7.60: 9 7.60 - 9.50: 6 Bond angle restraints: 15696 Sorted by residual: angle pdb=" N GLU A 470 " pdb=" CA GLU A 470 " pdb=" C GLU A 470 " ideal model delta sigma weight residual 111.28 120.78 -9.50 1.09e+00 8.42e-01 7.59e+01 angle pdb=" N LYS A 469 " pdb=" CA LYS A 469 " pdb=" C LYS A 469 " ideal model delta sigma weight residual 111.28 120.68 -9.40 1.09e+00 8.42e-01 7.44e+01 angle pdb=" N GLU B 470 " pdb=" CA GLU B 470 " pdb=" C GLU B 470 " ideal model delta sigma weight residual 111.28 119.74 -8.46 1.09e+00 8.42e-01 6.02e+01 angle pdb=" N LYS B 469 " pdb=" CA LYS B 469 " pdb=" C LYS B 469 " ideal model delta sigma weight residual 111.28 119.01 -7.73 1.09e+00 8.42e-01 5.02e+01 angle pdb=" N GLU B 468 " pdb=" CA GLU B 468 " pdb=" C GLU B 468 " ideal model delta sigma weight residual 111.28 117.62 -6.34 1.09e+00 8.42e-01 3.38e+01 ... (remaining 15691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6392 17.66 - 35.32: 525 35.32 - 52.97: 120 52.97 - 70.63: 25 70.63 - 88.29: 6 Dihedral angle restraints: 7068 sinusoidal: 2846 harmonic: 4222 Sorted by residual: dihedral pdb=" N SER A 651 " pdb=" C SER A 651 " pdb=" CA SER A 651 " pdb=" CB SER A 651 " ideal model delta harmonic sigma weight residual 122.80 131.50 -8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" C SER A 651 " pdb=" N SER A 651 " pdb=" CA SER A 651 " pdb=" CB SER A 651 " ideal model delta harmonic sigma weight residual -122.60 -130.77 8.17 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CA ASP A 94 " pdb=" CB ASP A 94 " pdb=" CG ASP A 94 " pdb=" OD1 ASP A 94 " ideal model delta sinusoidal sigma weight residual -30.00 -84.84 54.84 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1642 0.068 - 0.136: 189 0.136 - 0.204: 14 0.204 - 0.271: 3 0.271 - 0.339: 4 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA LYS A 469 " pdb=" N LYS A 469 " pdb=" C LYS A 469 " pdb=" CB LYS A 469 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA SER A 651 " pdb=" N SER A 651 " pdb=" C SER A 651 " pdb=" CB SER A 651 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA GLU A 470 " pdb=" N GLU A 470 " pdb=" C GLU A 470 " pdb=" CB GLU A 470 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1849 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 532 " -0.028 2.00e-02 2.50e+03 5.52e-02 3.04e+01 pdb=" C LEU A 532 " 0.095 2.00e-02 2.50e+03 pdb=" O LEU A 532 " -0.036 2.00e-02 2.50e+03 pdb=" N MET A 533 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C LEU A 710 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 710 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 711 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 328 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 329 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.025 5.00e-02 4.00e+02 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 13 2.36 - 2.99: 6068 2.99 - 3.63: 16922 3.63 - 4.26: 24023 4.26 - 4.90: 40984 Nonbonded interactions: 88010 Sorted by model distance: nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 1.719 2.170 nonbonded pdb=" OE1 GLN A 567 " pdb="MG MG A 802 " model vdw 1.823 2.170 nonbonded pdb=" O1B ATP A 801 " pdb="MG MG A 802 " model vdw 1.824 2.170 nonbonded pdb=" OD1 ASP B 647 " pdb=" N GLU B 648 " model vdw 2.116 3.120 nonbonded pdb=" N GLU A 669 " pdb=" OE1 GLU A 669 " model vdw 2.197 3.120 ... (remaining 88005 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.480 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.004 0.048 11636 Z= 0.245 Angle : 0.682 9.498 15696 Z= 0.433 Chirality : 0.047 0.339 1852 Planarity : 0.003 0.055 1944 Dihedral : 13.819 88.290 4356 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 0.72 % Allowed : 0.64 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.18 (0.22), residues: 1456 helix: 1.42 (0.19), residues: 832 sheet: -1.15 (0.42), residues: 138 loop : -1.81 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 132 HIS 0.005 0.001 HIS A 249 PHE 0.015 0.002 PHE A 83 TYR 0.013 0.001 TYR B 389 ARG 0.007 0.001 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 432 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ASN cc_start: 0.8092 (m-40) cc_final: 0.7519 (t0) REVERT: C 19 MET cc_start: 0.6545 (mmp) cc_final: 0.6144 (mmp) REVERT: B 39 LEU cc_start: 0.8705 (tp) cc_final: 0.8442 (tp) REVERT: B 518 VAL cc_start: 0.8792 (p) cc_final: 0.8563 (m) REVERT: B 598 MET cc_start: 0.7849 (mtp) cc_final: 0.7547 (mtt) outliers start: 9 outliers final: 1 residues processed: 439 average time/residue: 0.2539 time to fit residues: 154.1747 Evaluate side-chains 271 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 54 ASN A 99 HIS A 259 ASN A 305 ASN A 424 GLN A 450 GLN A 490 ASN A 602 HIS A 629 GLN A 704 HIS B 99 HIS B 259 ASN B 660 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11636 Z= 0.268 Angle : 0.627 6.887 15696 Z= 0.330 Chirality : 0.042 0.152 1852 Planarity : 0.004 0.068 1944 Dihedral : 7.233 87.348 1622 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.69 % Allowed : 15.25 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.60 (0.22), residues: 1456 helix: 1.73 (0.19), residues: 822 sheet: -1.01 (0.42), residues: 142 loop : -1.51 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 132 HIS 0.005 0.002 HIS A 602 PHE 0.016 0.002 PHE A 428 TYR 0.013 0.001 TYR B 319 ARG 0.013 0.001 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7652 (t80) REVERT: A 335 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6519 (ptp-110) REVERT: A 606 GLU cc_start: 0.7188 (mp0) cc_final: 0.6988 (mp0) REVERT: B 99 HIS cc_start: 0.7750 (t70) cc_final: 0.7471 (t70) REVERT: B 694 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7599 (ttpt) outliers start: 46 outliers final: 34 residues processed: 309 average time/residue: 0.2221 time to fit residues: 100.4300 Evaluate side-chains 277 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 105 optimal weight: 3.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS A 278 GLN A 419 ASN B 660 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11636 Z= 0.188 Angle : 0.562 6.987 15696 Z= 0.294 Chirality : 0.041 0.168 1852 Planarity : 0.003 0.057 1944 Dihedral : 6.295 76.876 1622 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.77 % Allowed : 19.82 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.74 (0.22), residues: 1456 helix: 1.86 (0.18), residues: 822 sheet: -0.86 (0.42), residues: 140 loop : -1.50 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 132 HIS 0.004 0.001 HIS B 660 PHE 0.012 0.001 PHE A 428 TYR 0.009 0.001 TYR A 319 ARG 0.009 0.001 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.8519 (t0) cc_final: 0.8273 (t0) REVERT: A 420 MET cc_start: 0.6015 (ttm) cc_final: 0.5669 (mtp) REVERT: B 269 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7314 (mtt90) REVERT: D 18 LEU cc_start: 0.8739 (mt) cc_final: 0.8457 (mm) outliers start: 47 outliers final: 32 residues processed: 279 average time/residue: 0.2163 time to fit residues: 88.0598 Evaluate side-chains 262 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 715 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 0.0870 chunk 139 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 124 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS B 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11636 Z= 0.201 Angle : 0.575 8.564 15696 Z= 0.295 Chirality : 0.041 0.143 1852 Planarity : 0.003 0.048 1944 Dihedral : 5.751 60.895 1622 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.74 % Allowed : 20.87 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.80 (0.22), residues: 1456 helix: 1.90 (0.18), residues: 822 sheet: -0.80 (0.42), residues: 140 loop : -1.47 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.003 0.001 HIS B 679 PHE 0.013 0.001 PHE A 213 TYR 0.009 0.001 TYR A 225 ARG 0.011 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 246 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.7465 (ttm) cc_final: 0.7148 (mtp) REVERT: A 340 ASP cc_start: 0.8473 (t0) cc_final: 0.8220 (t0) REVERT: A 420 MET cc_start: 0.6469 (ttm) cc_final: 0.6084 (mtp) REVERT: A 606 GLU cc_start: 0.6927 (mp0) cc_final: 0.6619 (mp0) REVERT: B 633 ILE cc_start: 0.8828 (mp) cc_final: 0.8600 (mp) outliers start: 59 outliers final: 42 residues processed: 281 average time/residue: 0.2158 time to fit residues: 88.4748 Evaluate side-chains 272 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 715 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 118 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 0.0770 chunk 35 optimal weight: 0.2980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 450 GLN B 54 ASN B 99 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11636 Z= 0.173 Angle : 0.559 8.559 15696 Z= 0.287 Chirality : 0.040 0.140 1852 Planarity : 0.003 0.045 1944 Dihedral : 5.467 59.701 1622 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.93 % Allowed : 23.19 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.88 (0.22), residues: 1456 helix: 1.99 (0.18), residues: 822 sheet: -0.78 (0.43), residues: 138 loop : -1.48 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.014 0.002 HIS B 660 PHE 0.017 0.001 PHE B 428 TYR 0.009 0.001 TYR A 225 ARG 0.008 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.7399 (ttm) cc_final: 0.7164 (mtp) REVERT: A 340 ASP cc_start: 0.8485 (t0) cc_final: 0.8269 (t0) REVERT: A 420 MET cc_start: 0.6463 (ttm) cc_final: 0.6059 (mtp) REVERT: A 450 GLN cc_start: 0.8140 (tp40) cc_final: 0.7875 (tp40) REVERT: A 606 GLU cc_start: 0.6821 (mp0) cc_final: 0.6274 (mp0) REVERT: D 18 LEU cc_start: 0.8696 (mt) cc_final: 0.8483 (mm) outliers start: 49 outliers final: 39 residues processed: 280 average time/residue: 0.2254 time to fit residues: 91.0175 Evaluate side-chains 274 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 715 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS B 278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11636 Z= 0.204 Angle : 0.590 8.849 15696 Z= 0.301 Chirality : 0.041 0.136 1852 Planarity : 0.003 0.046 1944 Dihedral : 5.389 59.528 1622 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.33 % Allowed : 23.19 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.89 (0.22), residues: 1456 helix: 1.96 (0.18), residues: 836 sheet: -0.74 (0.42), residues: 138 loop : -1.51 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.008 0.001 HIS B 660 PHE 0.013 0.001 PHE B 428 TYR 0.009 0.001 TYR A 225 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7338 (mtp) cc_final: 0.7134 (mtp) REVERT: A 340 ASP cc_start: 0.8449 (t0) cc_final: 0.8225 (t0) REVERT: A 420 MET cc_start: 0.6512 (ttm) cc_final: 0.6028 (mtp) REVERT: D 18 LEU cc_start: 0.8739 (mt) cc_final: 0.8514 (mm) outliers start: 54 outliers final: 45 residues processed: 271 average time/residue: 0.2245 time to fit residues: 88.2796 Evaluate side-chains 271 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 715 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 278 GLN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11636 Z= 0.223 Angle : 0.610 8.336 15696 Z= 0.311 Chirality : 0.041 0.144 1852 Planarity : 0.003 0.038 1944 Dihedral : 5.361 59.301 1622 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.09 % Allowed : 23.60 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.88 (0.22), residues: 1456 helix: 1.97 (0.18), residues: 836 sheet: -0.77 (0.43), residues: 138 loop : -1.54 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.009 0.001 HIS B 660 PHE 0.016 0.001 PHE B 173 TYR 0.011 0.001 TYR A 225 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7354 (mtp) cc_final: 0.7152 (mtp) REVERT: A 340 ASP cc_start: 0.8464 (t0) cc_final: 0.8224 (t0) REVERT: A 420 MET cc_start: 0.6526 (ttm) cc_final: 0.6021 (mtp) REVERT: A 655 SER cc_start: 0.8466 (m) cc_final: 0.8200 (p) REVERT: D 18 LEU cc_start: 0.8782 (mt) cc_final: 0.8560 (mm) outliers start: 51 outliers final: 42 residues processed: 266 average time/residue: 0.2136 time to fit residues: 83.8878 Evaluate side-chains 272 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 0.0020 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 249 HIS B 278 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11636 Z= 0.178 Angle : 0.607 8.500 15696 Z= 0.307 Chirality : 0.041 0.232 1852 Planarity : 0.003 0.038 1944 Dihedral : 5.243 58.623 1622 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.61 % Allowed : 24.48 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.95 (0.22), residues: 1456 helix: 2.03 (0.18), residues: 836 sheet: -0.83 (0.42), residues: 138 loop : -1.50 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.009 0.001 HIS B 660 PHE 0.014 0.001 PHE B 428 TYR 0.010 0.001 TYR A 225 ARG 0.008 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 MET cc_start: 0.6542 (ttm) cc_final: 0.6043 (mtp) REVERT: A 655 SER cc_start: 0.8434 (m) cc_final: 0.8187 (p) REVERT: D 18 LEU cc_start: 0.8751 (mt) cc_final: 0.8540 (mm) outliers start: 45 outliers final: 37 residues processed: 262 average time/residue: 0.2109 time to fit residues: 81.3017 Evaluate side-chains 262 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 715 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 129 optimal weight: 0.0470 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.0980 chunk 122 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11636 Z= 0.175 Angle : 0.616 8.945 15696 Z= 0.310 Chirality : 0.041 0.171 1852 Planarity : 0.003 0.038 1944 Dihedral : 5.177 57.817 1622 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.89 % Allowed : 25.36 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.98 (0.22), residues: 1456 helix: 2.04 (0.18), residues: 836 sheet: -0.77 (0.42), residues: 138 loop : -1.46 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.009 0.001 HIS B 660 PHE 0.024 0.001 PHE A 428 TYR 0.009 0.001 TYR A 225 ARG 0.007 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.7398 (tt0) cc_final: 0.7080 (tt0) REVERT: A 420 MET cc_start: 0.6490 (ttm) cc_final: 0.6030 (mtp) REVERT: A 655 SER cc_start: 0.8382 (m) cc_final: 0.8125 (p) outliers start: 36 outliers final: 32 residues processed: 262 average time/residue: 0.2187 time to fit residues: 84.7779 Evaluate side-chains 259 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 0.0570 chunk 11 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 278 GLN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11636 Z= 0.250 Angle : 0.682 16.646 15696 Z= 0.340 Chirality : 0.042 0.157 1852 Planarity : 0.003 0.036 1944 Dihedral : 5.277 58.559 1622 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.29 % Allowed : 25.52 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.89 (0.22), residues: 1456 helix: 1.99 (0.18), residues: 834 sheet: -0.82 (0.42), residues: 138 loop : -1.52 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.010 0.001 HIS B 660 PHE 0.024 0.002 PHE A 428 TYR 0.011 0.001 TYR A 225 ARG 0.008 0.001 ARG B 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7449 (mtm) cc_final: 0.7157 (mtm) REVERT: A 236 MET cc_start: 0.7373 (mtp) cc_final: 0.7157 (mtp) REVERT: A 420 MET cc_start: 0.6487 (ttm) cc_final: 0.6026 (mtp) REVERT: A 637 LEU cc_start: 0.8907 (mt) cc_final: 0.8570 (tp) REVERT: A 655 SER cc_start: 0.8484 (m) cc_final: 0.8255 (p) outliers start: 41 outliers final: 34 residues processed: 254 average time/residue: 0.2217 time to fit residues: 82.9328 Evaluate side-chains 260 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.0870 chunk 47 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 450 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 429 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.133923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109583 restraints weight = 27544.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.112364 restraints weight = 14339.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114224 restraints weight = 9178.094| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11636 Z= 0.192 Angle : 0.660 15.942 15696 Z= 0.330 Chirality : 0.042 0.185 1852 Planarity : 0.003 0.037 1944 Dihedral : 5.203 58.144 1622 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.81 % Allowed : 26.32 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.91 (0.22), residues: 1456 helix: 2.00 (0.18), residues: 832 sheet: -0.79 (0.42), residues: 138 loop : -1.49 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.010 0.001 HIS B 660 PHE 0.024 0.001 PHE A 428 TYR 0.009 0.001 TYR A 225 ARG 0.008 0.001 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.93 seconds wall clock time: 48 minutes 10.35 seconds (2890.35 seconds total)