Starting phenix.real_space_refine on Fri Jul 3 02:05:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t56_25696/07_2026/7t56_25696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t56_25696/07_2026/7t56_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_25696/07_2026/7t56_25696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t56_25696/07_2026/7t56_25696.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7t56_25696/07_2026/7t56_25696.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t56_25696/07_2026/7t56_25696.cif" model { file = "/net/cci-nas-00/data/ceres_data/7t56_25696/07_2026/7t56_25696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t56_25696/07_2026/7t56_25696.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.36, per 1000 atoms: 0.29 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: 0.98 Conformation dependent library (CDL) restraints added in 616.7 milliseconds 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: 0.36 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: 2.18 Time building geometry restraints manager: 1.33 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 - 16.07: 6301 16.07 - 32.14: 535 32.14 - 48.21: 133 48.21 - 64.28: 33 64.28 - 80.35: 4 Dihedral angle restraints: 7006 sinusoidal: 2784 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 7003 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: 0.03 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: 1.770 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.210 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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= 0.199 Angle : 0.682 9.498 15696 Z= 0.433 Chirality : 0.047 0.339 1852 Planarity : 0.003 0.055 1944 Dihedral : 13.024 80.347 4294 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 9.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG A 458 TYR 0.013 0.001 TYR B 389 PHE 0.015 0.002 PHE A 83 TRP 0.028 0.002 TRP B 132 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.20 (11636) covalent geometry : angle 0.68227 / 0.43 (15696) hydrogen bonds : bond 0.16305 / 11.29 ( 678) hydrogen bonds : angle 5.74859 / 4.01 ( 1962) *********************** 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 : 0.488 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: 0.1131 time to fit residues: 69.9890 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 : 0.462 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 54 ASN A 99 HIS A 259 ASN A 305 ASN A 419 ASN A 424 GLN A 450 GLN A 490 ASN ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 704 HIS B 99 HIS B 259 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.143112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119842 restraints weight = 30816.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.123113 restraints weight = 14503.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.125241 restraints weight = 8696.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.126475 restraints weight = 6104.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.127407 restraints weight = 4849.900| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11636 Z= 0.164 Angle : 0.610 6.745 15696 Z= 0.320 Chirality : 0.041 0.158 1852 Planarity : 0.004 0.067 1944 Dihedral : 4.816 80.814 1560 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.45 % Allowed : 15.57 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1456 helix: 1.78 (0.19), residues: 822 sheet: -0.99 (0.42), residues: 142 loop : -1.50 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 680 TYR 0.013 0.001 TYR B 319 PHE 0.016 0.002 PHE B 217 TRP 0.014 0.002 TRP A 718 HIS 0.005 0.002 HIS A 704 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (11636) covalent geometry : angle 0.61026 / 0.32 (15696) hydrogen bonds : bond 0.04854 / 3.27 ( 678) hydrogen bonds : angle 4.36807 / 3.10 ( 1962) *********************** 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 326 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.9366 (tp) cc_final: 0.9144 (tt) REVERT: A 305 ASN cc_start: 0.7500 (t0) cc_final: 0.7210 (t0) REVERT: A 335 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7027 (ptp-110) REVERT: A 606 GLU cc_start: 0.7662 (mp0) cc_final: 0.7379 (mp0) REVERT: A 679 HIS cc_start: 0.7612 (t-90) cc_final: 0.7367 (p90) REVERT: B 36 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7991 (mtpp) REVERT: B 49 ASP cc_start: 0.8524 (t0) cc_final: 0.8088 (p0) REVERT: B 99 HIS cc_start: 0.8177 (t70) cc_final: 0.7916 (t70) REVERT: B 239 ASP cc_start: 0.8897 (t0) cc_final: 0.8619 (t0) REVERT: B 660 HIS cc_start: 0.8117 (t70) cc_final: 0.7822 (t70) outliers start: 43 outliers final: 31 residues processed: 310 average time/residue: 0.0986 time to fit residues: 45.3479 Evaluate side-chains 276 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 316 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 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 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 97 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 99 HIS A 278 GLN A 602 HIS B 586 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.141193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.117749 restraints weight = 31314.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.120982 restraints weight = 14630.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.123057 restraints weight = 8772.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.124437 restraints weight = 6177.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.125172 restraints weight = 4870.622| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11636 Z= 0.147 Angle : 0.568 6.547 15696 Z= 0.296 Chirality : 0.041 0.185 1852 Planarity : 0.003 0.056 1944 Dihedral : 4.674 75.139 1560 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.25 % Allowed : 19.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.22), residues: 1456 helix: 1.84 (0.18), residues: 822 sheet: -0.81 (0.43), residues: 136 loop : -1.53 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.010 0.001 TYR A 319 PHE 0.012 0.001 PHE B 194 TRP 0.012 0.001 TRP B 132 HIS 0.004 0.001 HIS A 704 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (11636) covalent geometry : angle 0.56804 / 0.30 (15696) hydrogen bonds : bond 0.04592 / 3.11 ( 678) hydrogen bonds : angle 4.21033 / 2.99 ( 1962) *********************** 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 309 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8919 (tpp) cc_final: 0.8588 (tpp) REVERT: A 305 ASN cc_start: 0.7617 (t0) cc_final: 0.7364 (t0) REVERT: A 340 ASP cc_start: 0.8854 (t0) cc_final: 0.8452 (t0) REVERT: B 36 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7970 (mtpp) REVERT: B 49 ASP cc_start: 0.8658 (t0) cc_final: 0.8277 (p0) REVERT: B 269 ARG cc_start: 0.8396 (mtt90) cc_final: 0.7463 (mtt90) REVERT: B 637 LEU cc_start: 0.9359 (tp) cc_final: 0.8940 (pp) REVERT: D 18 LEU cc_start: 0.9201 (mt) cc_final: 0.8879 (mm) outliers start: 53 outliers final: 41 residues processed: 289 average time/residue: 0.0963 time to fit residues: 41.3222 Evaluate side-chains 275 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 18 LEU 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 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 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 ASN 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 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 271 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 99 HIS B 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.141573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.118106 restraints weight = 31272.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.121366 restraints weight = 14697.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.123475 restraints weight = 8779.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.124821 restraints weight = 6190.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.125564 restraints weight = 4900.592| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11636 Z= 0.126 Angle : 0.556 8.697 15696 Z= 0.285 Chirality : 0.041 0.140 1852 Planarity : 0.003 0.048 1944 Dihedral : 4.546 71.862 1560 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.65 % Allowed : 20.47 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.22), residues: 1456 helix: 1.96 (0.19), residues: 822 sheet: -0.76 (0.43), residues: 140 loop : -1.47 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.010 0.001 TYR A 189 PHE 0.013 0.001 PHE A 213 TRP 0.012 0.001 TRP B 132 HIS 0.003 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (11636) covalent geometry : angle 0.55596 / 0.29 (15696) hydrogen bonds : bond 0.04260 / 2.87 ( 678) hydrogen bonds : angle 4.03921 / 2.88 ( 1962) *********************** 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 319 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8850 (tpp) cc_final: 0.8635 (tpp) REVERT: A 340 ASP cc_start: 0.8792 (t0) cc_final: 0.8410 (t0) REVERT: B 36 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7978 (mtpp) REVERT: B 108 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7809 (p0) REVERT: B 637 LEU cc_start: 0.9290 (tp) cc_final: 0.9041 (pp) REVERT: B 660 HIS cc_start: 0.8067 (t-170) cc_final: 0.7832 (t-170) REVERT: D 18 LEU cc_start: 0.9158 (mt) cc_final: 0.8861 (mm) outliers start: 58 outliers final: 40 residues processed: 295 average time/residue: 0.0889 time to fit residues: 39.5455 Evaluate side-chains 283 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 99 HIS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 VAL 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 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 396 THR 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 97 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS B 54 ASN B 99 HIS B 278 GLN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.132819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108265 restraints weight = 27482.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111117 restraints weight = 13792.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113008 restraints weight = 8583.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.114226 restraints weight = 6211.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114912 restraints weight = 4996.055| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11636 Z= 0.125 Angle : 0.561 8.193 15696 Z= 0.288 Chirality : 0.041 0.149 1852 Planarity : 0.003 0.055 1944 Dihedral : 4.501 69.642 1560 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.93 % Allowed : 23.52 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.22), residues: 1456 helix: 2.01 (0.18), residues: 822 sheet: -0.76 (0.43), residues: 138 loop : -1.46 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 96 TYR 0.009 0.001 TYR A 225 PHE 0.011 0.001 PHE B 257 TRP 0.011 0.001 TRP B 132 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (11636) covalent geometry : angle 0.56128 / 0.29 (15696) hydrogen bonds : bond 0.04158 / 2.81 ( 678) hydrogen bonds : angle 3.95935 / 2.83 ( 1962) *********************** 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 300 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8691 (mmt-90) cc_final: 0.8388 (mmt-90) REVERT: A 293 MET cc_start: 0.8153 (ttm) cc_final: 0.7721 (mtp) REVERT: A 340 ASP cc_start: 0.8778 (t0) cc_final: 0.8390 (t0) REVERT: C 17 GLU cc_start: 0.8783 (pt0) cc_final: 0.8500 (pt0) REVERT: B 108 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7808 (p0) REVERT: B 269 ARG cc_start: 0.8391 (mtt90) cc_final: 0.7911 (mtt90) REVERT: B 637 LEU cc_start: 0.9311 (tp) cc_final: 0.9062 (pp) REVERT: B 660 HIS cc_start: 0.8208 (t-170) cc_final: 0.7970 (t-170) REVERT: D 18 LEU cc_start: 0.9125 (mt) cc_final: 0.8857 (mm) outliers start: 49 outliers final: 38 residues processed: 279 average time/residue: 0.0916 time to fit residues: 38.1398 Evaluate side-chains 279 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 337 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 426 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 108 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 VAL 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 432 LEU Chi-restraints excluded: chain B residue 502 LEU 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 84 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 8.9990 chunk 142 optimal weight: 0.0070 chunk 50 optimal weight: 0.0870 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 99 HIS A 249 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 278 GLN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.133724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109327 restraints weight = 27586.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112212 restraints weight = 13814.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.114125 restraints weight = 8573.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.115235 restraints weight = 6192.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.116043 restraints weight = 5032.508| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11636 Z= 0.110 Angle : 0.556 7.912 15696 Z= 0.283 Chirality : 0.040 0.150 1852 Planarity : 0.003 0.041 1944 Dihedral : 4.446 67.961 1560 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.29 % Allowed : 23.60 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1456 helix: 2.07 (0.19), residues: 822 sheet: -0.62 (0.43), residues: 138 loop : -1.39 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.009 0.001 TYR A 225 PHE 0.010 0.001 PHE A 257 TRP 0.011 0.001 TRP B 132 HIS 0.010 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (11636) covalent geometry : angle 0.55559 / 0.28 (15696) hydrogen bonds : bond 0.03887 / 2.63 ( 678) hydrogen bonds : angle 3.88146 / 2.77 ( 1962) *********************** 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 299 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8648 (mmt-90) cc_final: 0.8404 (mmt-90) REVERT: A 293 MET cc_start: 0.8032 (ttm) cc_final: 0.7738 (mtp) REVERT: A 340 ASP cc_start: 0.8796 (t0) cc_final: 0.8389 (t0) REVERT: B 108 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7666 (p0) REVERT: B 269 ARG cc_start: 0.8395 (mtt90) cc_final: 0.7921 (mtt90) REVERT: B 637 LEU cc_start: 0.9311 (tp) cc_final: 0.9074 (pp) REVERT: B 660 HIS cc_start: 0.8198 (t-170) cc_final: 0.7922 (t-170) REVERT: B 698 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7418 (tp) REVERT: D 18 LEU cc_start: 0.9119 (mt) cc_final: 0.8860 (mm) outliers start: 41 outliers final: 30 residues processed: 282 average time/residue: 0.0894 time to fit residues: 37.8989 Evaluate side-chains 272 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 426 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 108 ASN Chi-restraints excluded: chain B residue 113 VAL 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 350 GLU 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 543 ILE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 698 ILE 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 85 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.133524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.109101 restraints weight = 27411.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.111953 restraints weight = 13704.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113790 restraints weight = 8527.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115027 restraints weight = 6169.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115719 restraints weight = 4968.134| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11636 Z= 0.123 Angle : 0.576 7.857 15696 Z= 0.292 Chirality : 0.040 0.150 1852 Planarity : 0.003 0.038 1944 Dihedral : 4.349 66.774 1560 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.45 % Allowed : 24.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1456 helix: 2.03 (0.18), residues: 836 sheet: -0.66 (0.43), residues: 138 loop : -1.43 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.009 0.001 TYR A 225 PHE 0.010 0.001 PHE A 257 TRP 0.009 0.001 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11636) covalent geometry : angle 0.57593 / 0.29 (15696) hydrogen bonds : bond 0.03985 / 2.70 ( 678) hydrogen bonds : angle 3.87115 / 2.77 ( 1962) *********************** 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 279 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8660 (mmt-90) cc_final: 0.8434 (mmt-90) REVERT: A 293 MET cc_start: 0.7990 (ttm) cc_final: 0.7775 (mtp) REVERT: A 340 ASP cc_start: 0.8784 (t0) cc_final: 0.8396 (t0) REVERT: A 450 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8347 (tp40) REVERT: B 99 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7868 (t70) REVERT: B 108 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7747 (p0) REVERT: B 153 ASN cc_start: 0.7806 (t0) cc_final: 0.7549 (t0) REVERT: B 269 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7883 (mtt90) REVERT: B 637 LEU cc_start: 0.9357 (tp) cc_final: 0.9080 (pp) REVERT: B 660 HIS cc_start: 0.8238 (t-170) cc_final: 0.7978 (t-170) REVERT: B 698 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7478 (tp) REVERT: D 18 LEU cc_start: 0.9111 (mt) cc_final: 0.8863 (mm) outliers start: 43 outliers final: 35 residues processed: 261 average time/residue: 0.0969 time to fit residues: 37.8707 Evaluate side-chains 273 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 426 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 99 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 108 ASN 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 350 GLU 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 543 ILE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 715 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.0170 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 99 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.131020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106360 restraints weight = 27495.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109137 restraints weight = 14007.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.110961 restraints weight = 8850.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.112140 restraints weight = 6454.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.112786 restraints weight = 5236.277| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4823 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= 0.146 Angle : 0.592 8.305 15696 Z= 0.301 Chirality : 0.041 0.140 1852 Planarity : 0.003 0.037 1944 Dihedral : 4.349 67.021 1560 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.45 % Allowed : 24.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1456 helix: 2.06 (0.18), residues: 836 sheet: -0.72 (0.43), residues: 138 loop : -1.47 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 96 TYR 0.011 0.001 TYR A 225 PHE 0.013 0.001 PHE B 217 TRP 0.009 0.001 TRP B 132 HIS 0.008 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11636) covalent geometry : angle 0.59211 / 0.30 (15696) hydrogen bonds : bond 0.04268 / 2.91 ( 678) hydrogen bonds : angle 3.95987 / 2.82 ( 1962) *********************** 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 286 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8699 (mmt-90) cc_final: 0.8467 (mmt-90) REVERT: A 236 MET cc_start: 0.7993 (mtp) cc_final: 0.7778 (mtp) REVERT: A 293 MET cc_start: 0.8033 (ttm) cc_final: 0.7756 (mtp) REVERT: A 340 ASP cc_start: 0.8777 (t0) cc_final: 0.8413 (t0) REVERT: A 450 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8336 (tp40) REVERT: A 655 SER cc_start: 0.8872 (m) cc_final: 0.8622 (p) REVERT: A 679 HIS cc_start: 0.7897 (t-90) cc_final: 0.7575 (t-90) REVERT: C 17 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8537 (pt0) REVERT: B 108 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7846 (p0) REVERT: B 153 ASN cc_start: 0.7920 (t0) cc_final: 0.7531 (t0) REVERT: B 269 ARG cc_start: 0.8409 (mtt90) cc_final: 0.7826 (mtm-85) REVERT: B 660 HIS cc_start: 0.8262 (t-170) cc_final: 0.8016 (t-170) REVERT: D 18 LEU cc_start: 0.9119 (mt) cc_final: 0.8878 (mm) outliers start: 43 outliers final: 35 residues processed: 269 average time/residue: 0.0983 time to fit residues: 39.3808 Evaluate side-chains 270 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 426 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 C residue 16 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain B residue 108 ASN 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 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 663 ASP Chi-restraints excluded: chain B residue 698 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 140 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS A 305 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.131373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106779 restraints weight = 27554.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.109569 restraints weight = 13976.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.111408 restraints weight = 8791.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.112598 restraints weight = 6405.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113347 restraints weight = 5179.382| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11636 Z= 0.131 Angle : 0.620 16.118 15696 Z= 0.308 Chirality : 0.041 0.143 1852 Planarity : 0.003 0.037 1944 Dihedral : 4.318 66.491 1560 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.53 % Allowed : 24.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.22), residues: 1456 helix: 2.02 (0.18), residues: 836 sheet: -0.70 (0.43), residues: 138 loop : -1.46 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 335 TYR 0.011 0.001 TYR B 714 PHE 0.024 0.001 PHE B 715 TRP 0.010 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11636) covalent geometry : angle 0.61951 / 0.31 (15696) hydrogen bonds : bond 0.04201 / 2.86 ( 678) hydrogen bonds : angle 3.97076 / 2.84 ( 1962) *********************** 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 281 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8272 (tt0) cc_final: 0.7808 (tt0) REVERT: A 293 MET cc_start: 0.8015 (ttm) cc_final: 0.7795 (mtp) REVERT: A 340 ASP cc_start: 0.8768 (t0) cc_final: 0.8405 (t0) REVERT: A 450 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8295 (tp40) REVERT: A 655 SER cc_start: 0.8860 (m) cc_final: 0.8601 (p) REVERT: A 679 HIS cc_start: 0.7844 (t-90) cc_final: 0.7528 (t-90) REVERT: C 17 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: B 99 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7985 (t70) REVERT: B 108 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7781 (p0) REVERT: B 153 ASN cc_start: 0.8059 (t0) cc_final: 0.7565 (t0) REVERT: B 269 ARG cc_start: 0.8385 (mtt90) cc_final: 0.7815 (mtm-85) REVERT: B 461 GLU cc_start: 0.8468 (tp30) cc_final: 0.8167 (tp30) REVERT: B 660 HIS cc_start: 0.8250 (t-170) cc_final: 0.7975 (t-170) REVERT: D 18 LEU cc_start: 0.9147 (mt) cc_final: 0.8909 (mm) outliers start: 44 outliers final: 37 residues processed: 260 average time/residue: 0.1026 time to fit residues: 38.9249 Evaluate side-chains 266 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 426 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 C residue 16 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 108 ASN 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 445 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 692 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.131540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.106767 restraints weight = 27661.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109587 restraints weight = 14126.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.111449 restraints weight = 8896.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.112518 restraints weight = 6474.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113401 restraints weight = 5309.775| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5096 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= 0.137 Angle : 0.656 16.108 15696 Z= 0.328 Chirality : 0.042 0.191 1852 Planarity : 0.003 0.070 1944 Dihedral : 4.350 66.038 1560 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.45 % Allowed : 25.12 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.22), residues: 1456 helix: 1.99 (0.18), residues: 836 sheet: -0.70 (0.43), residues: 138 loop : -1.48 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 335 TYR 0.010 0.001 TYR B 714 PHE 0.017 0.001 PHE A 615 TRP 0.010 0.001 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (11636) covalent geometry : angle 0.65566 / 0.33 (15696) hydrogen bonds : bond 0.04282 / 2.90 ( 678) hydrogen bonds : angle 4.06329 / 2.88 ( 1962) ********************** 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 277 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8007 (ttm) cc_final: 0.7793 (mtp) REVERT: A 340 ASP cc_start: 0.8763 (t0) cc_final: 0.8407 (t0) REVERT: A 450 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8260 (tp40) REVERT: A 655 SER cc_start: 0.8831 (m) cc_final: 0.8577 (p) REVERT: A 679 HIS cc_start: 0.7795 (t-90) cc_final: 0.7488 (t-90) REVERT: C 17 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: B 99 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7919 (t70) REVERT: B 108 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7752 (p0) REVERT: B 153 ASN cc_start: 0.8110 (t0) cc_final: 0.7615 (t0) REVERT: B 154 MET cc_start: 0.8353 (ttp) cc_final: 0.8088 (ttm) REVERT: B 269 ARG cc_start: 0.8381 (mtt90) cc_final: 0.7821 (mtm-85) REVERT: B 461 GLU cc_start: 0.8459 (tp30) cc_final: 0.8100 (tp30) REVERT: B 660 HIS cc_start: 0.8227 (t-170) cc_final: 0.7946 (t-170) REVERT: D 18 LEU cc_start: 0.9134 (mt) cc_final: 0.8928 (mm) REVERT: D 19 MET cc_start: 0.8819 (mmm) cc_final: 0.8570 (mmm) outliers start: 43 outliers final: 35 residues processed: 259 average time/residue: 0.0951 time to fit residues: 37.0169 Evaluate side-chains 268 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 426 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 C residue 17 GLU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 108 ASN 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 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 445 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 103 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.130615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105732 restraints weight = 27946.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108535 restraints weight = 14289.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.110398 restraints weight = 9027.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111452 restraints weight = 6584.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112225 restraints weight = 5405.184| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11636 Z= 0.149 Angle : 0.648 16.044 15696 Z= 0.327 Chirality : 0.042 0.180 1852 Planarity : 0.003 0.056 1944 Dihedral : 4.331 66.243 1560 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.53 % Allowed : 24.88 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.22), residues: 1456 helix: 1.99 (0.18), residues: 836 sheet: -0.71 (0.40), residues: 158 loop : -1.57 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 335 TYR 0.010 0.001 TYR A 225 PHE 0.013 0.001 PHE B 428 TRP 0.009 0.001 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (11636) covalent geometry : angle 0.64764 / 0.33 (15696) hydrogen bonds : bond 0.04392 / 2.98 ( 678) hydrogen bonds : angle 4.14300 / 2.94 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.85 seconds wall clock time: 37 minutes 6.57 seconds (2226.57 seconds total)