Starting phenix.real_space_refine on Tue Jun 10 09:39:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t56_25696/06_2025/7t56_25696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t56_25696/06_2025/7t56_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_25696/06_2025/7t56_25696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t56_25696/06_2025/7t56_25696.map" model { file = "/net/cci-nas-00/data/ceres_data/7t56_25696/06_2025/7t56_25696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t56_25696/06_2025/7t56_25696.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 7382 2.51 5 N 1870 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.49, per 1000 atoms: 0.65 Number of scatterers: 11460 At special positions: 0 Unit cell: (109.18, 107.12, 138.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 6 15.00 Mg 2 11.99 O 2140 8.00 N 1870 7.00 C 7382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 8 sheets defined 61.3% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 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: 3.47 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3576 1.34 - 1.46: 1485 1.46 - 1.57: 6460 1.57 - 1.69: 11 1.69 - 1.81: 104 Bond restraints: 11636 Sorted by residual: bond pdb=" N MET A 533 " pdb=" CA MET A 533 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.26e-02 6.30e+03 9.59e+00 bond pdb=" N VAL A 672 " pdb=" CA VAL A 672 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.19e-02 7.06e+03 8.51e+00 bond pdb=" N VAL A 501 " pdb=" CA VAL A 501 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.59e+00 bond pdb=" N LEU A 502 " pdb=" CA LEU A 502 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.22e-02 6.72e+03 7.43e+00 bond pdb=" N ILE A 505 " pdb=" CA ILE A 505 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.19e+00 ... (remaining 11631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 15333 1.90 - 3.80: 312 3.80 - 5.70: 36 5.70 - 7.60: 9 7.60 - 9.50: 6 Bond angle restraints: 15696 Sorted by residual: angle pdb=" N GLU A 470 " pdb=" CA GLU A 470 " pdb=" C GLU A 470 " ideal model delta sigma weight residual 111.28 120.78 -9.50 1.09e+00 8.42e-01 7.59e+01 angle pdb=" N LYS A 469 " pdb=" CA LYS A 469 " pdb=" C LYS A 469 " ideal model delta sigma weight residual 111.28 120.68 -9.40 1.09e+00 8.42e-01 7.44e+01 angle pdb=" N GLU B 470 " pdb=" CA GLU B 470 " pdb=" C GLU B 470 " ideal model delta sigma weight residual 111.28 119.74 -8.46 1.09e+00 8.42e-01 6.02e+01 angle pdb=" N LYS B 469 " pdb=" CA LYS B 469 " pdb=" C LYS B 469 " ideal model delta sigma weight residual 111.28 119.01 -7.73 1.09e+00 8.42e-01 5.02e+01 angle pdb=" N GLU B 468 " pdb=" CA GLU B 468 " pdb=" C GLU B 468 " ideal model delta sigma weight residual 111.28 117.62 -6.34 1.09e+00 8.42e-01 3.38e+01 ... (remaining 15691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6392 17.66 - 35.32: 525 35.32 - 52.97: 120 52.97 - 70.63: 25 70.63 - 88.29: 6 Dihedral angle restraints: 7068 sinusoidal: 2846 harmonic: 4222 Sorted by residual: dihedral pdb=" N SER A 651 " pdb=" C SER A 651 " pdb=" CA SER A 651 " pdb=" CB SER A 651 " ideal model delta harmonic sigma weight residual 122.80 131.50 -8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" C SER A 651 " pdb=" N SER A 651 " pdb=" CA SER A 651 " pdb=" CB SER A 651 " ideal model delta harmonic sigma weight residual -122.60 -130.77 8.17 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CA ASP A 94 " pdb=" CB ASP A 94 " pdb=" CG ASP A 94 " pdb=" OD1 ASP A 94 " ideal model delta sinusoidal sigma weight residual -30.00 -84.84 54.84 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1642 0.068 - 0.136: 189 0.136 - 0.204: 14 0.204 - 0.271: 3 0.271 - 0.339: 4 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA LYS A 469 " pdb=" N LYS A 469 " pdb=" C LYS A 469 " pdb=" CB LYS A 469 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA SER A 651 " pdb=" N SER A 651 " pdb=" C SER A 651 " pdb=" CB SER A 651 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA GLU A 470 " pdb=" N GLU A 470 " pdb=" C GLU A 470 " pdb=" CB GLU A 470 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1849 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 532 " -0.028 2.00e-02 2.50e+03 5.52e-02 3.04e+01 pdb=" C LEU A 532 " 0.095 2.00e-02 2.50e+03 pdb=" O LEU A 532 " -0.036 2.00e-02 2.50e+03 pdb=" N MET A 533 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C LEU A 710 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 710 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 711 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 328 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 329 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.025 5.00e-02 4.00e+02 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 13 2.36 - 2.99: 6068 2.99 - 3.63: 16922 3.63 - 4.26: 24023 4.26 - 4.90: 40984 Nonbonded interactions: 88010 Sorted by model distance: nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 1.719 2.170 nonbonded pdb=" OE1 GLN A 567 " pdb="MG MG A 802 " model vdw 1.823 2.170 nonbonded pdb=" O1B ATP A 801 " pdb="MG MG A 802 " model vdw 1.824 2.170 nonbonded pdb=" OD1 ASP B 647 " pdb=" N GLU B 648 " model vdw 2.116 3.120 nonbonded pdb=" N GLU A 669 " pdb=" OE1 GLU A 669 " model vdw 2.197 3.120 ... (remaining 88005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.760 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11636 Z= 0.199 Angle : 0.682 9.498 15696 Z= 0.433 Chirality : 0.047 0.339 1852 Planarity : 0.003 0.055 1944 Dihedral : 13.819 88.290 4356 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 0.72 % Allowed : 0.64 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1456 helix: 1.42 (0.19), residues: 832 sheet: -1.15 (0.42), residues: 138 loop : -1.81 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 132 HIS 0.005 0.001 HIS A 249 PHE 0.015 0.002 PHE A 83 TYR 0.013 0.001 TYR B 389 ARG 0.007 0.001 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.16305 ( 678) hydrogen bonds : angle 5.74859 ( 1962) covalent geometry : bond 0.00375 (11636) covalent geometry : angle 0.68227 (15696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 432 time to evaluate : 1.347 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: 0.2460 time to fit residues: 150.7339 Evaluate side-chains 271 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 54 ASN A 99 HIS A 259 ASN A 305 ASN A 424 GLN A 450 GLN A 490 ASN A 602 HIS A 629 GLN A 704 HIS B 99 HIS B 259 ASN B 660 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.141744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118346 restraints weight = 30586.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.121615 restraints weight = 14483.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.123686 restraints weight = 8689.281| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11636 Z= 0.186 Angle : 0.627 6.887 15696 Z= 0.330 Chirality : 0.042 0.152 1852 Planarity : 0.004 0.068 1944 Dihedral : 7.233 87.348 1622 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.69 % Allowed : 15.25 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.22), residues: 1456 helix: 1.73 (0.19), residues: 822 sheet: -1.01 (0.42), residues: 142 loop : -1.51 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 132 HIS 0.005 0.002 HIS A 602 PHE 0.016 0.002 PHE A 428 TYR 0.013 0.001 TYR B 319 ARG 0.013 0.001 ARG B 680 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 678) hydrogen bonds : angle 4.42675 ( 1962) covalent geometry : bond 0.00413 (11636) covalent geometry : angle 0.62690 (15696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8254 (t80) REVERT: A 305 ASN cc_start: 0.7626 (t0) cc_final: 0.7352 (t0) REVERT: A 335 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7111 (ptp-110) REVERT: A 606 GLU cc_start: 0.7936 (mp0) cc_final: 0.7607 (mp0) REVERT: B 36 LYS cc_start: 0.8409 (ttmt) cc_final: 0.7933 (mtpp) REVERT: B 49 ASP cc_start: 0.8549 (t0) cc_final: 0.8310 (t70) REVERT: B 51 GLN cc_start: 0.8238 (mt0) cc_final: 0.8028 (mt0) REVERT: B 99 HIS cc_start: 0.8192 (t70) cc_final: 0.7925 (t70) REVERT: B 660 HIS cc_start: 0.7967 (t-90) cc_final: 0.7741 (t70) REVERT: B 694 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8136 (ttpt) outliers start: 46 outliers final: 34 residues processed: 309 average time/residue: 0.2161 time to fit residues: 97.4480 Evaluate side-chains 280 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 37 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.142176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.118684 restraints weight = 31322.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.121915 restraints weight = 14695.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124032 restraints weight = 8824.255| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11636 Z= 0.130 Angle : 0.561 7.076 15696 Z= 0.292 Chirality : 0.040 0.167 1852 Planarity : 0.003 0.056 1944 Dihedral : 6.293 76.844 1622 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.69 % Allowed : 19.82 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1456 helix: 1.87 (0.18), residues: 822 sheet: -0.86 (0.42), residues: 140 loop : -1.50 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 132 HIS 0.004 0.001 HIS A 704 PHE 0.012 0.001 PHE A 428 TYR 0.009 0.001 TYR A 319 ARG 0.006 0.001 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 678) hydrogen bonds : angle 4.15422 ( 1962) covalent geometry : bond 0.00285 (11636) covalent geometry : angle 0.56076 (15696) *********************** 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 300 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASN cc_start: 0.7474 (t0) cc_final: 0.7239 (t0) REVERT: A 340 ASP cc_start: 0.8858 (t0) cc_final: 0.8438 (t0) REVERT: B 36 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7923 (mtpp) REVERT: B 51 GLN cc_start: 0.8372 (mt0) cc_final: 0.8105 (mt0) REVERT: B 637 LEU cc_start: 0.9295 (tp) cc_final: 0.8972 (pp) REVERT: B 660 HIS cc_start: 0.7958 (t-90) cc_final: 0.7644 (t-170) REVERT: D 18 LEU cc_start: 0.9242 (mt) cc_final: 0.8896 (mm) outliers start: 46 outliers final: 32 residues processed: 280 average time/residue: 0.2095 time to fit residues: 85.9985 Evaluate side-chains 264 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 0.0070 chunk 94 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS A 278 GLN A 419 ASN B 99 HIS B 627 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.114141 restraints weight = 31045.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.117236 restraints weight = 15141.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119211 restraints weight = 9306.102| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11636 Z= 0.158 Angle : 0.589 8.376 15696 Z= 0.304 Chirality : 0.041 0.136 1852 Planarity : 0.003 0.054 1944 Dihedral : 5.763 61.387 1622 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.06 % Allowed : 20.71 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1456 helix: 1.87 (0.18), residues: 822 sheet: -0.82 (0.43), residues: 140 loop : -1.51 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.003 0.001 HIS A 704 PHE 0.013 0.002 PHE B 428 TYR 0.010 0.001 TYR A 225 ARG 0.011 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 678) hydrogen bonds : angle 4.19618 ( 1962) covalent geometry : bond 0.00359 (11636) covalent geometry : angle 0.58933 (15696) *********************** 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 312 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8184 (ttm) cc_final: 0.7764 (mtp) REVERT: A 340 ASP cc_start: 0.8910 (t0) cc_final: 0.8478 (t0) REVERT: A 606 GLU cc_start: 0.7594 (mp0) cc_final: 0.7265 (mp0) REVERT: B 36 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7884 (mtpp) REVERT: B 108 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7740 (p0) REVERT: B 340 ASP cc_start: 0.8660 (t0) cc_final: 0.8434 (t0) REVERT: B 627 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8363 (mp10) outliers start: 63 outliers final: 44 residues processed: 286 average time/residue: 0.2200 time to fit residues: 92.6209 Evaluate side-chains 270 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 MET 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 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 431 LEU 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 627 GLN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 0.9980 chunk 26 optimal weight: 0.0000 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 130 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS B 54 ASN B 99 HIS B 249 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106884 restraints weight = 27779.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.109753 restraints weight = 14085.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.111671 restraints weight = 8839.140| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4376 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= 0.116 Angle : 0.563 8.490 15696 Z= 0.289 Chirality : 0.040 0.140 1852 Planarity : 0.003 0.043 1944 Dihedral : 5.480 59.338 1622 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.69 % Allowed : 23.43 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1456 helix: 1.99 (0.18), residues: 822 sheet: -0.76 (0.43), residues: 138 loop : -1.49 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 132 HIS 0.009 0.001 HIS B 99 PHE 0.028 0.001 PHE B 715 TYR 0.010 0.001 TYR B 714 ARG 0.009 0.000 ARG B 269 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 678) hydrogen bonds : angle 3.95890 ( 1962) covalent geometry : bond 0.00247 (11636) covalent geometry : angle 0.56343 (15696) *********************** 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 304 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8692 (mmt-90) cc_final: 0.8418 (mmt-90) REVERT: A 41 LYS cc_start: 0.8923 (mmtm) cc_final: 0.8413 (mmmt) REVERT: A 293 MET cc_start: 0.8102 (ttm) cc_final: 0.7784 (mtp) REVERT: A 340 ASP cc_start: 0.8918 (t0) cc_final: 0.8510 (t0) REVERT: A 606 GLU cc_start: 0.7592 (mp0) cc_final: 0.7205 (mp0) REVERT: C 17 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8695 (pt0) REVERT: B 108 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7734 (p0) REVERT: B 189 TYR cc_start: 0.8990 (t80) cc_final: 0.8780 (t80) REVERT: B 269 ARG cc_start: 0.8561 (mtt90) cc_final: 0.7993 (mtm-85) REVERT: B 340 ASP cc_start: 0.8657 (t0) cc_final: 0.8386 (t0) REVERT: B 379 MET cc_start: 0.8767 (mmp) cc_final: 0.8472 (mmp) REVERT: B 627 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: B 637 LEU cc_start: 0.9347 (tp) cc_final: 0.9063 (pp) REVERT: B 660 HIS cc_start: 0.8400 (t-170) cc_final: 0.8182 (t-170) REVERT: D 18 LEU cc_start: 0.9164 (mt) cc_final: 0.8877 (mm) outliers start: 46 outliers final: 33 residues processed: 282 average time/residue: 0.2099 time to fit residues: 86.6792 Evaluate side-chains 278 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain C residue 17 GLU 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 221 ILE 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 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 627 GLN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 0.0060 chunk 51 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 125 optimal weight: 0.0070 chunk 52 optimal weight: 0.8980 overall best weight: 0.5214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 450 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 278 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.134123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.109727 restraints weight = 27657.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.112619 restraints weight = 13934.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.114540 restraints weight = 8676.573| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4532 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= 0.114 Angle : 0.564 8.900 15696 Z= 0.287 Chirality : 0.040 0.141 1852 Planarity : 0.003 0.040 1944 Dihedral : 5.299 58.390 1622 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.61 % Allowed : 23.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1456 helix: 2.04 (0.18), residues: 824 sheet: -0.67 (0.42), residues: 138 loop : -1.49 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.008 0.001 HIS B 99 PHE 0.014 0.001 PHE B 715 TYR 0.009 0.001 TYR A 225 ARG 0.007 0.001 ARG B 269 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 678) hydrogen bonds : angle 3.89357 ( 1962) covalent geometry : bond 0.00244 (11636) covalent geometry : angle 0.56430 (15696) *********************** 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: 45 poor density : 254 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8281 (tt0) cc_final: 0.7826 (tt0) REVERT: A 293 MET cc_start: 0.8093 (ttm) cc_final: 0.7850 (mtp) REVERT: A 340 ASP cc_start: 0.8880 (t0) cc_final: 0.8490 (t0) REVERT: A 450 GLN cc_start: 0.8780 (tp40) cc_final: 0.8397 (tp40) REVERT: A 606 GLU cc_start: 0.7289 (mp0) cc_final: 0.6974 (mp0) REVERT: C 17 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8625 (pt0) REVERT: B 99 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7627 (t70) REVERT: B 108 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7784 (p0) REVERT: B 189 TYR cc_start: 0.8973 (t80) cc_final: 0.8731 (t80) REVERT: B 340 ASP cc_start: 0.8666 (t0) cc_final: 0.8326 (t0) REVERT: B 637 LEU cc_start: 0.9356 (tp) cc_final: 0.9092 (pp) REVERT: B 660 HIS cc_start: 0.8436 (t-170) cc_final: 0.8226 (t-170) REVERT: D 18 LEU cc_start: 0.9147 (mt) cc_final: 0.8869 (mm) outliers start: 45 outliers final: 34 residues processed: 282 average time/residue: 0.2172 time to fit residues: 88.9421 Evaluate side-chains 274 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain C residue 17 GLU 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 221 ILE 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 355 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** 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 = 0.3903 r_free = 0.3903 target = 0.132667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107850 restraints weight = 27826.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110637 restraints weight = 14217.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.112559 restraints weight = 8996.988| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11636 Z= 0.131 Angle : 0.588 8.571 15696 Z= 0.298 Chirality : 0.041 0.141 1852 Planarity : 0.003 0.039 1944 Dihedral : 5.274 58.264 1622 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.77 % Allowed : 23.92 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1456 helix: 2.01 (0.18), residues: 836 sheet: -0.60 (0.43), residues: 138 loop : -1.50 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.025 0.001 PHE A 428 TYR 0.010 0.001 TYR A 225 ARG 0.006 0.001 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 678) hydrogen bonds : angle 3.92297 ( 1962) covalent geometry : bond 0.00298 (11636) covalent geometry : angle 0.58813 (15696) *********************** 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 280 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8516 (mmt-90) cc_final: 0.8294 (mmm160) REVERT: A 293 MET cc_start: 0.8076 (ttm) cc_final: 0.7829 (mtp) REVERT: A 340 ASP cc_start: 0.8870 (t0) cc_final: 0.8493 (t0) REVERT: A 450 GLN cc_start: 0.8763 (tp40) cc_final: 0.8530 (tp40) REVERT: C 17 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8598 (pt0) REVERT: B 108 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7805 (p0) REVERT: B 189 TYR cc_start: 0.9003 (t80) cc_final: 0.8762 (t80) REVERT: B 340 ASP cc_start: 0.8660 (t0) cc_final: 0.8311 (t0) REVERT: B 660 HIS cc_start: 0.8458 (t-170) cc_final: 0.8244 (t-170) REVERT: D 18 LEU cc_start: 0.9156 (mt) cc_final: 0.8875 (mm) outliers start: 47 outliers final: 40 residues processed: 262 average time/residue: 0.2444 time to fit residues: 96.0878 Evaluate side-chains 272 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 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 C residue 17 GLU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 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 543 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS B 99 HIS 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 = 0.3844 r_free = 0.3844 target = 0.133837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109473 restraints weight = 27735.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112163 restraints weight = 14404.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113931 restraints weight = 9149.316| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11636 Z= 0.193 Angle : 0.655 8.844 15696 Z= 0.333 Chirality : 0.042 0.176 1852 Planarity : 0.003 0.047 1944 Dihedral : 5.472 60.769 1622 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.33 % Allowed : 23.92 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1456 helix: 1.89 (0.18), residues: 836 sheet: -0.88 (0.42), residues: 138 loop : -1.61 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.005 0.001 HIS B 249 PHE 0.020 0.002 PHE A 428 TYR 0.012 0.001 TYR A 225 ARG 0.007 0.001 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 678) hydrogen bonds : angle 4.28851 ( 1962) covalent geometry : bond 0.00444 (11636) covalent geometry : angle 0.65545 (15696) *********************** 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 292 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 238 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8574 (mmt-90) cc_final: 0.8187 (mmm160) REVERT: A 118 LYS cc_start: 0.9275 (ptpp) cc_final: 0.8688 (ptpp) REVERT: A 317 LEU cc_start: 0.9389 (tp) cc_final: 0.9084 (tt) REVERT: A 336 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 340 ASP cc_start: 0.8824 (t0) cc_final: 0.8399 (t0) REVERT: A 450 GLN cc_start: 0.8806 (tp40) cc_final: 0.8348 (tp40) REVERT: A 655 SER cc_start: 0.8905 (m) cc_final: 0.8657 (p) REVERT: A 679 HIS cc_start: 0.7892 (t-90) cc_final: 0.7561 (t-90) REVERT: B 108 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7802 (p0) REVERT: B 173 PHE cc_start: 0.8496 (t80) cc_final: 0.8264 (t80) REVERT: B 316 ILE cc_start: 0.9542 (tp) cc_final: 0.9332 (tp) REVERT: B 340 ASP cc_start: 0.8690 (t0) cc_final: 0.8414 (t0) REVERT: B 368 GLU cc_start: 0.8227 (pp20) cc_final: 0.7989 (pp20) REVERT: B 457 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8963 (t0) REVERT: B 660 HIS cc_start: 0.8468 (t-170) cc_final: 0.8252 (t-170) outliers start: 54 outliers final: 38 residues processed: 272 average time/residue: 0.2230 time to fit residues: 88.4819 Evaluate side-chains 270 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 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 221 ILE Chi-restraints excluded: chain B residue 278 GLN 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 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 457 ASN Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 0.0010 chunk 43 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 305 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110985 restraints weight = 27894.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.113778 restraints weight = 14281.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115681 restraints weight = 9016.652| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11636 Z= 0.129 Angle : 0.637 8.841 15696 Z= 0.320 Chirality : 0.041 0.182 1852 Planarity : 0.003 0.038 1944 Dihedral : 5.278 59.265 1622 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.05 % Allowed : 26.00 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1456 helix: 1.96 (0.18), residues: 836 sheet: -0.83 (0.42), residues: 138 loop : -1.52 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 132 HIS 0.005 0.001 HIS B 99 PHE 0.020 0.001 PHE A 428 TYR 0.012 0.001 TYR A 150 ARG 0.010 0.001 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 678) hydrogen bonds : angle 4.06864 ( 1962) covalent geometry : bond 0.00291 (11636) covalent geometry : angle 0.63686 (15696) *********************** 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 275 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8596 (mmt-90) cc_final: 0.8349 (mmm160) REVERT: A 118 LYS cc_start: 0.9286 (ptpp) cc_final: 0.8723 (ptpp) REVERT: A 335 ARG cc_start: 0.7601 (ptp90) cc_final: 0.7361 (ptp-110) REVERT: A 336 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7444 (tm-30) REVERT: A 340 ASP cc_start: 0.8786 (t0) cc_final: 0.8438 (t0) REVERT: A 387 MET cc_start: 0.8121 (tpp) cc_final: 0.7881 (tpt) REVERT: A 655 SER cc_start: 0.8832 (m) cc_final: 0.8558 (p) REVERT: A 679 HIS cc_start: 0.7915 (t-90) cc_final: 0.7594 (t-90) REVERT: C 17 GLU cc_start: 0.8769 (pt0) cc_final: 0.8562 (pt0) REVERT: B 108 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7771 (p0) REVERT: B 154 MET cc_start: 0.8405 (ttp) cc_final: 0.8112 (ttm) REVERT: B 173 PHE cc_start: 0.8408 (t80) cc_final: 0.8166 (t80) REVERT: B 251 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9078 (mm) REVERT: B 316 ILE cc_start: 0.9501 (tp) cc_final: 0.9279 (tp) REVERT: B 340 ASP cc_start: 0.8610 (t0) cc_final: 0.8280 (t0) REVERT: B 660 HIS cc_start: 0.8437 (t-170) cc_final: 0.8207 (t-170) outliers start: 38 outliers final: 31 residues processed: 263 average time/residue: 0.2812 time to fit residues: 107.9109 Evaluate side-chains 255 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 251 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 104 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.137181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.113139 restraints weight = 27474.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115982 restraints weight = 13908.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.117836 restraints weight = 8643.283| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 11636 Z= 0.125 Angle : 0.660 12.698 15696 Z= 0.327 Chirality : 0.041 0.182 1852 Planarity : 0.003 0.037 1944 Dihedral : 5.172 58.256 1622 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.73 % Allowed : 26.32 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1456 helix: 2.04 (0.18), residues: 836 sheet: -0.78 (0.42), residues: 138 loop : -1.51 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.003 0.001 HIS B 679 PHE 0.020 0.001 PHE A 428 TYR 0.010 0.001 TYR A 225 ARG 0.013 0.001 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 678) hydrogen bonds : angle 3.98976 ( 1962) covalent geometry : bond 0.00285 (11636) covalent geometry : angle 0.66029 (15696) ********************** 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 269 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8623 (mmt-90) cc_final: 0.8346 (mmm160) REVERT: A 118 LYS cc_start: 0.9267 (ptpp) cc_final: 0.8801 (ptpp) REVERT: A 335 ARG cc_start: 0.7645 (ptp90) cc_final: 0.7444 (ptp-110) REVERT: A 336 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 340 ASP cc_start: 0.8793 (t0) cc_final: 0.8455 (t0) REVERT: A 655 SER cc_start: 0.8876 (m) cc_final: 0.8616 (p) REVERT: A 679 HIS cc_start: 0.7908 (t-90) cc_final: 0.7659 (t-90) REVERT: C 20 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7992 (mm-30) REVERT: B 108 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7783 (p0) REVERT: B 154 MET cc_start: 0.8370 (ttp) cc_final: 0.8115 (ttm) REVERT: B 316 ILE cc_start: 0.9492 (tp) cc_final: 0.9288 (tp) REVERT: B 340 ASP cc_start: 0.8641 (t0) cc_final: 0.8303 (t0) REVERT: B 660 HIS cc_start: 0.8450 (t-170) cc_final: 0.8224 (t-170) outliers start: 34 outliers final: 31 residues processed: 256 average time/residue: 0.2547 time to fit residues: 96.7658 Evaluate side-chains 262 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 2.388 ------------------------------------------------------------------------------- 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 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 389 TYR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 356 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** 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 = 0.3690 r_free = 0.3690 target = 0.121064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094285 restraints weight = 29548.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097351 restraints weight = 14085.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.099365 restraints weight = 8550.885| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 11636 Z= 0.150 Angle : 0.669 12.502 15696 Z= 0.336 Chirality : 0.042 0.169 1852 Planarity : 0.003 0.036 1944 Dihedral : 5.190 58.819 1622 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.81 % Allowed : 26.57 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1456 helix: 2.00 (0.18), residues: 836 sheet: -0.83 (0.39), residues: 158 loop : -1.57 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.012 0.001 HIS B 99 PHE 0.019 0.001 PHE A 428 TYR 0.011 0.001 TYR A 225 ARG 0.011 0.001 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 678) hydrogen bonds : angle 4.10460 ( 1962) covalent geometry : bond 0.00356 (11636) covalent geometry : angle 0.66880 (15696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.17 seconds wall clock time: 97 minutes 12.68 seconds (5832.68 seconds total)