Starting phenix.real_space_refine on Tue May 20 00:57:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liu_63123/05_2025/9liu_63123.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liu_63123/05_2025/9liu_63123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9liu_63123/05_2025/9liu_63123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liu_63123/05_2025/9liu_63123.map" model { file = "/net/cci-nas-00/data/ceres_data/9liu_63123/05_2025/9liu_63123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liu_63123/05_2025/9liu_63123.cif" } resolution = 2.7 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= 0.009 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 298 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 11469 2.51 5 N 3565 2.21 5 O 4215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19587 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3738 Classifications: {'peptide': 455} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 437} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3738 Classifications: {'peptide': 455} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 437} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" 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: "N" 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: 10.44, per 1000 atoms: 0.53 Number of scatterers: 19587 At special positions: 0 Unit cell: (119.075, 124.487, 186.19, 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 38 16.00 P 298 15.00 Mg 2 11.99 O 4215 8.00 N 3565 7.00 C 11469 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.66 Conformation dependent library (CDL) restraints added in 1.7 seconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 14 sheets defined 60.8% alpha, 6.6% beta 144 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 8.10 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.599A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 15 through 19 removed outlier: 3.838A pdb=" N HIS B 18 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG B 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 15 through 19' Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.087A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.645A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.519A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 15 through 19 removed outlier: 3.882A pdb=" N HIS F 18 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG F 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 15 through 19' Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.106A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.543A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.590A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 214 Processing helix chain 'K' and resid 226 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 Processing helix chain 'K' and resid 309 through 314 removed outlier: 3.637A pdb=" N LEU K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 Processing helix chain 'K' and resid 334 through 341 Processing helix chain 'K' and resid 360 through 371 removed outlier: 3.643A pdb=" N TRP K 364 " --> pdb=" O LEU K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 384 Processing helix chain 'K' and resid 397 through 406 removed outlier: 3.591A pdb=" N LEU K 405 " --> pdb=" O LEU K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 467 through 478 removed outlier: 3.525A pdb=" N GLN K 471 " --> pdb=" O ASN K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 495 through 500 removed outlier: 4.004A pdb=" N TYR K 499 " --> pdb=" O GLU K 495 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN K 500 " --> pdb=" O HIS K 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 495 through 500' Processing helix chain 'K' and resid 501 through 518 removed outlier: 3.669A pdb=" N LYS K 509 " --> pdb=" O GLN K 505 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 542 Processing helix chain 'K' and resid 553 through 565 Processing helix chain 'K' and resid 601 through 611 removed outlier: 3.815A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 649 removed outlier: 3.958A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 214 Processing helix chain 'N' and resid 226 through 241 Processing helix chain 'N' and resid 253 through 255 No H-bonds generated for 'chain 'N' and resid 253 through 255' Processing helix chain 'N' and resid 256 through 268 Processing helix chain 'N' and resid 279 through 290 Processing helix chain 'N' and resid 303 through 309 Processing helix chain 'N' and resid 309 through 314 removed outlier: 3.636A pdb=" N LEU N 313 " --> pdb=" O GLU N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 330 Processing helix chain 'N' and resid 334 through 341 Processing helix chain 'N' and resid 360 through 371 removed outlier: 3.643A pdb=" N TRP N 364 " --> pdb=" O LEU N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 378 through 384 Processing helix chain 'N' and resid 397 through 406 removed outlier: 3.591A pdb=" N LEU N 405 " --> pdb=" O LEU N 401 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 446 Processing helix chain 'N' and resid 467 through 478 removed outlier: 3.523A pdb=" N GLN N 471 " --> pdb=" O ASN N 467 " (cutoff:3.500A) Processing helix chain 'N' and resid 479 through 482 Processing helix chain 'N' and resid 495 through 500 removed outlier: 4.004A pdb=" N TYR N 499 " --> pdb=" O GLU N 495 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN N 500 " --> pdb=" O HIS N 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 495 through 500' Processing helix chain 'N' and resid 501 through 518 removed outlier: 3.669A pdb=" N LYS N 509 " --> pdb=" O GLN N 505 " (cutoff:3.500A) Processing helix chain 'N' and resid 527 through 542 Processing helix chain 'N' and resid 553 through 565 Processing helix chain 'N' and resid 601 through 611 removed outlier: 3.815A pdb=" N ASP N 605 " --> pdb=" O ASN N 601 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 649 removed outlier: 3.958A pdb=" N LYS N 635 " --> pdb=" O SER N 631 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP N 647 " --> pdb=" O LYS N 643 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.629A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.197A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.769A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.913A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.080A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 273 through 275 removed outlier: 6.420A pdb=" N PHE K 274 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N SER K 302 " --> pdb=" O PHE K 274 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TRP K 318 " --> pdb=" O ARG K 346 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ARG K 348 " --> pdb=" O TRP K 318 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR K 320 " --> pdb=" O ARG K 348 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N LEU K 350 " --> pdb=" O TYR K 320 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ILE K 322 " --> pdb=" O LEU K 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 425 through 431 removed outlier: 6.267A pdb=" N LYS K 425 " --> pdb=" O VAL K 623 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ARG K 625 " --> pdb=" O LYS K 425 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU K 427 " --> pdb=" O ARG K 625 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL K 627 " --> pdb=" O LEU K 427 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU K 429 " --> pdb=" O VAL K 627 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL K 593 " --> pdb=" O PHE K 624 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU K 626 " --> pdb=" O VAL K 593 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU K 595 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N THR K 628 " --> pdb=" O LEU K 595 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU K 522 " --> pdb=" O VAL K 594 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 273 through 275 removed outlier: 6.421A pdb=" N PHE N 274 " --> pdb=" O ILE N 300 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N SER N 302 " --> pdb=" O PHE N 274 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N TRP N 318 " --> pdb=" O ARG N 346 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG N 348 " --> pdb=" O TRP N 318 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR N 320 " --> pdb=" O ARG N 348 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N LEU N 350 " --> pdb=" O TYR N 320 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ILE N 322 " --> pdb=" O LEU N 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 425 through 431 removed outlier: 6.267A pdb=" N LYS N 425 " --> pdb=" O VAL N 623 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ARG N 625 " --> pdb=" O LYS N 425 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU N 427 " --> pdb=" O ARG N 625 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL N 627 " --> pdb=" O LEU N 427 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU N 429 " --> pdb=" O VAL N 627 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL N 593 " --> pdb=" O PHE N 624 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU N 626 " --> pdb=" O VAL N 593 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU N 595 " --> pdb=" O LEU N 626 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N THR N 628 " --> pdb=" O LEU N 595 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU N 522 " --> pdb=" O VAL N 594 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 2082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 9.72 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3747 1.33 - 1.45: 6134 1.45 - 1.57: 10006 1.57 - 1.69: 592 1.69 - 1.82: 64 Bond restraints: 20543 Sorted by residual: bond pdb=" C4 ATP N1202 " pdb=" C5 ATP N1202 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C4 ATP K1202 " pdb=" C5 ATP K1202 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 bond pdb=" C5 ATP K1202 " pdb=" C6 ATP K1202 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.22e+01 bond pdb=" C5 ATP N1202 " pdb=" C6 ATP N1202 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.19e+01 bond pdb=" C5 ATP K1202 " pdb=" N7 ATP K1202 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.19e+01 ... (remaining 20538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 28957 4.84 - 9.68: 58 9.68 - 14.53: 0 14.53 - 19.37: 0 19.37 - 24.21: 4 Bond angle restraints: 29019 Sorted by residual: angle pdb=" PA ATP K1202 " pdb=" O3A ATP K1202 " pdb=" PB ATP K1202 " ideal model delta sigma weight residual 136.83 112.62 24.21 1.00e+00 1.00e+00 5.86e+02 angle pdb=" PA ATP N1202 " pdb=" O3A ATP N1202 " pdb=" PB ATP N1202 " ideal model delta sigma weight residual 136.83 112.64 24.19 1.00e+00 1.00e+00 5.85e+02 angle pdb=" PB ATP N1202 " pdb=" O3B ATP N1202 " pdb=" PG ATP N1202 " ideal model delta sigma weight residual 139.87 120.22 19.65 1.00e+00 1.00e+00 3.86e+02 angle pdb=" PB ATP K1202 " pdb=" O3B ATP K1202 " pdb=" PG ATP K1202 " ideal model delta sigma weight residual 139.87 120.28 19.59 1.00e+00 1.00e+00 3.84e+02 angle pdb=" C5 ATP N1202 " pdb=" C4 ATP N1202 " pdb=" N3 ATP N1202 " ideal model delta sigma weight residual 126.80 118.52 8.28 1.00e+00 1.00e+00 6.85e+01 ... (remaining 29014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.60: 9823 31.60 - 63.20: 1824 63.20 - 94.80: 55 94.80 - 126.40: 0 126.40 - 158.00: 2 Dihedral angle restraints: 11704 sinusoidal: 6790 harmonic: 4914 Sorted by residual: dihedral pdb=" CA ILE N 585 " pdb=" C ILE N 585 " pdb=" N ASN N 586 " pdb=" CA ASN N 586 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE K 585 " pdb=" C ILE K 585 " pdb=" N ASN K 586 " pdb=" CA ASN K 586 " ideal model delta harmonic sigma weight residual -180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 11701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1815 0.037 - 0.073: 1058 0.073 - 0.110: 338 0.110 - 0.147: 65 0.147 - 0.184: 5 Chirality restraints: 3281 Sorted by residual: chirality pdb=" CA ILE K 548 " pdb=" N ILE K 548 " pdb=" C ILE K 548 " pdb=" CB ILE K 548 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CG LEU K 465 " pdb=" CB LEU K 465 " pdb=" CD1 LEU K 465 " pdb=" CD2 LEU K 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CG LEU N 465 " pdb=" CB LEU N 465 " pdb=" CD1 LEU N 465 " pdb=" CD2 LEU N 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 3278 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER N 188 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.51e+01 pdb=" N PRO N 189 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO N 189 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO N 189 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 188 " -0.064 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO K 189 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO K 189 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO K 189 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 50 " -0.018 2.00e-02 2.50e+03 2.19e-02 9.63e+00 pdb=" CG TYR C 50 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR C 50 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 50 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C 50 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR C 50 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 50 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 50 " -0.002 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 291 2.59 - 3.17: 16725 3.17 - 3.74: 33752 3.74 - 4.32: 47783 4.32 - 4.90: 70993 Nonbonded interactions: 169544 Sorted by model distance: nonbonded pdb=" N2 DG I 6 " pdb=" O2 DC J 142 " model vdw 2.011 2.496 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.011 3.040 nonbonded pdb="MG MG N1201 " pdb=" O3A ATP N1202 " model vdw 2.031 2.170 nonbonded pdb="MG MG K1201 " pdb=" O3A ATP K1202 " model vdw 2.031 2.170 nonbonded pdb="MG MG K1201 " pdb=" O1G ATP K1202 " model vdw 2.051 2.170 ... (remaining 169539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 15 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = chain 'K' selection = chain 'N' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.030 Extract box with map and model: 1.490 Check model and map are aligned: 0.000 Set scattering table: 0.050 Process input model: 49.940 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:13.540 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.014 0.855 20545 Z= 0.975 Angle : 0.887 24.211 29019 Z= 0.566 Chirality : 0.048 0.184 3281 Planarity : 0.005 0.097 2661 Dihedral : 24.805 158.001 8518 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.71 % Allowed : 1.51 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1650 helix: 0.87 (0.17), residues: 947 sheet: -0.71 (0.46), residues: 128 loop : -1.65 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 364 HIS 0.013 0.002 HIS G 31 PHE 0.020 0.002 PHE N 574 TYR 0.051 0.002 TYR C 50 ARG 0.009 0.001 ARG N 520 Details of bonding type rmsd hydrogen bonds : bond 0.12109 ( 1076) hydrogen bonds : angle 4.86837 ( 2814) covalent geometry : bond 0.01112 (20543) covalent geometry : angle 0.88731 (29019) Misc. bond : bond 0.83883 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 1.977 Fit side-chains REVERT: D 65 ASP cc_start: 0.8229 (t0) cc_final: 0.8017 (t0) REVERT: N 260 TRP cc_start: 0.8698 (m100) cc_final: 0.8483 (m100) REVERT: N 350 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8559 (mt) outliers start: 54 outliers final: 5 residues processed: 236 average time/residue: 1.5523 time to fit residues: 404.6550 Evaluate side-chains 148 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 577 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 75 HIS G 24 GLN K 467 ASN K 642 GLN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 642 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.090230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.063385 restraints weight = 57988.000| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.33 r_work: 0.3079 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20545 Z= 0.198 Angle : 0.620 7.373 29019 Z= 0.349 Chirality : 0.039 0.157 3281 Planarity : 0.004 0.056 2661 Dihedral : 27.906 158.287 5121 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.51 % Allowed : 11.27 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.68 (0.21), residues: 1650 helix: 1.66 (0.17), residues: 960 sheet: -0.85 (0.46), residues: 132 loop : -1.37 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.007 0.001 HIS B 18 PHE 0.015 0.001 PHE N 540 TYR 0.012 0.001 TYR K 499 ARG 0.006 0.000 ARG N 614 Details of bonding type rmsd hydrogen bonds : bond 0.04963 ( 1076) hydrogen bonds : angle 3.69249 ( 2814) covalent geometry : bond 0.00449 (20543) covalent geometry : angle 0.61957 (29019) Misc. bond : bond 0.00302 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 1.664 Fit side-chains REVERT: A 59 GLU cc_start: 0.8902 (pm20) cc_final: 0.8651 (pm20) REVERT: B 93 GLN cc_start: 0.8092 (mt0) cc_final: 0.7879 (mm-40) REVERT: C 90 ASP cc_start: 0.8707 (t0) cc_final: 0.8418 (t0) REVERT: C 92 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: D 117 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8100 (tttp) REVERT: E 58 THR cc_start: 0.8817 (p) cc_final: 0.8583 (t) REVERT: E 133 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: F 93 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: G 95 LYS cc_start: 0.9230 (ttpt) cc_final: 0.8816 (tptt) REVERT: H 110 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8110 (mt-10) outliers start: 22 outliers final: 4 residues processed: 188 average time/residue: 1.6123 time to fit residues: 334.1256 Evaluate side-chains 151 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 24 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.089659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.062719 restraints weight = 58287.690| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.33 r_work: 0.3075 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20545 Z= 0.223 Angle : 0.609 6.123 29019 Z= 0.344 Chirality : 0.039 0.143 3281 Planarity : 0.004 0.042 2661 Dihedral : 27.889 154.699 5108 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.68 % Allowed : 13.13 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.82 (0.21), residues: 1650 helix: 1.79 (0.17), residues: 964 sheet: -0.95 (0.45), residues: 132 loop : -1.33 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 364 HIS 0.011 0.002 HIS N 554 PHE 0.014 0.001 PHE N 540 TYR 0.011 0.001 TYR B 51 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05338 ( 1076) hydrogen bonds : angle 3.56232 ( 2814) covalent geometry : bond 0.00508 (20543) covalent geometry : angle 0.60883 (29019) Misc. bond : bond 0.00320 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8926 (pm20) cc_final: 0.8641 (pm20) REVERT: A 105 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8259 (mt-10) REVERT: B 93 GLN cc_start: 0.8209 (mt0) cc_final: 0.8006 (mm-40) REVERT: C 78 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8525 (mp) REVERT: C 90 ASP cc_start: 0.8815 (t0) cc_final: 0.8350 (t0) REVERT: D 90 GLU cc_start: 0.8760 (mp0) cc_final: 0.8503 (mp0) REVERT: E 58 THR cc_start: 0.8724 (p) cc_final: 0.8459 (t) REVERT: E 133 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: F 92 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8371 (ttp80) REVERT: F 93 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: G 24 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7874 (mm-40) REVERT: G 95 LYS cc_start: 0.9238 (ttpt) cc_final: 0.8824 (tptt) outliers start: 39 outliers final: 14 residues processed: 184 average time/residue: 1.5424 time to fit residues: 313.8334 Evaluate side-chains 161 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Chi-restraints excluded: chain N residue 609 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 137 optimal weight: 0.2980 chunk 164 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 72 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN G 24 GLN H 92 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.091685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.065031 restraints weight = 58106.473| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.35 r_work: 0.3129 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20545 Z= 0.137 Angle : 0.564 6.292 29019 Z= 0.320 Chirality : 0.037 0.142 3281 Planarity : 0.004 0.043 2661 Dihedral : 27.480 152.516 5108 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.06 % Allowed : 14.71 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 1.11 (0.22), residues: 1650 helix: 2.05 (0.17), residues: 968 sheet: -0.93 (0.45), residues: 132 loop : -1.26 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.010 0.001 HIS N 554 PHE 0.016 0.001 PHE K 183 TYR 0.010 0.001 TYR N 545 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 1076) hydrogen bonds : angle 3.28794 ( 2814) covalent geometry : bond 0.00302 (20543) covalent geometry : angle 0.56403 (29019) Misc. bond : bond 0.00231 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8869 (pm20) cc_final: 0.8559 (pm20) REVERT: A 105 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8152 (mt-10) REVERT: B 31 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7700 (tttm) REVERT: C 78 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8590 (mp) REVERT: C 90 ASP cc_start: 0.8714 (t0) cc_final: 0.8308 (t0) REVERT: D 90 GLU cc_start: 0.8733 (mp0) cc_final: 0.8480 (mp0) REVERT: D 117 LYS cc_start: 0.8343 (ttpt) cc_final: 0.8089 (tttm) REVERT: E 133 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: F 74 GLU cc_start: 0.8688 (pt0) cc_final: 0.8469 (mt-10) REVERT: F 93 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: G 24 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7892 (mm110) REVERT: G 72 ASP cc_start: 0.7822 (m-30) cc_final: 0.7588 (m-30) REVERT: G 95 LYS cc_start: 0.9232 (ttpt) cc_final: 0.8809 (tptt) REVERT: K 309 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8485 (mp0) REVERT: K 335 MET cc_start: 0.8465 (ttm) cc_final: 0.8115 (ttt) outliers start: 30 outliers final: 5 residues processed: 182 average time/residue: 1.5619 time to fit residues: 314.9568 Evaluate side-chains 156 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain N residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 121 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN G 31 HIS H 92 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.089409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.062282 restraints weight = 58438.326| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.35 r_work: 0.3077 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20545 Z= 0.233 Angle : 0.605 8.192 29019 Z= 0.342 Chirality : 0.039 0.146 3281 Planarity : 0.004 0.041 2661 Dihedral : 27.775 151.414 5107 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.34 % Allowed : 15.46 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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 (0.21), residues: 1650 helix: 1.93 (0.17), residues: 968 sheet: -1.05 (0.45), residues: 132 loop : -1.32 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.012 0.001 HIS N 554 PHE 0.014 0.001 PHE N 540 TYR 0.010 0.001 TYR N 596 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05370 ( 1076) hydrogen bonds : angle 3.49571 ( 2814) covalent geometry : bond 0.00534 (20543) covalent geometry : angle 0.60483 (29019) Misc. bond : bond 0.00289 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8917 (pm20) cc_final: 0.8526 (pm20) REVERT: A 105 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8264 (mt-10) REVERT: B 31 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7752 (tttm) REVERT: B 91 LYS cc_start: 0.9250 (ttmm) cc_final: 0.9034 (ttpp) REVERT: C 78 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8493 (mp) REVERT: C 90 ASP cc_start: 0.8786 (t0) cc_final: 0.8318 (t0) REVERT: D 102 GLU cc_start: 0.8223 (mp0) cc_final: 0.7855 (pm20) REVERT: D 117 LYS cc_start: 0.8396 (ttpt) cc_final: 0.8105 (tttp) REVERT: E 133 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: F 93 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: G 72 ASP cc_start: 0.7874 (m-30) cc_final: 0.7646 (m-30) REVERT: G 95 LYS cc_start: 0.9234 (ttpt) cc_final: 0.8802 (tptt) REVERT: K 309 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: K 465 LEU cc_start: 0.8848 (mt) cc_final: 0.8456 (pt) outliers start: 34 outliers final: 16 residues processed: 172 average time/residue: 1.5785 time to fit residues: 300.5617 Evaluate side-chains 159 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 129 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.090217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.063302 restraints weight = 58042.579| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.33 r_work: 0.3100 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20545 Z= 0.163 Angle : 0.586 8.326 29019 Z= 0.331 Chirality : 0.038 0.142 3281 Planarity : 0.004 0.040 2661 Dihedral : 27.712 149.461 5107 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.99 % Allowed : 16.56 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 1.03 (0.21), residues: 1650 helix: 1.96 (0.17), residues: 968 sheet: -0.98 (0.45), residues: 130 loop : -1.22 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.014 0.001 HIS N 554 PHE 0.014 0.001 PHE N 540 TYR 0.013 0.001 TYR F 51 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 1076) hydrogen bonds : angle 3.39995 ( 2814) covalent geometry : bond 0.00367 (20543) covalent geometry : angle 0.58604 (29019) Misc. bond : bond 0.00282 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8909 (pm20) cc_final: 0.8565 (pm20) REVERT: A 105 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 31 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7720 (tttm) REVERT: B 91 LYS cc_start: 0.9237 (ttmm) cc_final: 0.9020 (ttpp) REVERT: C 78 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8565 (mp) REVERT: C 90 ASP cc_start: 0.8777 (t0) cc_final: 0.8321 (t0) REVERT: D 102 GLU cc_start: 0.8273 (mp0) cc_final: 0.7924 (pm20) REVERT: D 117 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8096 (tttm) REVERT: E 120 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7658 (mtp) REVERT: E 133 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: F 93 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: G 72 ASP cc_start: 0.7880 (m-30) cc_final: 0.7631 (m-30) REVERT: G 92 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7550 (mt-10) REVERT: H 102 GLU cc_start: 0.7916 (pp20) cc_final: 0.7484 (pp20) REVERT: K 309 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: K 465 LEU cc_start: 0.8793 (mt) cc_final: 0.8394 (pt) REVERT: K 596 TYR cc_start: 0.8871 (t80) cc_final: 0.8613 (t80) REVERT: N 478 HIS cc_start: 0.8306 (t70) cc_final: 0.8005 (t70) outliers start: 29 outliers final: 16 residues processed: 169 average time/residue: 1.6655 time to fit residues: 310.9356 Evaluate side-chains 162 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.091067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.064306 restraints weight = 58078.205| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.34 r_work: 0.3124 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20545 Z= 0.147 Angle : 0.567 8.056 29019 Z= 0.323 Chirality : 0.037 0.137 3281 Planarity : 0.004 0.038 2661 Dihedral : 27.527 148.947 5107 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.27 % Allowed : 16.70 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 1.16 (0.22), residues: 1650 helix: 2.04 (0.17), residues: 968 sheet: -0.88 (0.46), residues: 134 loop : -1.16 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.014 0.001 HIS N 554 PHE 0.013 0.001 PHE N 540 TYR 0.008 0.001 TYR H 37 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 1076) hydrogen bonds : angle 3.30276 ( 2814) covalent geometry : bond 0.00329 (20543) covalent geometry : angle 0.56732 (29019) Misc. bond : bond 0.00253 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8855 (pm20) cc_final: 0.8528 (pm20) REVERT: A 105 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8182 (mt-10) REVERT: B 31 LYS cc_start: 0.8160 (ttmm) cc_final: 0.7716 (tttm) REVERT: B 91 LYS cc_start: 0.9207 (ttmm) cc_final: 0.8989 (ttpp) REVERT: C 78 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8569 (mp) REVERT: C 90 ASP cc_start: 0.8755 (t0) cc_final: 0.8283 (t0) REVERT: D 102 GLU cc_start: 0.8270 (mp0) cc_final: 0.7974 (pm20) REVERT: D 117 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8099 (tttm) REVERT: E 120 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7536 (mtp) REVERT: F 93 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7188 (mp10) REVERT: G 72 ASP cc_start: 0.7852 (m-30) cc_final: 0.7595 (m-30) REVERT: G 92 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7674 (mt-10) REVERT: G 95 LYS cc_start: 0.9244 (ttmt) cc_final: 0.8837 (tptt) REVERT: H 102 GLU cc_start: 0.7913 (pp20) cc_final: 0.7518 (pp20) REVERT: K 309 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8502 (mp0) REVERT: K 465 LEU cc_start: 0.8827 (mt) cc_final: 0.8397 (pt) REVERT: K 546 CYS cc_start: 0.8457 (t) cc_final: 0.7834 (t) REVERT: K 596 TYR cc_start: 0.8857 (t80) cc_final: 0.8575 (t80) REVERT: N 478 HIS cc_start: 0.8322 (t70) cc_final: 0.7967 (t70) outliers start: 33 outliers final: 19 residues processed: 173 average time/residue: 1.6322 time to fit residues: 315.4776 Evaluate side-chains 165 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 182 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** 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 = 0.3815 r_free = 0.3815 target = 0.090721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.063784 restraints weight = 58584.306| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.35 r_work: 0.3105 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20545 Z= 0.172 Angle : 0.587 10.623 29019 Z= 0.330 Chirality : 0.037 0.140 3281 Planarity : 0.004 0.040 2661 Dihedral : 27.520 148.237 5107 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.27 % Allowed : 17.18 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 1.12 (0.21), residues: 1650 helix: 2.00 (0.17), residues: 971 sheet: -0.90 (0.46), residues: 130 loop : -1.15 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP N 364 HIS 0.014 0.001 HIS N 554 PHE 0.012 0.001 PHE N 540 TYR 0.008 0.001 TYR H 37 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 1076) hydrogen bonds : angle 3.30707 ( 2814) covalent geometry : bond 0.00392 (20543) covalent geometry : angle 0.58701 (29019) Misc. bond : bond 0.00259 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8845 (pm20) cc_final: 0.8480 (pm20) REVERT: A 105 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8163 (mt-10) REVERT: B 31 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7730 (tttm) REVERT: C 78 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8585 (mp) REVERT: C 90 ASP cc_start: 0.8774 (t0) cc_final: 0.8349 (t0) REVERT: D 102 GLU cc_start: 0.8266 (mp0) cc_final: 0.7943 (pm20) REVERT: D 117 LYS cc_start: 0.8342 (ttpt) cc_final: 0.8071 (tttp) REVERT: E 120 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7591 (mtp) REVERT: F 77 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8667 (mtmt) REVERT: F 93 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: G 72 ASP cc_start: 0.7842 (m-30) cc_final: 0.7583 (m-30) REVERT: G 92 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7628 (mt-10) REVERT: G 95 LYS cc_start: 0.9252 (ttmt) cc_final: 0.8856 (tptt) REVERT: H 102 GLU cc_start: 0.7961 (pp20) cc_final: 0.7581 (pp20) REVERT: K 309 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: K 465 LEU cc_start: 0.8824 (mt) cc_final: 0.8417 (pt) REVERT: K 546 CYS cc_start: 0.8489 (t) cc_final: 0.7842 (t) REVERT: K 596 TYR cc_start: 0.8851 (t80) cc_final: 0.8513 (t80) REVERT: N 364 TRP cc_start: 0.9265 (t60) cc_final: 0.9013 (t60) REVERT: N 478 HIS cc_start: 0.8330 (t70) cc_final: 0.7933 (t70) outliers start: 33 outliers final: 21 residues processed: 170 average time/residue: 1.5634 time to fit residues: 294.8485 Evaluate side-chains 168 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 352 THR Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 185 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** 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 = 0.3833 r_free = 0.3833 target = 0.091433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064826 restraints weight = 58234.822| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.32 r_work: 0.3115 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20545 Z= 0.150 Angle : 0.582 9.673 29019 Z= 0.328 Chirality : 0.037 0.258 3281 Planarity : 0.004 0.039 2661 Dihedral : 27.517 147.834 5107 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.13 % Allowed : 17.39 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 1.13 (0.21), residues: 1650 helix: 2.01 (0.17), residues: 969 sheet: -0.89 (0.46), residues: 130 loop : -1.16 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 364 HIS 0.014 0.001 HIS N 554 PHE 0.012 0.001 PHE N 540 TYR 0.010 0.001 TYR B 88 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 1076) hydrogen bonds : angle 3.31211 ( 2814) covalent geometry : bond 0.00337 (20543) covalent geometry : angle 0.58153 (29019) Misc. bond : bond 0.00258 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8838 (pm20) cc_final: 0.8478 (pm20) REVERT: A 105 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8152 (mt-10) REVERT: B 31 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7710 (tttm) REVERT: C 78 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8588 (mp) REVERT: C 90 ASP cc_start: 0.8769 (t0) cc_final: 0.8306 (t0) REVERT: D 102 GLU cc_start: 0.8249 (mp0) cc_final: 0.7915 (pm20) REVERT: D 117 LYS cc_start: 0.8339 (ttpt) cc_final: 0.8070 (tttp) REVERT: E 120 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7576 (mtp) REVERT: F 93 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7170 (mp10) REVERT: G 72 ASP cc_start: 0.7842 (m-30) cc_final: 0.7582 (m-30) REVERT: G 92 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7725 (mt-10) REVERT: H 102 GLU cc_start: 0.7974 (pp20) cc_final: 0.7616 (pp20) REVERT: K 309 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: K 465 LEU cc_start: 0.8843 (mt) cc_final: 0.8442 (pt) REVERT: K 546 CYS cc_start: 0.8485 (t) cc_final: 0.7822 (t) REVERT: K 596 TYR cc_start: 0.8880 (t80) cc_final: 0.8595 (t80) REVERT: K 615 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8266 (pt) REVERT: N 364 TRP cc_start: 0.9266 (t60) cc_final: 0.9006 (t60) REVERT: N 478 HIS cc_start: 0.8325 (t70) cc_final: 0.7911 (t70) outliers start: 31 outliers final: 21 residues processed: 167 average time/residue: 1.5561 time to fit residues: 287.6172 Evaluate side-chains 168 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** 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 = 0.3834 r_free = 0.3834 target = 0.091489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.064891 restraints weight = 58078.767| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.31 r_work: 0.3122 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20545 Z= 0.158 Angle : 0.580 7.820 29019 Z= 0.328 Chirality : 0.037 0.137 3281 Planarity : 0.004 0.039 2661 Dihedral : 27.477 147.418 5107 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.99 % Allowed : 17.53 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 1.14 (0.21), residues: 1650 helix: 2.00 (0.17), residues: 971 sheet: -0.88 (0.46), residues: 130 loop : -1.11 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 364 HIS 0.014 0.001 HIS N 554 PHE 0.012 0.001 PHE N 540 TYR 0.009 0.001 TYR D 37 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 1076) hydrogen bonds : angle 3.31151 ( 2814) covalent geometry : bond 0.00358 (20543) covalent geometry : angle 0.58001 (29019) Misc. bond : bond 0.00254 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8832 (pm20) cc_final: 0.8475 (pm20) REVERT: A 105 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8174 (mt-10) REVERT: B 31 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7714 (tttm) REVERT: C 78 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8566 (mp) REVERT: C 90 ASP cc_start: 0.8773 (t0) cc_final: 0.8300 (t0) REVERT: D 102 GLU cc_start: 0.8256 (mp0) cc_final: 0.7955 (pm20) REVERT: D 117 LYS cc_start: 0.8337 (ttpt) cc_final: 0.8072 (tttm) REVERT: F 93 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: G 24 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7843 (mm110) REVERT: G 72 ASP cc_start: 0.7843 (m-30) cc_final: 0.7582 (m-30) REVERT: G 92 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7631 (mt-10) REVERT: G 95 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8840 (tptt) REVERT: H 102 GLU cc_start: 0.7952 (pp20) cc_final: 0.7585 (pp20) REVERT: K 309 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8487 (mp0) REVERT: K 335 MET cc_start: 0.8597 (ttm) cc_final: 0.8331 (ttt) REVERT: K 436 MET cc_start: 0.9283 (mtp) cc_final: 0.8790 (pmm) REVERT: K 465 LEU cc_start: 0.8846 (mt) cc_final: 0.8439 (pt) REVERT: K 546 CYS cc_start: 0.8473 (t) cc_final: 0.7805 (t) REVERT: K 596 TYR cc_start: 0.8874 (t80) cc_final: 0.8584 (t80) REVERT: K 615 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8268 (pt) REVERT: N 364 TRP cc_start: 0.9262 (t60) cc_final: 0.9018 (t60) REVERT: N 478 HIS cc_start: 0.8341 (t70) cc_final: 0.7902 (t70) outliers start: 29 outliers final: 22 residues processed: 171 average time/residue: 1.5308 time to fit residues: 290.3817 Evaluate side-chains 169 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 352 THR Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** 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 = 0.3814 r_free = 0.3814 target = 0.090646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.063722 restraints weight = 58292.362| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.35 r_work: 0.3099 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20545 Z= 0.185 Angle : 0.595 10.699 29019 Z= 0.335 Chirality : 0.037 0.163 3281 Planarity : 0.004 0.049 2661 Dihedral : 27.519 147.578 5107 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.20 % Allowed : 17.66 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 1.10 (0.21), residues: 1650 helix: 1.98 (0.17), residues: 969 sheet: -0.91 (0.46), residues: 130 loop : -1.15 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.014 0.001 HIS N 554 PHE 0.012 0.001 PHE N 540 TYR 0.009 0.001 TYR F 88 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 1076) hydrogen bonds : angle 3.34990 ( 2814) covalent geometry : bond 0.00425 (20543) covalent geometry : angle 0.59498 (29019) Misc. bond : bond 0.00267 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12909.78 seconds wall clock time: 222 minutes 40.20 seconds (13360.20 seconds total)