Starting phenix.real_space_refine on Sat Jul 4 07:24:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liu_63123/07_2026/9liu_63123.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liu_63123/07_2026/9liu_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 { model { file = "/net/cci-nas-00/data/ceres_data/9liu_63123/07_2026/9liu_63123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liu_63123/07_2026/9liu_63123.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9liu_63123/07_2026/9liu_63123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liu_63123/07_2026/9liu_63123.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.60, per 1000 atoms: 0.18 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: 1.80 Conformation dependent library (CDL) restraints added in 564.1 milliseconds 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: 2.48 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: 3.73 Time building geometry restraints manager: 2.29 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=" C3' DG J 70 " pdb=" O3' DG J 70 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.24e+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 - 0.039: 1786 0.039 - 0.078: 996 0.078 - 0.117: 376 0.117 - 0.156: 100 0.156 - 0.195: 23 Chirality restraints: 3281 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" C3' DG I 126 " pdb=" C4' DG I 126 " pdb=" O3' DG I 126 " pdb=" C2' DG I 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" C3' DA I 98 " pdb=" C4' DA I 98 " pdb=" O3' DA I 98 " pdb=" C2' DA I 98 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.07e-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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.730 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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= 1.188 Angle : 0.967 24.211 29019 Z= 0.748 Chirality : 0.055 0.195 3281 Planarity : 0.005 0.097 2661 Dihedral : 24.805 158.001 8518 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (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 ARG 0.009 0.001 ARG N 520 TYR 0.051 0.002 TYR C 50 PHE 0.020 0.002 PHE N 574 TRP 0.018 0.002 TRP K 364 HIS 0.013 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01139 / 0.85 (20543) covalent geometry : angle 0.96723 / 0.75 (29019) hydrogen bonds : bond 0.12109 / 8.14 ( 1076) hydrogen bonds : angle 4.86837 / 3.51 ( 2814) Misc. bond : bond 0.83883 / 42.18 ( 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 : 0.581 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: 0.6677 time to fit residues: 174.6316 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 : 0.392 ------------------------------------------------------------------------------- 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 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 ASN 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 = 0.090214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.063266 restraints weight = 57673.746| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.34 r_work: 0.3089 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20545 Z= 0.160 Angle : 0.690 7.993 29019 Z= 0.378 Chirality : 0.048 0.274 3281 Planarity : 0.005 0.074 2661 Dihedral : 28.444 162.652 5121 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.31 % Allowed : 11.62 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1650 helix: 1.44 (0.17), residues: 967 sheet: -1.04 (0.45), residues: 132 loop : -1.32 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 63 TYR 0.013 0.001 TYR F 51 PHE 0.011 0.001 PHE N 369 TRP 0.017 0.001 TRP K 364 HIS 0.010 0.002 HIS N 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (20543) covalent geometry : angle 0.68996 / 0.38 (29019) hydrogen bonds : bond 0.05462 / 3.79 ( 1076) hydrogen bonds : angle 3.86366 / 2.77 ( 2814) Misc. bond : bond 0.00389 / 0.19 ( 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 190 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.633 Fit side-chains REVERT: A 59 GLU cc_start: 0.8746 (pm20) cc_final: 0.8464 (pm20) REVERT: D 117 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8045 (tttp) REVERT: H 90 GLU cc_start: 0.8142 (mp0) cc_final: 0.7634 (mp0) REVERT: K 546 CYS cc_start: 0.8766 (t) cc_final: 0.8372 (t) REVERT: N 605 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8264 (p0) outliers start: 19 outliers final: 8 residues processed: 186 average time/residue: 0.6937 time to fit residues: 142.6122 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 : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 349 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 Chi-restraints excluded: chain N residue 605 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 175 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** 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 = 0.3797 r_free = 0.3797 target = 0.089309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.062186 restraints weight = 57920.232| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.35 r_work: 0.3061 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1475 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= 0.212 Angle : 0.669 7.356 29019 Z= 0.367 Chirality : 0.047 0.279 3281 Planarity : 0.004 0.049 2661 Dihedral : 28.321 163.237 5108 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.23 % Allowed : 11.75 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.21), residues: 1650 helix: 1.69 (0.17), residues: 958 sheet: -1.08 (0.45), residues: 132 loop : -1.26 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.010 0.001 TYR B 51 PHE 0.015 0.001 PHE N 540 TRP 0.018 0.001 TRP K 364 HIS 0.013 0.002 HIS N 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (20543) covalent geometry : angle 0.66850 / 0.37 (29019) hydrogen bonds : bond 0.06234 / 4.32 ( 1076) hydrogen bonds : angle 3.74320 / 2.71 ( 2814) Misc. bond : bond 0.00405 / 0.20 ( 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 196 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.635 Fit side-chains REVERT: A 59 GLU cc_start: 0.8900 (pm20) cc_final: 0.8569 (pm20) REVERT: B 77 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8638 (mtmt) REVERT: B 93 GLN cc_start: 0.8145 (mt0) cc_final: 0.7866 (mt0) REVERT: C 78 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8406 (mp) REVERT: C 90 ASP cc_start: 0.8467 (t0) cc_final: 0.8183 (t0) REVERT: F 93 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: G 95 LYS cc_start: 0.9257 (ttmt) cc_final: 0.8845 (tptt) REVERT: H 76 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8377 (ptp-170) REVERT: H 90 GLU cc_start: 0.8274 (mp0) cc_final: 0.7672 (mp0) REVERT: K 465 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8627 (pt) REVERT: K 546 CYS cc_start: 0.8835 (t) cc_final: 0.8327 (t) REVERT: N 436 MET cc_start: 0.7756 (mtp) cc_final: 0.7358 (mtp) REVERT: N 478 HIS cc_start: 0.8251 (t70) cc_final: 0.7930 (t70) outliers start: 47 outliers final: 16 residues processed: 184 average time/residue: 0.6553 time to fit residues: 133.7560 Evaluate side-chains 166 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 58 THR 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 93 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 465 LEU 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 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 159 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 23 optimal weight: 0.0070 chunk 45 optimal weight: 0.0970 chunk 81 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 145 optimal weight: 0.0070 chunk 132 optimal weight: 3.9990 overall best weight: 1.0218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3819 r_free = 0.3819 target = 0.090517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.063665 restraints weight = 57938.468| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.34 r_work: 0.3120 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20545 Z= 0.143 Angle : 0.630 7.238 29019 Z= 0.349 Chirality : 0.045 0.273 3281 Planarity : 0.004 0.045 2661 Dihedral : 28.199 162.296 5108 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.54 % Allowed : 13.68 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1650 helix: 1.81 (0.17), residues: 963 sheet: -1.09 (0.45), residues: 132 loop : -1.17 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.009 0.001 TYR N 499 PHE 0.013 0.001 PHE N 540 TRP 0.017 0.001 TRP K 364 HIS 0.014 0.001 HIS N 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (20543) covalent geometry : angle 0.62962 / 0.35 (29019) hydrogen bonds : bond 0.04865 / 3.38 ( 1076) hydrogen bonds : angle 3.56086 / 2.55 ( 2814) Misc. bond : bond 0.00421 / 0.22 ( 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 196 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8923 (pm20) cc_final: 0.8577 (pm20) REVERT: B 84 MET cc_start: 0.8604 (mmm) cc_final: 0.7812 (mmm) REVERT: B 93 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7897 (mm-40) REVERT: C 78 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8580 (mp) REVERT: C 90 ASP cc_start: 0.8533 (t0) cc_final: 0.8143 (t0) REVERT: D 65 ASP cc_start: 0.8561 (t0) cc_final: 0.8359 (t0) REVERT: E 58 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8381 (t) REVERT: F 93 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: G 95 LYS cc_start: 0.9277 (ttmt) cc_final: 0.8881 (tptt) REVERT: K 465 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8518 (pt) REVERT: K 546 CYS cc_start: 0.8763 (t) cc_final: 0.8309 (t) REVERT: N 436 MET cc_start: 0.7728 (mtp) cc_final: 0.7374 (mtp) REVERT: N 478 HIS cc_start: 0.8306 (t70) cc_final: 0.8063 (t70) outliers start: 37 outliers final: 11 residues processed: 184 average time/residue: 0.7302 time to fit residues: 147.9488 Evaluate side-chains 159 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 446 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 7 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 24 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** 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 = 0.3773 r_free = 0.3773 target = 0.088015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.060742 restraints weight = 57928.276| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.39 r_work: 0.3024 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 20545 Z= 0.338 Angle : 0.752 7.727 29019 Z= 0.402 Chirality : 0.051 0.269 3281 Planarity : 0.005 0.070 2661 Dihedral : 28.449 161.008 5108 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.23 % Allowed : 14.85 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1650 helix: 1.53 (0.17), residues: 960 sheet: -1.24 (0.45), residues: 132 loop : -1.35 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 341 TYR 0.012 0.002 TYR N 545 PHE 0.014 0.002 PHE N 540 TRP 0.019 0.001 TRP K 364 HIS 0.014 0.002 HIS N 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.34 (20543) covalent geometry : angle 0.75169 / 0.40 (29019) hydrogen bonds : bond 0.07994 / 5.55 ( 1076) hydrogen bonds : angle 3.87249 / 2.79 ( 2814) Misc. bond : bond 0.00427 / 0.22 ( 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 191 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8921 (pm20) cc_final: 0.8543 (pm20) REVERT: B 91 LYS cc_start: 0.9252 (ttmm) cc_final: 0.9031 (ttpp) REVERT: B 93 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8070 (mm-40) REVERT: C 78 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8432 (mp) REVERT: C 90 ASP cc_start: 0.8669 (t0) cc_final: 0.8228 (t0) REVERT: F 93 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: G 95 LYS cc_start: 0.9245 (ttmt) cc_final: 0.8829 (tptt) REVERT: K 444 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8747 (mp) REVERT: K 465 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8633 (pt) REVERT: K 546 CYS cc_start: 0.8873 (t) cc_final: 0.8305 (t) REVERT: N 436 MET cc_start: 0.7883 (mtp) cc_final: 0.7533 (mtp) REVERT: N 478 HIS cc_start: 0.8229 (t70) cc_final: 0.7919 (t70) outliers start: 47 outliers final: 21 residues processed: 175 average time/residue: 0.7303 time to fit residues: 141.8582 Evaluate side-chains 165 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN 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 H residue 98 LEU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 444 ILE Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain N residue 446 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 24 GLN E 76 GLN G 24 GLN G 31 HIS ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.090214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.063251 restraints weight = 57604.032| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.35 r_work: 0.3065 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20545 Z= 0.142 Angle : 0.639 8.384 29019 Z= 0.352 Chirality : 0.045 0.273 3281 Planarity : 0.004 0.046 2661 Dihedral : 28.269 160.811 5108 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.47 % Allowed : 15.67 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1650 helix: 1.80 (0.17), residues: 962 sheet: -1.29 (0.44), residues: 132 loop : -1.20 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.010 0.001 TYR N 545 PHE 0.012 0.001 PHE N 540 TRP 0.014 0.001 TRP K 364 HIS 0.012 0.001 HIS N 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (20543) covalent geometry : angle 0.63949 / 0.35 (29019) hydrogen bonds : bond 0.04865 / 3.39 ( 1076) hydrogen bonds : angle 3.55708 / 2.56 ( 2814) Misc. bond : bond 0.00336 / 0.18 ( 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 191 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8901 (pm20) cc_final: 0.8534 (pm20) REVERT: B 84 MET cc_start: 0.8587 (mmm) cc_final: 0.7778 (mmm) REVERT: B 93 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.8006 (mm-40) REVERT: C 24 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: C 78 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8448 (mp) REVERT: C 90 ASP cc_start: 0.8656 (t0) cc_final: 0.8208 (t0) REVERT: E 58 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8420 (t) REVERT: F 93 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7106 (mp10) REVERT: G 95 LYS cc_start: 0.9267 (ttmt) cc_final: 0.8832 (tptt) REVERT: K 465 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8447 (pt) REVERT: K 546 CYS cc_start: 0.8783 (t) cc_final: 0.8262 (t) REVERT: N 436 MET cc_start: 0.7783 (mtp) cc_final: 0.7431 (mtp) REVERT: N 478 HIS cc_start: 0.8310 (t70) cc_final: 0.8007 (t70) outliers start: 36 outliers final: 16 residues processed: 178 average time/residue: 0.7970 time to fit residues: 156.2230 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 : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 24 ASP 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 446 GLU Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 446 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 20 optimal weight: 0.1980 chunk 128 optimal weight: 0.3980 chunk 86 optimal weight: 30.0000 chunk 164 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 76 GLN G 24 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.090821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.064003 restraints weight = 58050.182| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.35 r_work: 0.3086 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20545 Z= 0.134 Angle : 0.631 10.849 29019 Z= 0.350 Chirality : 0.044 0.270 3281 Planarity : 0.004 0.043 2661 Dihedral : 28.082 159.886 5108 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.20 % Allowed : 16.49 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1650 helix: 1.87 (0.17), residues: 964 sheet: -1.24 (0.45), residues: 132 loop : -1.18 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.019 0.001 TYR N 545 PHE 0.015 0.001 PHE N 540 TRP 0.014 0.001 TRP N 364 HIS 0.013 0.001 HIS N 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (20543) covalent geometry : angle 0.63086 / 0.35 (29019) hydrogen bonds : bond 0.04616 / 3.22 ( 1076) hydrogen bonds : angle 3.48094 / 2.50 ( 2814) Misc. bond : bond 0.00292 / 0.15 ( 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 184 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8927 (pm20) cc_final: 0.8557 (pm20) REVERT: B 31 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7634 (tttm) REVERT: C 90 ASP cc_start: 0.8680 (t0) cc_final: 0.8227 (t0) REVERT: E 58 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8474 (t) REVERT: E 133 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: F 93 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: G 95 LYS cc_start: 0.9276 (ttmt) cc_final: 0.8867 (tptt) REVERT: N 364 TRP cc_start: 0.9283 (t60) cc_final: 0.8897 (t60) REVERT: N 436 MET cc_start: 0.7830 (mtp) cc_final: 0.7451 (mtp) REVERT: N 478 HIS cc_start: 0.8349 (t70) cc_final: 0.8023 (t70) outliers start: 32 outliers final: 14 residues processed: 171 average time/residue: 0.7771 time to fit residues: 146.6362 Evaluate side-chains 158 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 58 THR 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 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 446 GLU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 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 0 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 76 GLN ** K 288 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 = 0.3823 r_free = 0.3823 target = 0.090899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.064106 restraints weight = 57972.183| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.33 r_work: 0.3086 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20545 Z= 0.142 Angle : 0.634 11.169 29019 Z= 0.350 Chirality : 0.044 0.265 3281 Planarity : 0.004 0.042 2661 Dihedral : 28.019 158.869 5107 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.86 % Allowed : 17.87 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1650 helix: 1.90 (0.17), residues: 967 sheet: -1.09 (0.45), residues: 130 loop : -1.14 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 341 TYR 0.010 0.001 TYR D 37 PHE 0.013 0.001 PHE N 540 TRP 0.014 0.001 TRP K 364 HIS 0.015 0.001 HIS N 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (20543) covalent geometry : angle 0.63417 / 0.35 (29019) hydrogen bonds : bond 0.04669 / 3.26 ( 1076) hydrogen bonds : angle 3.43888 / 2.47 ( 2814) Misc. bond : bond 0.00278 / 0.15 ( 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 176 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8926 (pm20) cc_final: 0.8556 (pm20) REVERT: B 31 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7596 (tttm) REVERT: C 90 ASP cc_start: 0.8706 (t0) cc_final: 0.8256 (t0) REVERT: E 58 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8449 (t) REVERT: F 93 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7110 (mp10) REVERT: G 24 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7931 (mm110) REVERT: G 95 LYS cc_start: 0.9252 (ttmt) cc_final: 0.8830 (tptt) REVERT: K 309 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8451 (mp0) REVERT: K 465 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8441 (pt) REVERT: N 352 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7797 (m) REVERT: N 436 MET cc_start: 0.7822 (mtp) cc_final: 0.7466 (mtp) REVERT: N 478 HIS cc_start: 0.8351 (t70) cc_final: 0.8007 (t70) outliers start: 27 outliers final: 13 residues processed: 167 average time/residue: 0.7343 time to fit residues: 135.0327 Evaluate side-chains 157 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 58 THR 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 446 GLU Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 352 THR Chi-restraints excluded: chain N residue 446 GLU 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 88 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 76 GLN ** 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 = 0.3823 r_free = 0.3823 target = 0.090834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064054 restraints weight = 57595.779| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.31 r_work: 0.3087 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20545 Z= 0.146 Angle : 0.633 8.613 29019 Z= 0.350 Chirality : 0.044 0.265 3281 Planarity : 0.004 0.043 2661 Dihedral : 28.021 158.678 5107 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.79 % Allowed : 18.42 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1650 helix: 1.89 (0.17), residues: 971 sheet: -1.02 (0.46), residues: 130 loop : -1.16 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 341 TYR 0.015 0.001 TYR N 545 PHE 0.014 0.001 PHE N 540 TRP 0.024 0.001 TRP N 364 HIS 0.015 0.001 HIS N 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (20543) covalent geometry : angle 0.63260 / 0.35 (29019) hydrogen bonds : bond 0.04665 / 3.25 ( 1076) hydrogen bonds : angle 3.42394 / 2.46 ( 2814) Misc. bond : bond 0.00272 / 0.14 ( 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 168 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8931 (pm20) cc_final: 0.8557 (pm20) REVERT: B 31 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7587 (tttm) REVERT: B 84 MET cc_start: 0.8565 (mmm) cc_final: 0.7782 (tmm) REVERT: C 90 ASP cc_start: 0.8731 (t0) cc_final: 0.8302 (t0) REVERT: E 58 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8479 (t) REVERT: E 133 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: F 93 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: G 95 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8811 (tptt) REVERT: K 309 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8452 (mp0) REVERT: K 465 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8488 (pt) REVERT: N 478 HIS cc_start: 0.8379 (t70) cc_final: 0.8022 (t70) outliers start: 26 outliers final: 16 residues processed: 160 average time/residue: 0.7903 time to fit residues: 139.3772 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 : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 133 GLU 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 62 ILE 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 374 ILE Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 431 VAL Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 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 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 184 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 76 GLN ** 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 = 0.3829 r_free = 0.3829 target = 0.091216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064453 restraints weight = 58069.984| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.34 r_work: 0.3098 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20545 Z= 0.130 Angle : 0.630 10.215 29019 Z= 0.348 Chirality : 0.044 0.266 3281 Planarity : 0.004 0.060 2661 Dihedral : 28.000 157.269 5107 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.51 % Allowed : 18.49 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1650 helix: 1.92 (0.17), residues: 969 sheet: -1.02 (0.46), residues: 130 loop : -1.19 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.010 0.001 TYR N 545 PHE 0.013 0.001 PHE N 540 TRP 0.024 0.001 TRP N 364 HIS 0.015 0.001 HIS N 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (20543) covalent geometry : angle 0.63043 / 0.35 (29019) hydrogen bonds : bond 0.04470 / 3.13 ( 1076) hydrogen bonds : angle 3.39960 / 2.44 ( 2814) Misc. bond : bond 0.00273 / 0.14 ( 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 169 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8938 (pm20) cc_final: 0.8569 (pm20) REVERT: B 31 LYS cc_start: 0.8122 (ttmm) cc_final: 0.7627 (tttm) REVERT: C 64 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7895 (tm-30) REVERT: C 90 ASP cc_start: 0.8756 (t0) cc_final: 0.8306 (t0) REVERT: E 58 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8507 (t) REVERT: E 133 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: F 93 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7152 (mp10) REVERT: G 95 LYS cc_start: 0.9251 (ttmt) cc_final: 0.8836 (tptt) REVERT: K 309 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8451 (mp0) REVERT: K 465 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8482 (pt) REVERT: N 314 LYS cc_start: 0.9222 (ttmt) cc_final: 0.9000 (mtmm) REVERT: N 478 HIS cc_start: 0.8401 (t70) cc_final: 0.8036 (t70) outliers start: 22 outliers final: 15 residues processed: 161 average time/residue: 0.8270 time to fit residues: 146.5626 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 : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 133 GLU 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 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 446 GLU Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 431 VAL Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 185 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN E 76 GLN N 184 GLN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.091309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064535 restraints weight = 58039.400| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.33 r_work: 0.3098 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20545 Z= 0.139 Angle : 0.623 8.655 29019 Z= 0.345 Chirality : 0.043 0.264 3281 Planarity : 0.004 0.041 2661 Dihedral : 27.970 158.021 5107 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.44 % Allowed : 18.56 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.22), residues: 1650 helix: 1.94 (0.17), residues: 971 sheet: -1.00 (0.46), residues: 130 loop : -1.16 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 341 TYR 0.012 0.001 TYR D 37 PHE 0.014 0.001 PHE N 540 TRP 0.021 0.001 TRP N 364 HIS 0.015 0.001 HIS N 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (20543) covalent geometry : angle 0.62311 / 0.35 (29019) hydrogen bonds : bond 0.04525 / 3.17 ( 1076) hydrogen bonds : angle 3.38767 / 2.43 ( 2814) Misc. bond : bond 0.00267 / 0.14 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5988.28 seconds wall clock time: 102 minutes 48.60 seconds (6168.60 seconds total)