Starting phenix.real_space_refine on Tue Jun 17 00:13:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liu_63123/06_2025/9liu_63123.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liu_63123/06_2025/9liu_63123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9liu_63123/06_2025/9liu_63123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liu_63123/06_2025/9liu_63123.map" model { file = "/net/cci-nas-00/data/ceres_data/9liu_63123/06_2025/9liu_63123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liu_63123/06_2025/9liu_63123.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 298 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 11469 2.51 5 N 3565 2.21 5 O 4215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19587 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3738 Classifications: {'peptide': 455} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 437} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3738 Classifications: {'peptide': 455} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 437} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.66, per 1000 atoms: 0.75 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: 7.89 Conformation dependent library (CDL) restraints added in 2.1 seconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 14 sheets defined 60.8% alpha, 6.6% beta 144 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 11.85 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: 15.20 Time building geometry restraints manager: 8.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3747 1.33 - 1.45: 6134 1.45 - 1.57: 10006 1.57 - 1.69: 592 1.69 - 1.82: 64 Bond restraints: 20543 Sorted by residual: bond pdb=" C4 ATP N1202 " pdb=" C5 ATP N1202 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C4 ATP K1202 " pdb=" C5 ATP K1202 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 bond pdb=" C5 ATP K1202 " pdb=" C6 ATP K1202 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.22e+01 bond pdb=" C5 ATP N1202 " pdb=" C6 ATP N1202 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.19e+01 bond pdb=" C5 ATP K1202 " pdb=" N7 ATP K1202 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.19e+01 ... (remaining 20538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 28957 4.84 - 9.68: 58 9.68 - 14.53: 0 14.53 - 19.37: 0 19.37 - 24.21: 4 Bond angle restraints: 29019 Sorted by residual: angle pdb=" PA ATP K1202 " pdb=" O3A ATP K1202 " pdb=" PB ATP K1202 " ideal model delta sigma weight residual 136.83 112.62 24.21 1.00e+00 1.00e+00 5.86e+02 angle pdb=" PA ATP N1202 " pdb=" O3A ATP N1202 " pdb=" PB ATP N1202 " ideal model delta sigma weight residual 136.83 112.64 24.19 1.00e+00 1.00e+00 5.85e+02 angle pdb=" PB ATP N1202 " pdb=" O3B ATP N1202 " pdb=" PG ATP N1202 " ideal model delta sigma weight residual 139.87 120.22 19.65 1.00e+00 1.00e+00 3.86e+02 angle pdb=" PB ATP K1202 " pdb=" O3B ATP K1202 " pdb=" PG ATP K1202 " ideal model delta sigma weight residual 139.87 120.28 19.59 1.00e+00 1.00e+00 3.84e+02 angle pdb=" C5 ATP N1202 " pdb=" C4 ATP N1202 " pdb=" N3 ATP N1202 " ideal model delta sigma weight residual 126.80 118.52 8.28 1.00e+00 1.00e+00 6.85e+01 ... (remaining 29014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.60: 9823 31.60 - 63.20: 1824 63.20 - 94.80: 55 94.80 - 126.40: 0 126.40 - 158.00: 2 Dihedral angle restraints: 11704 sinusoidal: 6790 harmonic: 4914 Sorted by residual: dihedral pdb=" CA ILE N 585 " pdb=" C ILE N 585 " pdb=" N ASN N 586 " pdb=" CA ASN N 586 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE K 585 " pdb=" C ILE K 585 " pdb=" N ASN K 586 " pdb=" CA ASN K 586 " ideal model delta harmonic sigma weight residual -180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 11701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1815 0.037 - 0.073: 1058 0.073 - 0.110: 338 0.110 - 0.147: 65 0.147 - 0.184: 5 Chirality restraints: 3281 Sorted by residual: chirality pdb=" CA ILE K 548 " pdb=" N ILE K 548 " pdb=" C ILE K 548 " pdb=" CB ILE K 548 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CG LEU K 465 " pdb=" CB LEU K 465 " pdb=" CD1 LEU K 465 " pdb=" CD2 LEU K 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CG LEU N 465 " pdb=" CB LEU N 465 " pdb=" CD1 LEU N 465 " pdb=" CD2 LEU N 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 3278 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER N 188 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.51e+01 pdb=" N PRO N 189 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO N 189 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO N 189 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 188 " -0.064 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO K 189 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO K 189 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO K 189 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 50 " -0.018 2.00e-02 2.50e+03 2.19e-02 9.63e+00 pdb=" CG TYR C 50 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR C 50 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 50 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C 50 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR C 50 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 50 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 50 " -0.002 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 291 2.59 - 3.17: 16725 3.17 - 3.74: 33752 3.74 - 4.32: 47783 4.32 - 4.90: 70993 Nonbonded interactions: 169544 Sorted by model distance: nonbonded pdb=" N2 DG I 6 " pdb=" O2 DC J 142 " model vdw 2.011 2.496 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.011 3.040 nonbonded pdb="MG MG N1201 " pdb=" O3A ATP N1202 " model vdw 2.031 2.170 nonbonded pdb="MG MG K1201 " pdb=" O3A ATP K1202 " model vdw 2.031 2.170 nonbonded pdb="MG MG K1201 " pdb=" O1G ATP K1202 " model vdw 2.051 2.170 ... (remaining 169539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 15 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 69.190 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:18.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.855 20545 Z= 0.975 Angle : 0.887 24.211 29019 Z= 0.566 Chirality : 0.048 0.184 3281 Planarity : 0.005 0.097 2661 Dihedral : 24.805 158.001 8518 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.71 % Allowed : 1.51 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1650 helix: 0.87 (0.17), residues: 947 sheet: -0.71 (0.46), residues: 128 loop : -1.65 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 364 HIS 0.013 0.002 HIS G 31 PHE 0.020 0.002 PHE N 574 TYR 0.051 0.002 TYR C 50 ARG 0.009 0.001 ARG N 520 Details of bonding type rmsd hydrogen bonds : bond 0.12109 ( 1076) hydrogen bonds : angle 4.86837 ( 2814) covalent geometry : bond 0.01112 (20543) covalent geometry : angle 0.88731 (29019) Misc. bond : bond 0.83883 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 2.527 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: 2.0271 time to fit residues: 529.5304 Evaluate side-chains 148 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 577 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 75 HIS G 24 GLN K 467 ASN K 642 GLN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 642 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.090195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.063415 restraints weight = 57856.605| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.32 r_work: 0.3073 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20545 Z= 0.199 Angle : 0.620 7.410 29019 Z= 0.349 Chirality : 0.039 0.160 3281 Planarity : 0.004 0.056 2661 Dihedral : 27.919 158.216 5121 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.51 % Allowed : 11.34 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1650 helix: 1.65 (0.17), residues: 960 sheet: -0.85 (0.45), residues: 132 loop : -1.36 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.007 0.001 HIS G 31 PHE 0.014 0.001 PHE N 540 TYR 0.011 0.001 TYR K 499 ARG 0.007 0.000 ARG N 614 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 1076) hydrogen bonds : angle 3.70028 ( 2814) covalent geometry : bond 0.00451 (20543) covalent geometry : angle 0.62036 (29019) Misc. bond : bond 0.00321 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 1.792 Fit side-chains REVERT: A 59 GLU cc_start: 0.8916 (pm20) cc_final: 0.8670 (pm20) REVERT: B 93 GLN cc_start: 0.8093 (mt0) cc_final: 0.7881 (mm-40) REVERT: C 90 ASP cc_start: 0.8703 (t0) cc_final: 0.8412 (t0) REVERT: C 92 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: D 117 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8101 (tttp) REVERT: E 58 THR cc_start: 0.8824 (p) cc_final: 0.8586 (t) REVERT: E 133 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: F 93 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: H 110 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8111 (mt-10) outliers start: 22 outliers final: 4 residues processed: 188 average time/residue: 1.8500 time to fit residues: 383.4583 Evaluate side-chains 151 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 24 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.090841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.064161 restraints weight = 57666.000| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.32 r_work: 0.3100 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20545 Z= 0.167 Angle : 0.580 6.334 29019 Z= 0.328 Chirality : 0.038 0.141 3281 Planarity : 0.004 0.041 2661 Dihedral : 27.672 155.326 5108 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.13 % Allowed : 13.54 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1650 helix: 1.91 (0.17), residues: 964 sheet: -0.86 (0.45), residues: 132 loop : -1.28 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.010 0.001 HIS N 554 PHE 0.014 0.001 PHE N 540 TYR 0.010 0.001 TYR B 51 ARG 0.006 0.000 ARG K 341 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 1076) hydrogen bonds : angle 3.44932 ( 2814) covalent geometry : bond 0.00375 (20543) covalent geometry : angle 0.57958 (29019) Misc. bond : bond 0.00286 ( 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 191 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8904 (pm20) cc_final: 0.8619 (pm20) REVERT: B 93 GLN cc_start: 0.8101 (mt0) cc_final: 0.7880 (mm-40) REVERT: C 64 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7939 (tm-30) REVERT: C 78 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8601 (mp) REVERT: C 90 ASP cc_start: 0.8725 (t0) cc_final: 0.8319 (t0) REVERT: D 90 GLU cc_start: 0.8741 (mp0) cc_final: 0.8517 (mp0) REVERT: E 133 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: F 74 GLU cc_start: 0.8790 (pt0) cc_final: 0.8475 (mt-10) REVERT: F 93 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: G 24 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7821 (mm-40) REVERT: G 95 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8860 (tptt) REVERT: H 65 ASP cc_start: 0.8831 (t0) cc_final: 0.8626 (t0) REVERT: K 570 LYS cc_start: 0.8652 (mmpt) cc_final: 0.8443 (mmpt) REVERT: K 615 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8449 (pt) outliers start: 31 outliers final: 9 residues processed: 180 average time/residue: 1.6148 time to fit residues: 322.0557 Evaluate side-chains 154 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Chi-restraints excluded: chain N residue 609 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 137 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN G 24 GLN H 64 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.091294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.064581 restraints weight = 58039.782| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.32 r_work: 0.3106 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20545 Z= 0.161 Angle : 0.568 6.972 29019 Z= 0.323 Chirality : 0.037 0.142 3281 Planarity : 0.004 0.041 2661 Dihedral : 27.576 153.222 5108 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.82 % Allowed : 13.75 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.22), residues: 1650 helix: 2.00 (0.17), residues: 968 sheet: -0.86 (0.45), residues: 132 loop : -1.27 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.010 0.001 HIS N 554 PHE 0.017 0.001 PHE K 183 TYR 0.009 0.001 TYR B 51 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 1076) hydrogen bonds : angle 3.32396 ( 2814) covalent geometry : bond 0.00363 (20543) covalent geometry : angle 0.56849 (29019) Misc. bond : bond 0.00261 ( 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 198 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8912 (pm20) cc_final: 0.8580 (pm20) REVERT: A 105 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8217 (mt-10) REVERT: B 31 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7706 (tttm) REVERT: B 93 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7913 (mm-40) REVERT: C 64 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7866 (tm-30) REVERT: C 78 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8591 (mp) REVERT: C 90 ASP cc_start: 0.8769 (t0) cc_final: 0.8294 (t0) REVERT: D 90 GLU cc_start: 0.8734 (mp0) cc_final: 0.8522 (mp0) REVERT: D 117 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8089 (tttp) REVERT: E 120 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7547 (mtp) REVERT: F 92 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8310 (ttp80) REVERT: F 93 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: G 24 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7825 (mm-40) REVERT: G 72 ASP cc_start: 0.7834 (m-30) cc_final: 0.7627 (m-30) REVERT: G 95 LYS cc_start: 0.9249 (ttmt) cc_final: 0.8856 (tptt) REVERT: K 309 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8465 (mp0) REVERT: K 615 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8446 (pt) REVERT: N 478 HIS cc_start: 0.8280 (t70) cc_final: 0.8033 (t70) REVERT: N 527 MET cc_start: 0.7345 (mpt) cc_final: 0.7035 (mpp) outliers start: 41 outliers final: 13 residues processed: 185 average time/residue: 1.6450 time to fit residues: 336.9420 Evaluate side-chains 165 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 E residue 120 MET Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain 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 516 GLU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 615 ILE 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 517 GLU 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 121 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 158 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.088566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.061520 restraints weight = 58858.673| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.35 r_work: 0.3042 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 20545 Z= 0.324 Angle : 0.658 7.620 29019 Z= 0.369 Chirality : 0.042 0.152 3281 Planarity : 0.005 0.043 2661 Dihedral : 28.041 151.990 5108 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.16 % Allowed : 14.85 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1650 helix: 1.74 (0.17), residues: 968 sheet: -1.02 (0.45), residues: 130 loop : -1.35 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 364 HIS 0.012 0.002 HIS N 554 PHE 0.014 0.002 PHE N 540 TYR 0.013 0.002 TYR E 54 ARG 0.005 0.001 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.06318 ( 1076) hydrogen bonds : angle 3.66366 ( 2814) covalent geometry : bond 0.00741 (20543) covalent geometry : angle 0.65781 (29019) Misc. bond : bond 0.00337 ( 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 196 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8942 (pm20) cc_final: 0.8552 (pm20) REVERT: A 105 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8260 (mt-10) REVERT: B 31 LYS cc_start: 0.8297 (ttmm) cc_final: 0.7788 (tttm) REVERT: C 64 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7854 (tm-30) REVERT: C 78 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8491 (mp) REVERT: C 90 ASP cc_start: 0.8826 (t0) cc_final: 0.8383 (t0) REVERT: C 92 GLU cc_start: 0.8603 (tp30) cc_final: 0.8348 (mm-30) REVERT: E 129 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8229 (tmt170) REVERT: F 92 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8372 (ttp80) REVERT: F 93 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: G 24 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7839 (mm-40) REVERT: G 95 LYS cc_start: 0.9261 (ttmt) cc_final: 0.8859 (tptt) REVERT: N 436 MET cc_start: 0.7580 (mtp) cc_final: 0.7343 (ptp) REVERT: N 478 HIS cc_start: 0.8383 (t70) cc_final: 0.8069 (t70) outliers start: 46 outliers final: 22 residues processed: 181 average time/residue: 1.6224 time to fit residues: 324.5227 Evaluate side-chains 169 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 F residue 24 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 517 GLU Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 64 ASN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.091034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.064344 restraints weight = 58612.703| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.34 r_work: 0.3112 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20545 Z= 0.158 Angle : 0.575 8.288 29019 Z= 0.326 Chirality : 0.037 0.139 3281 Planarity : 0.004 0.040 2661 Dihedral : 27.545 149.626 5108 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.06 % Allowed : 16.36 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1650 helix: 1.98 (0.17), residues: 968 sheet: -1.04 (0.45), residues: 130 loop : -1.22 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 364 HIS 0.013 0.001 HIS N 554 PHE 0.014 0.001 PHE G 25 TYR 0.010 0.001 TYR N 545 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 1076) hydrogen bonds : angle 3.34143 ( 2814) covalent geometry : bond 0.00357 (20543) covalent geometry : angle 0.57491 (29019) Misc. bond : bond 0.00242 ( 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 186 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8869 (pm20) cc_final: 0.8545 (pm20) REVERT: A 105 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8217 (mt-10) REVERT: B 31 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7699 (tttm) REVERT: C 78 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8592 (mp) REVERT: C 90 ASP cc_start: 0.8777 (t0) cc_final: 0.8331 (t0) REVERT: E 120 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7544 (mtp) REVERT: F 92 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8271 (ttp80) REVERT: F 93 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: G 72 ASP cc_start: 0.7848 (m-30) cc_final: 0.7603 (m-30) REVERT: G 92 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7676 (mt-10) REVERT: G 95 LYS cc_start: 0.9264 (ttmt) cc_final: 0.8849 (tptt) REVERT: H 102 GLU cc_start: 0.7926 (pp20) cc_final: 0.7554 (pp20) REVERT: K 335 MET cc_start: 0.8620 (ttm) cc_final: 0.8316 (ttt) REVERT: K 465 LEU cc_start: 0.8841 (mt) cc_final: 0.8415 (pt) REVERT: K 546 CYS cc_start: 0.8434 (t) cc_final: 0.7793 (t) REVERT: K 596 TYR cc_start: 0.8911 (t80) cc_final: 0.8562 (t80) REVERT: N 478 HIS cc_start: 0.8477 (t70) cc_final: 0.8079 (t70) outliers start: 30 outliers final: 16 residues processed: 176 average time/residue: 1.6863 time to fit residues: 328.5573 Evaluate side-chains 162 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 92 ARG 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 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 517 GLU Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS H 64 ASN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.090162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.063206 restraints weight = 58093.959| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.34 r_work: 0.3094 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20545 Z= 0.185 Angle : 0.583 7.466 29019 Z= 0.330 Chirality : 0.038 0.159 3281 Planarity : 0.004 0.040 2661 Dihedral : 27.623 148.965 5107 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.68 % Allowed : 16.77 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1650 helix: 1.99 (0.17), residues: 968 sheet: -1.03 (0.45), residues: 130 loop : -1.19 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 364 HIS 0.012 0.001 HIS N 554 PHE 0.013 0.001 PHE N 540 TYR 0.009 0.001 TYR D 37 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 1076) hydrogen bonds : angle 3.36856 ( 2814) covalent geometry : bond 0.00421 (20543) covalent geometry : angle 0.58343 (29019) Misc. bond : bond 0.00272 ( 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 190 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8857 (pm20) cc_final: 0.8486 (pm20) REVERT: A 105 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8209 (mt-10) REVERT: B 31 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7731 (tttm) REVERT: C 64 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7910 (tm-30) REVERT: C 90 ASP cc_start: 0.8824 (t0) cc_final: 0.8335 (t0) REVERT: E 120 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7634 (mtp) REVERT: F 92 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8274 (ttp80) REVERT: F 93 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: G 72 ASP cc_start: 0.7818 (m-30) cc_final: 0.7563 (m-30) REVERT: G 92 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7696 (mt-10) REVERT: G 95 LYS cc_start: 0.9270 (ttmt) cc_final: 0.8851 (tptt) REVERT: H 102 GLU cc_start: 0.7937 (pp20) cc_final: 0.7555 (pp20) REVERT: K 309 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8529 (mp0) REVERT: K 465 LEU cc_start: 0.8874 (mt) cc_final: 0.8389 (pt) REVERT: K 546 CYS cc_start: 0.8491 (t) cc_final: 0.7805 (t) REVERT: K 596 TYR cc_start: 0.8867 (t80) cc_final: 0.8542 (t80) REVERT: N 478 HIS cc_start: 0.8492 (t70) cc_final: 0.8117 (t70) outliers start: 39 outliers final: 23 residues processed: 177 average time/residue: 2.2557 time to fit residues: 437.3230 Evaluate side-chains 170 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 3.269 ------------------------------------------------------------------------------- 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 99 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain 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 320 TYR Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 517 GLU Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 182 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 113 optimal weight: 0.0010 chunk 188 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN H 64 ASN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.090940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.064111 restraints weight = 58437.442| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.34 r_work: 0.3111 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20545 Z= 0.143 Angle : 0.585 10.134 29019 Z= 0.329 Chirality : 0.037 0.154 3281 Planarity : 0.004 0.039 2661 Dihedral : 27.593 147.317 5107 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.41 % Allowed : 17.66 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.22), residues: 1650 helix: 2.01 (0.17), residues: 968 sheet: -1.02 (0.46), residues: 130 loop : -1.14 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 364 HIS 0.013 0.001 HIS N 554 PHE 0.012 0.001 PHE N 540 TYR 0.011 0.001 TYR F 88 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 1076) hydrogen bonds : angle 3.32199 ( 2814) covalent geometry : bond 0.00321 (20543) covalent geometry : angle 0.58545 (29019) Misc. bond : bond 0.00258 ( 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 184 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8835 (pm20) cc_final: 0.8469 (pm20) REVERT: A 105 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8197 (mt-10) REVERT: B 31 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7699 (tttm) REVERT: C 64 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7841 (tm-30) REVERT: C 90 ASP cc_start: 0.8810 (t0) cc_final: 0.8342 (t0) REVERT: E 120 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7548 (mtp) REVERT: F 92 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8237 (ttp80) REVERT: F 93 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: G 72 ASP cc_start: 0.7859 (m-30) cc_final: 0.7604 (m-30) REVERT: G 92 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7692 (mt-10) REVERT: G 95 LYS cc_start: 0.9260 (ttmt) cc_final: 0.8832 (tptt) REVERT: H 102 GLU cc_start: 0.7925 (pp20) cc_final: 0.7538 (pp20) REVERT: K 309 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8534 (mp0) REVERT: K 436 MET cc_start: 0.9325 (mtp) cc_final: 0.8873 (pmm) REVERT: K 465 LEU cc_start: 0.8839 (mt) cc_final: 0.8356 (pt) REVERT: K 527 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8250 (mtt) REVERT: K 546 CYS cc_start: 0.8476 (t) cc_final: 0.7799 (t) REVERT: K 596 TYR cc_start: 0.8884 (t80) cc_final: 0.8523 (t80) REVERT: N 478 HIS cc_start: 0.8487 (t70) cc_final: 0.8137 (t70) outliers start: 35 outliers final: 24 residues processed: 174 average time/residue: 2.6545 time to fit residues: 514.2570 Evaluate side-chains 171 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 2.961 ------------------------------------------------------------------------------- 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 D residue 99 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG 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 320 TYR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 527 MET Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain N residue 352 THR Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 517 GLU Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 587 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 185 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN H 64 ASN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.090965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.064147 restraints weight = 58038.771| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.33 r_work: 0.3115 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20545 Z= 0.163 Angle : 0.586 7.473 29019 Z= 0.331 Chirality : 0.037 0.166 3281 Planarity : 0.004 0.037 2661 Dihedral : 27.507 146.896 5107 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.13 % Allowed : 18.21 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1650 helix: 2.02 (0.17), residues: 971 sheet: -0.91 (0.46), residues: 130 loop : -1.14 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 364 HIS 0.013 0.001 HIS N 554 PHE 0.012 0.001 PHE N 540 TYR 0.010 0.001 TYR F 88 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04351 ( 1076) hydrogen bonds : angle 3.33176 ( 2814) covalent geometry : bond 0.00371 (20543) covalent geometry : angle 0.58552 (29019) Misc. bond : bond 0.00255 ( 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 179 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8818 (pm20) cc_final: 0.8460 (pm20) REVERT: A 105 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8194 (mt-10) REVERT: B 31 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7693 (tttm) REVERT: C 64 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 90 ASP cc_start: 0.8825 (t0) cc_final: 0.8351 (t0) REVERT: D 117 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8121 (tttp) REVERT: E 120 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7579 (mtp) REVERT: F 92 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8269 (ttp80) REVERT: F 93 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: G 72 ASP cc_start: 0.7853 (m-30) cc_final: 0.7601 (m-30) REVERT: G 95 LYS cc_start: 0.9262 (ttmt) cc_final: 0.8840 (tptt) REVERT: K 309 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8526 (mp0) REVERT: K 335 MET cc_start: 0.8595 (ttm) cc_final: 0.8351 (ttt) REVERT: K 436 MET cc_start: 0.9308 (mtp) cc_final: 0.8866 (pmm) REVERT: K 465 LEU cc_start: 0.8795 (mt) cc_final: 0.8396 (pt) REVERT: K 546 CYS cc_start: 0.8460 (t) cc_final: 0.7771 (t) REVERT: K 596 TYR cc_start: 0.8856 (t80) cc_final: 0.8531 (t80) REVERT: N 364 TRP cc_start: 0.9268 (t60) cc_final: 0.9062 (t60) REVERT: N 478 HIS cc_start: 0.8535 (t70) cc_final: 0.8150 (t70) outliers start: 31 outliers final: 20 residues processed: 170 average time/residue: 1.7175 time to fit residues: 323.7898 Evaluate side-chains 167 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG 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 320 TYR 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 K residue 615 ILE 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 517 GLU Chi-restraints excluded: chain N residue 577 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN H 64 ASN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.091400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.064683 restraints weight = 58344.973| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.33 r_work: 0.3120 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20545 Z= 0.162 Angle : 0.595 11.676 29019 Z= 0.333 Chirality : 0.037 0.160 3281 Planarity : 0.004 0.039 2661 Dihedral : 27.498 146.752 5107 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.86 % Allowed : 18.63 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.22), residues: 1650 helix: 2.02 (0.17), residues: 971 sheet: -0.91 (0.46), residues: 130 loop : -1.10 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.013 0.001 HIS N 554 PHE 0.012 0.001 PHE N 540 TYR 0.011 0.001 TYR F 88 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 1076) hydrogen bonds : angle 3.34037 ( 2814) covalent geometry : bond 0.00369 (20543) covalent geometry : angle 0.59498 (29019) Misc. bond : bond 0.00261 ( 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 171 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8820 (pm20) cc_final: 0.8462 (pm20) REVERT: A 105 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8187 (mt-10) REVERT: B 31 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7674 (tttm) REVERT: C 64 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7814 (tm-30) REVERT: C 90 ASP cc_start: 0.8815 (t0) cc_final: 0.8332 (t0) REVERT: D 117 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8109 (tttp) REVERT: E 120 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7585 (mtp) REVERT: F 92 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8262 (ttp80) REVERT: F 93 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7164 (mp10) REVERT: G 72 ASP cc_start: 0.7852 (m-30) cc_final: 0.7599 (m-30) REVERT: G 95 LYS cc_start: 0.9257 (ttmt) cc_final: 0.8833 (tptt) REVERT: K 309 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8541 (mp0) REVERT: K 335 MET cc_start: 0.8599 (ttm) cc_final: 0.8357 (ttt) REVERT: K 436 MET cc_start: 0.9287 (mtp) cc_final: 0.8853 (pmm) REVERT: K 465 LEU cc_start: 0.8792 (mt) cc_final: 0.8390 (pt) REVERT: K 546 CYS cc_start: 0.8457 (t) cc_final: 0.7759 (t) REVERT: K 596 TYR cc_start: 0.8842 (t80) cc_final: 0.8517 (t80) REVERT: N 478 HIS cc_start: 0.8539 (t70) cc_final: 0.8148 (t70) outliers start: 27 outliers final: 20 residues processed: 163 average time/residue: 1.6886 time to fit residues: 303.3365 Evaluate side-chains 164 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG 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 320 TYR 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 K residue 615 ILE Chi-restraints excluded: chain N residue 352 THR Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 517 GLU Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 609 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN H 64 ASN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.091626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.064951 restraints weight = 58708.806| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.34 r_work: 0.3125 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20545 Z= 0.161 Angle : 0.584 7.727 29019 Z= 0.329 Chirality : 0.037 0.144 3281 Planarity : 0.004 0.038 2661 Dihedral : 27.458 146.690 5107 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.06 % Allowed : 18.42 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1650 helix: 2.03 (0.17), residues: 971 sheet: -0.89 (0.46), residues: 130 loop : -1.08 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP N 364 HIS 0.013 0.001 HIS N 554 PHE 0.011 0.001 PHE N 540 TYR 0.011 0.001 TYR F 88 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 1076) hydrogen bonds : angle 3.32496 ( 2814) covalent geometry : bond 0.00364 (20543) covalent geometry : angle 0.58365 (29019) Misc. bond : bond 0.00251 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15397.58 seconds wall clock time: 271 minutes 6.70 seconds (16266.70 seconds total)