Starting phenix.real_space_refine on Thu Sep 18 18:50:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liu_63123/09_2025/9liu_63123.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liu_63123/09_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_63123/09_2025/9liu_63123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liu_63123/09_2025/9liu_63123.map" model { file = "/net/cci-nas-00/data/ceres_data/9liu_63123/09_2025/9liu_63123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liu_63123/09_2025/9liu_63123.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 298 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 11469 2.51 5 N 3565 2.21 5 O 4215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19587 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3738 Classifications: {'peptide': 455} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 437} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3738 Classifications: {'peptide': 455} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 437} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.22, per 1000 atoms: 0.22 Number of scatterers: 19587 At special positions: 0 Unit cell: (119.075, 124.487, 186.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 298 15.00 Mg 2 11.99 O 4215 8.00 N 3565 7.00 C 11469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 402.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 14 sheets defined 60.8% alpha, 6.6% beta 144 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 2.78 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: 4.32 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3747 1.33 - 1.45: 6134 1.45 - 1.57: 10006 1.57 - 1.69: 592 1.69 - 1.82: 64 Bond restraints: 20543 Sorted by residual: bond pdb=" C4 ATP N1202 " pdb=" C5 ATP N1202 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C4 ATP K1202 " pdb=" C5 ATP K1202 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 bond pdb=" C5 ATP K1202 " pdb=" C6 ATP K1202 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.22e+01 bond pdb=" C5 ATP N1202 " pdb=" C6 ATP N1202 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.19e+01 bond pdb=" C5 ATP K1202 " pdb=" N7 ATP K1202 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.19e+01 ... (remaining 20538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 28957 4.84 - 9.68: 58 9.68 - 14.53: 0 14.53 - 19.37: 0 19.37 - 24.21: 4 Bond angle restraints: 29019 Sorted by residual: angle pdb=" PA ATP K1202 " pdb=" O3A ATP K1202 " pdb=" PB ATP K1202 " ideal model delta sigma weight residual 136.83 112.62 24.21 1.00e+00 1.00e+00 5.86e+02 angle pdb=" PA ATP N1202 " pdb=" O3A ATP N1202 " pdb=" PB ATP N1202 " ideal model delta sigma weight residual 136.83 112.64 24.19 1.00e+00 1.00e+00 5.85e+02 angle pdb=" PB ATP N1202 " pdb=" O3B ATP N1202 " pdb=" PG ATP N1202 " ideal model delta sigma weight residual 139.87 120.22 19.65 1.00e+00 1.00e+00 3.86e+02 angle pdb=" PB ATP K1202 " pdb=" O3B ATP K1202 " pdb=" PG ATP K1202 " ideal model delta sigma weight residual 139.87 120.28 19.59 1.00e+00 1.00e+00 3.84e+02 angle pdb=" C5 ATP N1202 " pdb=" C4 ATP N1202 " pdb=" N3 ATP N1202 " ideal model delta sigma weight residual 126.80 118.52 8.28 1.00e+00 1.00e+00 6.85e+01 ... (remaining 29014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.60: 9823 31.60 - 63.20: 1824 63.20 - 94.80: 55 94.80 - 126.40: 0 126.40 - 158.00: 2 Dihedral angle restraints: 11704 sinusoidal: 6790 harmonic: 4914 Sorted by residual: dihedral pdb=" CA ILE N 585 " pdb=" C ILE N 585 " pdb=" N ASN N 586 " pdb=" CA ASN N 586 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE K 585 " pdb=" C ILE K 585 " pdb=" N ASN K 586 " pdb=" CA ASN K 586 " ideal model delta harmonic sigma weight residual -180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 11701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1815 0.037 - 0.073: 1058 0.073 - 0.110: 338 0.110 - 0.147: 65 0.147 - 0.184: 5 Chirality restraints: 3281 Sorted by residual: chirality pdb=" CA ILE K 548 " pdb=" N ILE K 548 " pdb=" C ILE K 548 " pdb=" CB ILE K 548 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CG LEU K 465 " pdb=" CB LEU K 465 " pdb=" CD1 LEU K 465 " pdb=" CD2 LEU K 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CG LEU N 465 " pdb=" CB LEU N 465 " pdb=" CD1 LEU N 465 " pdb=" CD2 LEU N 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 3278 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER N 188 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.51e+01 pdb=" N PRO N 189 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO N 189 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO N 189 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 188 " -0.064 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO K 189 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO K 189 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO K 189 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 50 " -0.018 2.00e-02 2.50e+03 2.19e-02 9.63e+00 pdb=" CG TYR C 50 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR C 50 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 50 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C 50 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR C 50 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 50 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 50 " -0.002 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 291 2.59 - 3.17: 16725 3.17 - 3.74: 33752 3.74 - 4.32: 47783 4.32 - 4.90: 70993 Nonbonded interactions: 169544 Sorted by model distance: nonbonded pdb=" N2 DG I 6 " pdb=" O2 DC J 142 " model vdw 2.011 2.496 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.011 3.040 nonbonded pdb="MG MG N1201 " pdb=" O3A ATP N1202 " model vdw 2.031 2.170 nonbonded pdb="MG MG K1201 " pdb=" O3A ATP K1202 " model vdw 2.031 2.170 nonbonded pdb="MG MG K1201 " pdb=" O1G ATP K1202 " model vdw 2.051 2.170 ... (remaining 169539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 15 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.330 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.050 ------------------------------------------------------------------------------- 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 : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.71 % Allowed : 1.51 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.20), residues: 1650 helix: 0.87 (0.17), residues: 947 sheet: -0.71 (0.46), residues: 128 loop : -1.65 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 520 TYR 0.051 0.002 TYR C 50 PHE 0.020 0.002 PHE N 574 TRP 0.018 0.002 TRP K 364 HIS 0.013 0.002 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.01112 (20543) covalent geometry : angle 0.88731 (29019) hydrogen bonds : bond 0.12109 ( 1076) hydrogen bonds : angle 4.86837 ( 2814) 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 : 0.474 Fit side-chains REVERT: D 65 ASP cc_start: 0.8229 (t0) cc_final: 0.8017 (t0) REVERT: N 260 TRP cc_start: 0.8698 (m100) cc_final: 0.8483 (m100) REVERT: N 350 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8559 (mt) outliers start: 54 outliers final: 5 residues processed: 236 average time/residue: 0.7539 time to fit residues: 195.9690 Evaluate side-chains 148 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 577 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 K 467 ASN K 642 GLN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.091309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.064763 restraints weight = 57828.483| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.32 r_work: 0.3107 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20545 Z= 0.158 Angle : 0.604 8.333 29019 Z= 0.340 Chirality : 0.038 0.156 3281 Planarity : 0.004 0.057 2661 Dihedral : 27.740 158.815 5121 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.17 % Allowed : 11.20 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.21), residues: 1650 helix: 1.75 (0.17), residues: 960 sheet: -0.79 (0.46), residues: 132 loop : -1.32 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 63 TYR 0.012 0.001 TYR K 499 PHE 0.014 0.001 PHE N 540 TRP 0.014 0.001 TRP K 364 HIS 0.007 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00351 (20543) covalent geometry : angle 0.60386 (29019) hydrogen bonds : bond 0.04425 ( 1076) hydrogen bonds : angle 3.60362 ( 2814) Misc. bond : bond 0.00241 ( 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 199 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8919 (pm20) cc_final: 0.8680 (pm20) REVERT: C 90 ASP cc_start: 0.8654 (t0) cc_final: 0.8405 (t0) REVERT: C 92 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: D 117 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8112 (tttm) REVERT: F 93 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7283 (mp10) REVERT: H 102 GLU cc_start: 0.7803 (pp20) cc_final: 0.7580 (pp20) REVERT: H 110 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8118 (mt-10) REVERT: K 653 GLN cc_start: 0.7777 (pt0) cc_final: 0.7567 (pm20) REVERT: N 436 MET cc_start: 0.7867 (mtp) cc_final: 0.7374 (mtp) REVERT: N 527 MET cc_start: 0.7440 (mtm) cc_final: 0.7170 (mpt) outliers start: 17 outliers final: 4 residues processed: 194 average time/residue: 0.7696 time to fit residues: 164.4480 Evaluate side-chains 153 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 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 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.090160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.063340 restraints weight = 58090.215| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.32 r_work: 0.3077 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20545 Z= 0.204 Angle : 0.595 6.490 29019 Z= 0.336 Chirality : 0.038 0.141 3281 Planarity : 0.004 0.042 2661 Dihedral : 27.806 155.060 5108 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.68 % Allowed : 13.33 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.21), residues: 1650 helix: 1.87 (0.17), residues: 964 sheet: -0.86 (0.45), residues: 132 loop : -1.34 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 341 TYR 0.010 0.001 TYR B 51 PHE 0.014 0.001 PHE N 540 TRP 0.016 0.001 TRP K 364 HIS 0.010 0.001 HIS N 554 Details of bonding type rmsd covalent geometry : bond 0.00465 (20543) covalent geometry : angle 0.59520 (29019) hydrogen bonds : bond 0.05014 ( 1076) hydrogen bonds : angle 3.50448 ( 2814) Misc. bond : bond 0.00304 ( 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 190 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8986 (pm20) cc_final: 0.8684 (pm20) REVERT: B 93 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7844 (mm-40) REVERT: C 78 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8505 (mp) REVERT: C 90 ASP cc_start: 0.8775 (t0) cc_final: 0.8366 (t0) REVERT: E 133 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: F 68 ASP cc_start: 0.9121 (m-30) cc_final: 0.8916 (m-30) REVERT: F 74 GLU cc_start: 0.8927 (pt0) cc_final: 0.8602 (mt-10) REVERT: F 93 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: G 95 LYS cc_start: 0.9265 (ttmt) cc_final: 0.8847 (tptt) REVERT: H 65 ASP cc_start: 0.8857 (t0) cc_final: 0.8657 (t0) REVERT: K 615 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8672 (mp) REVERT: N 436 MET cc_start: 0.7896 (mtp) cc_final: 0.7469 (mtp) outliers start: 39 outliers final: 13 residues processed: 178 average time/residue: 0.7168 time to fit residues: 141.1519 Evaluate side-chains 158 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain 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 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 159 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 100 optimal weight: 0.0070 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.090821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063958 restraints weight = 58778.776| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.35 r_work: 0.3105 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2146 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= 0.175 Angle : 0.577 6.695 29019 Z= 0.327 Chirality : 0.038 0.145 3281 Planarity : 0.004 0.040 2661 Dihedral : 27.649 152.754 5108 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.82 % Allowed : 14.02 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.21), residues: 1650 helix: 1.96 (0.17), residues: 968 sheet: -0.92 (0.45), residues: 132 loop : -1.28 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 341 TYR 0.011 0.001 TYR N 545 PHE 0.017 0.001 PHE K 183 TRP 0.017 0.001 TRP K 364 HIS 0.011 0.001 HIS N 554 Details of bonding type rmsd covalent geometry : bond 0.00398 (20543) covalent geometry : angle 0.57705 (29019) hydrogen bonds : bond 0.04558 ( 1076) hydrogen bonds : angle 3.36945 ( 2814) Misc. bond : bond 0.00275 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9001 (pm20) cc_final: 0.8712 (pm20) REVERT: B 93 GLN cc_start: 0.8325 (mt0) cc_final: 0.8119 (mm-40) REVERT: C 78 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8594 (mp) REVERT: C 90 ASP cc_start: 0.8785 (t0) cc_final: 0.8383 (t0) REVERT: D 117 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8112 (tttm) REVERT: E 133 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: F 92 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8336 (ttp80) REVERT: F 93 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7209 (mp10) REVERT: G 72 ASP cc_start: 0.7827 (m-30) cc_final: 0.7609 (m-30) REVERT: G 95 LYS cc_start: 0.9265 (ttmt) cc_final: 0.8861 (tptt) REVERT: K 309 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8490 (mp0) REVERT: N 436 MET cc_start: 0.7870 (mtp) cc_final: 0.7438 (mtp) REVERT: N 478 HIS cc_start: 0.8295 (t70) cc_final: 0.8049 (t70) outliers start: 41 outliers final: 18 residues processed: 181 average time/residue: 0.8008 time to fit residues: 159.6222 Evaluate side-chains 164 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 E residue 133 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 LYS 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 110 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 517 GLU Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 517 GLU Chi-restraints excluded: chain N residue 587 LEU Chi-restraints excluded: chain N residue 609 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 7 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.089017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.061932 restraints weight = 58290.920| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.34 r_work: 0.3061 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20545 Z= 0.251 Angle : 0.620 7.627 29019 Z= 0.350 Chirality : 0.040 0.139 3281 Planarity : 0.004 0.042 2661 Dihedral : 27.869 151.052 5107 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.96 % Allowed : 14.78 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.21), residues: 1650 helix: 1.88 (0.17), residues: 968 sheet: -0.99 (0.45), residues: 130 loop : -1.29 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.010 0.001 TYR E 54 PHE 0.014 0.002 PHE N 540 TRP 0.017 0.001 TRP K 364 HIS 0.013 0.001 HIS N 554 Details of bonding type rmsd covalent geometry : bond 0.00576 (20543) covalent geometry : angle 0.62038 (29019) hydrogen bonds : bond 0.05598 ( 1076) hydrogen bonds : angle 3.52649 ( 2814) Misc. bond : bond 0.00307 ( 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 193 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8975 (pm20) cc_final: 0.8650 (pm20) REVERT: B 31 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7762 (tttm) REVERT: C 78 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8503 (mp) REVERT: C 90 ASP cc_start: 0.8803 (t0) cc_final: 0.8358 (t0) REVERT: F 92 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8357 (ttp80) REVERT: F 93 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: G 95 LYS cc_start: 0.9253 (ttmt) cc_final: 0.8866 (tptt) REVERT: K 309 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: N 478 HIS cc_start: 0.8348 (t70) cc_final: 0.8043 (t70) outliers start: 43 outliers final: 21 residues processed: 178 average time/residue: 0.7629 time to fit residues: 150.2821 Evaluate side-chains 165 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 F residue 24 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 517 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 125 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.091293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.064629 restraints weight = 58420.484| |-----------------------------------------------------------------------------| 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: 0.8211 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20545 Z= 0.155 Angle : 0.578 8.753 29019 Z= 0.328 Chirality : 0.037 0.165 3281 Planarity : 0.004 0.041 2661 Dihedral : 27.500 149.127 5107 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.06 % Allowed : 16.43 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.21), residues: 1650 helix: 2.07 (0.17), residues: 968 sheet: -0.98 (0.45), residues: 130 loop : -1.19 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.009 0.001 TYR N 596 PHE 0.014 0.001 PHE N 540 TRP 0.016 0.001 TRP K 364 HIS 0.012 0.001 HIS N 554 Details of bonding type rmsd covalent geometry : bond 0.00349 (20543) covalent geometry : angle 0.57759 (29019) hydrogen bonds : bond 0.04237 ( 1076) hydrogen bonds : angle 3.34054 ( 2814) Misc. bond : bond 0.00256 ( 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 189 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8991 (pm20) cc_final: 0.8660 (pm20) REVERT: B 31 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7737 (tttm) REVERT: C 78 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8576 (mp) REVERT: C 90 ASP cc_start: 0.8761 (t0) cc_final: 0.8315 (t0) REVERT: D 117 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8104 (tttm) REVERT: F 92 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8255 (ttp80) REVERT: F 93 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: G 72 ASP cc_start: 0.7841 (m-30) cc_final: 0.7595 (m-30) REVERT: G 95 LYS cc_start: 0.9263 (ttmt) cc_final: 0.8868 (tptt) REVERT: H 102 GLU cc_start: 0.7496 (pp20) cc_final: 0.7195 (pp20) REVERT: K 309 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8509 (mp0) REVERT: K 546 CYS cc_start: 0.8469 (t) cc_final: 0.7822 (t) REVERT: K 596 TYR cc_start: 0.8894 (t80) cc_final: 0.8541 (t80) REVERT: K 613 HIS cc_start: 0.8403 (t-170) cc_final: 0.8156 (t-170) REVERT: N 478 HIS cc_start: 0.8434 (t70) cc_final: 0.8117 (t70) outliers start: 30 outliers final: 18 residues processed: 179 average time/residue: 0.7113 time to fit residues: 140.6629 Evaluate side-chains 164 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 65 ASP 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 19 SER Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 517 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.091966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065384 restraints weight = 58706.104| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.34 r_work: 0.3135 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20545 Z= 0.145 Angle : 0.571 7.597 29019 Z= 0.324 Chirality : 0.037 0.221 3281 Planarity : 0.004 0.039 2661 Dihedral : 27.400 148.184 5107 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.13 % Allowed : 17.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.21), residues: 1650 helix: 2.11 (0.17), residues: 971 sheet: -0.89 (0.46), residues: 130 loop : -1.11 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.009 0.001 TYR D 37 PHE 0.013 0.001 PHE N 540 TRP 0.017 0.001 TRP N 364 HIS 0.012 0.001 HIS N 554 Details of bonding type rmsd covalent geometry : bond 0.00325 (20543) covalent geometry : angle 0.57134 (29019) hydrogen bonds : bond 0.04039 ( 1076) hydrogen bonds : angle 3.27782 ( 2814) Misc. bond : bond 0.00244 ( 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 188 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.653 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: 0.8983 (pm20) cc_final: 0.8658 (pm20) REVERT: B 31 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7706 (tttm) REVERT: C 90 ASP cc_start: 0.8742 (t0) cc_final: 0.8308 (t0) REVERT: D 117 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8057 (tttm) REVERT: F 93 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: G 72 ASP cc_start: 0.7831 (m-30) cc_final: 0.7583 (m-30) REVERT: G 95 LYS cc_start: 0.9249 (ttmt) cc_final: 0.8829 (tptt) REVERT: H 102 GLU cc_start: 0.7541 (pp20) cc_final: 0.7331 (pp20) REVERT: K 309 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8487 (mp0) REVERT: K 335 MET cc_start: 0.8539 (ttm) cc_final: 0.8301 (ttt) REVERT: K 436 MET cc_start: 0.9269 (mtp) cc_final: 0.8805 (pmm) REVERT: K 465 LEU cc_start: 0.8822 (mt) cc_final: 0.8424 (pt) REVERT: K 546 CYS cc_start: 0.8464 (t) cc_final: 0.7802 (t) REVERT: K 596 TYR cc_start: 0.8854 (t80) cc_final: 0.8529 (t80) REVERT: K 613 HIS cc_start: 0.8368 (t-170) cc_final: 0.8127 (t-170) REVERT: N 478 HIS cc_start: 0.8418 (t70) cc_final: 0.8074 (t70) outliers start: 31 outliers final: 19 residues processed: 177 average time/residue: 0.7507 time to fit residues: 146.4125 Evaluate side-chains 164 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 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 568 ASP Chi-restraints excluded: chain K residue 587 LEU Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 517 GLU Chi-restraints excluded: chain N residue 577 THR Chi-restraints excluded: chain N residue 609 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 156 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 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 ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.091566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064895 restraints weight = 58713.628| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.34 r_work: 0.3123 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20545 Z= 0.162 Angle : 0.590 11.199 29019 Z= 0.332 Chirality : 0.037 0.197 3281 Planarity : 0.004 0.039 2661 Dihedral : 27.429 147.168 5107 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.06 % Allowed : 17.73 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1650 helix: 2.10 (0.17), residues: 971 sheet: -0.89 (0.46), residues: 130 loop : -1.12 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.009 0.001 TYR D 37 PHE 0.012 0.001 PHE N 540 TRP 0.028 0.001 TRP N 364 HIS 0.013 0.001 HIS N 554 Details of bonding type rmsd covalent geometry : bond 0.00369 (20543) covalent geometry : angle 0.58989 (29019) hydrogen bonds : bond 0.04325 ( 1076) hydrogen bonds : angle 3.30191 ( 2814) 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 182 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.573 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: 0.8979 (pm20) cc_final: 0.8610 (pm20) REVERT: B 31 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7703 (tttm) REVERT: C 90 ASP cc_start: 0.8787 (t0) cc_final: 0.8310 (t0) REVERT: D 117 LYS cc_start: 0.8327 (ttpt) cc_final: 0.8068 (tttm) REVERT: F 93 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: G 24 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8042 (mm110) REVERT: G 72 ASP cc_start: 0.7813 (m-30) cc_final: 0.7563 (m-30) REVERT: G 92 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7510 (mt-10) REVERT: G 95 LYS cc_start: 0.9262 (ttmt) cc_final: 0.8836 (tptt) REVERT: H 102 GLU cc_start: 0.7557 (pp20) cc_final: 0.7245 (pp20) REVERT: K 309 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8507 (mp0) REVERT: K 335 MET cc_start: 0.8583 (ttm) cc_final: 0.8356 (ttt) REVERT: K 436 MET cc_start: 0.9260 (mtp) cc_final: 0.8816 (pmm) REVERT: K 465 LEU cc_start: 0.8841 (mt) cc_final: 0.8421 (pt) REVERT: K 546 CYS cc_start: 0.8510 (t) cc_final: 0.7830 (t) REVERT: K 596 TYR cc_start: 0.8837 (t80) cc_final: 0.8556 (t80) REVERT: K 613 HIS cc_start: 0.8379 (t-170) cc_final: 0.8138 (t-170) REVERT: N 478 HIS cc_start: 0.8466 (t70) cc_final: 0.8158 (t70) REVERT: N 514 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9025 (tm) outliers start: 30 outliers final: 19 residues processed: 173 average time/residue: 0.7324 time to fit residues: 139.6721 Evaluate side-chains 168 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain 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 N residue 446 GLU Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 514 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 88 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 167 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 51 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.092085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065641 restraints weight = 58042.773| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.31 r_work: 0.3122 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20545 Z= 0.140 Angle : 0.594 11.111 29019 Z= 0.334 Chirality : 0.037 0.300 3281 Planarity : 0.004 0.048 2661 Dihedral : 27.419 146.718 5107 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.86 % Allowed : 18.08 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.21), residues: 1650 helix: 2.08 (0.17), residues: 969 sheet: -0.90 (0.46), residues: 130 loop : -1.10 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 197 TYR 0.010 0.001 TYR K 199 PHE 0.012 0.001 PHE N 540 TRP 0.035 0.001 TRP N 364 HIS 0.013 0.001 HIS N 554 Details of bonding type rmsd covalent geometry : bond 0.00312 (20543) covalent geometry : angle 0.59399 (29019) hydrogen bonds : bond 0.04130 ( 1076) hydrogen bonds : angle 3.30176 ( 2814) Misc. bond : bond 0.00256 ( 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 180 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.634 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: 0.8947 (pm20) cc_final: 0.8563 (pm20) REVERT: B 31 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7592 (tttm) REVERT: C 90 ASP cc_start: 0.8751 (t0) cc_final: 0.8273 (t0) REVERT: D 117 LYS cc_start: 0.8245 (ttpt) cc_final: 0.7989 (tttm) REVERT: F 93 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.6989 (mp10) REVERT: G 24 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7992 (mm110) REVERT: G 72 ASP cc_start: 0.7780 (m-30) cc_final: 0.7525 (m-30) REVERT: G 92 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7411 (mt-10) REVERT: G 95 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8789 (tptt) REVERT: H 102 GLU cc_start: 0.7480 (pp20) cc_final: 0.7223 (pp20) REVERT: K 309 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8473 (mp0) REVERT: K 335 MET cc_start: 0.8540 (ttm) cc_final: 0.8308 (ttt) REVERT: K 436 MET cc_start: 0.9259 (mtp) cc_final: 0.8810 (pmm) REVERT: K 465 LEU cc_start: 0.8847 (mt) cc_final: 0.8414 (pt) REVERT: K 546 CYS cc_start: 0.8517 (t) cc_final: 0.7824 (t) REVERT: K 596 TYR cc_start: 0.8816 (t80) cc_final: 0.8484 (t80) REVERT: K 613 HIS cc_start: 0.8343 (t-170) cc_final: 0.8099 (t-170) REVERT: N 478 HIS cc_start: 0.8439 (t70) cc_final: 0.8118 (t70) REVERT: N 514 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9015 (tm) outliers start: 27 outliers final: 20 residues processed: 172 average time/residue: 0.7732 time to fit residues: 146.2289 Evaluate side-chains 171 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 65 ASP Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain 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 587 LEU Chi-restraints excluded: chain N residue 352 THR Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 514 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 62 optimal weight: 0.0370 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.092347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.065822 restraints weight = 58647.545| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.33 r_work: 0.3145 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20545 Z= 0.147 Angle : 0.589 10.124 29019 Z= 0.332 Chirality : 0.037 0.245 3281 Planarity : 0.004 0.050 2661 Dihedral : 27.336 146.424 5107 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.65 % Allowed : 18.56 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.21), residues: 1650 helix: 2.07 (0.17), residues: 971 sheet: -0.85 (0.46), residues: 130 loop : -1.06 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.010 0.001 TYR D 37 PHE 0.012 0.001 PHE N 540 TRP 0.031 0.001 TRP N 364 HIS 0.014 0.001 HIS N 554 Details of bonding type rmsd covalent geometry : bond 0.00331 (20543) covalent geometry : angle 0.58897 (29019) hydrogen bonds : bond 0.04069 ( 1076) hydrogen bonds : angle 3.30467 ( 2814) Misc. bond : bond 0.00248 ( 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 177 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.492 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: 0.8963 (pm20) cc_final: 0.8589 (pm20) REVERT: B 31 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7682 (tttm) REVERT: C 64 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7955 (tm-30) REVERT: C 90 ASP cc_start: 0.8798 (t0) cc_final: 0.8338 (t0) REVERT: D 117 LYS cc_start: 0.8295 (ttpt) cc_final: 0.8041 (tttm) REVERT: F 93 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: G 24 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8005 (mm110) REVERT: G 72 ASP cc_start: 0.7819 (m-30) cc_final: 0.7569 (m-30) REVERT: G 92 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7504 (mt-10) REVERT: G 95 LYS cc_start: 0.9237 (ttmt) cc_final: 0.8821 (tptt) REVERT: H 102 GLU cc_start: 0.7504 (pp20) cc_final: 0.7261 (pp20) REVERT: K 309 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8485 (mp0) REVERT: K 335 MET cc_start: 0.8603 (ttm) cc_final: 0.8373 (ttt) REVERT: K 436 MET cc_start: 0.9262 (mtp) cc_final: 0.8827 (pmm) REVERT: K 465 LEU cc_start: 0.8827 (mt) cc_final: 0.8384 (pt) REVERT: K 546 CYS cc_start: 0.8493 (t) cc_final: 0.7811 (t) REVERT: K 596 TYR cc_start: 0.8826 (t80) cc_final: 0.8506 (t80) REVERT: K 613 HIS cc_start: 0.8352 (t-170) cc_final: 0.8128 (t-90) REVERT: N 478 HIS cc_start: 0.8487 (t70) cc_final: 0.8126 (t70) REVERT: N 514 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9013 (tm) outliers start: 24 outliers final: 16 residues processed: 170 average time/residue: 0.7229 time to fit residues: 135.4395 Evaluate side-chains 167 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain 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 N residue 352 THR Chi-restraints excluded: chain N residue 446 GLU Chi-restraints excluded: chain N residue 514 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 185 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 31 HIS ** 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 = 0.3837 r_free = 0.3837 target = 0.091719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.064945 restraints weight = 58702.463| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.35 r_work: 0.3119 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20545 Z= 0.167 Angle : 0.602 10.870 29019 Z= 0.337 Chirality : 0.037 0.239 3281 Planarity : 0.004 0.038 2661 Dihedral : 27.425 147.026 5107 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.65 % Allowed : 18.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1650 helix: 2.08 (0.17), residues: 969 sheet: -0.83 (0.46), residues: 130 loop : -1.10 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.015 0.001 TYR B 88 PHE 0.011 0.001 PHE N 540 TRP 0.028 0.001 TRP N 364 HIS 0.013 0.001 HIS N 554 Details of bonding type rmsd covalent geometry : bond 0.00382 (20543) covalent geometry : angle 0.60180 (29019) hydrogen bonds : bond 0.04463 ( 1076) hydrogen bonds : angle 3.34416 ( 2814) Misc. bond : bond 0.00272 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6696.34 seconds wall clock time: 114 minutes 30.15 seconds (6870.15 seconds total)