Starting phenix.real_space_refine on Tue Feb 11 07:47:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ssx_10307/02_2025/6ssx_10307.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ssx_10307/02_2025/6ssx_10307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ssx_10307/02_2025/6ssx_10307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ssx_10307/02_2025/6ssx_10307.map" model { file = "/net/cci-nas-00/data/ceres_data/6ssx_10307/02_2025/6ssx_10307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ssx_10307/02_2025/6ssx_10307.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 3050 2.51 5 N 860 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4900 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 2.02, per 1000 atoms: 0.41 Number of scatterers: 4900 At special positions: 0 Unit cell: (75.48, 117.623, 40.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 990 8.00 N 860 7.00 C 3050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 672.3 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 63.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 removed outlier: 6.132A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA B 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR B 22 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS A 21 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N THR C 22 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 21 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA D 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR D 22 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS C 21 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 57 removed outlier: 9.080A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N GLU B 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 45 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N VAL B 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N HIS B 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL B 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY A 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N THR B 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ALA A 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N ALA B 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N VAL A 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N VAL B 37 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N VAL C 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N SER C 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N THR C 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N GLU C 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N HIS C 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLY B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N THR C 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ALA B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ALA C 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N VAL B 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N VAL C 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N VAL D 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 9.944A pdb=" N SER D 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N THR D 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N GLU D 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS C 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL D 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS D 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL C 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL D 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLY C 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N THR D 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N ALA C 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N ALA D 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N VAL C 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N GLU E 46 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS D 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N VAL E 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N HIS E 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL D 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL E 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY D 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N THR E 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA D 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N ALA E 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL D 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 93 Processing sheet with id=AA7, first strand: chain 'F' and resid 15 through 23 removed outlier: 6.129A pdb=" N VAL F 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA G 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA F 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLU G 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA F 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N THR G 22 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS F 21 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL H 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA I 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA H 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLU I 20 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA H 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR I 22 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS H 21 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL I 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA J 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLU J 20 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA I 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR J 22 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS I 21 " --> pdb=" O THR J 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 37 through 57 removed outlier: 9.084A pdb=" N VAL F 37 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL G 40 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N TYR F 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N SER G 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLY F 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N THR G 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LYS F 43 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLU G 46 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS F 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL G 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS G 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL F 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL G 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY F 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N THR G 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N ALA F 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ALA G 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N VAL F 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N VAL G 37 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N VAL H 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N SER H 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N GLU H 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS H 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N THR H 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N ALA G 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ALA H 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N VAL G 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N VAL H 37 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N VAL I 40 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N TYR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N SER I 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N GLY H 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N THR I 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N LYS H 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 10.621A pdb=" N GLU I 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS H 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL I 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY H 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS I 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL H 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL I 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY H 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N THR I 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N ALA H 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ALA I 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N VAL H 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N VAL I 37 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N VAL J 40 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N SER J 42 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N GLY I 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N THR J 44 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS I 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU J 46 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS I 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N VAL J 48 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N HIS J 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL I 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL J 52 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY I 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N THR J 54 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ALA I 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N ALA J 56 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N VAL I 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AB1, first strand: chain 'F' and resid 69 through 71 Processing sheet with id=AB2, first strand: chain 'F' and resid 75 through 79 Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 93 160 hydrogen bonds defined for protein. 480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 870 1.29 - 1.35: 770 1.35 - 1.41: 180 1.41 - 1.48: 831 1.48 - 1.54: 2259 Bond restraints: 4910 Sorted by residual: bond pdb=" CG LEU F 38 " pdb=" CD1 LEU F 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.58e+00 bond pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG LEU H 38 " pdb=" CD1 LEU H 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG LEU I 38 " pdb=" CD1 LEU I 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.55e+00 ... (remaining 4905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 5668 1.09 - 2.19: 720 2.19 - 3.28: 127 3.28 - 4.38: 70 4.38 - 5.47: 45 Bond angle restraints: 6630 Sorted by residual: angle pdb=" N THR I 44 " pdb=" CA THR I 44 " pdb=" C THR I 44 " ideal model delta sigma weight residual 109.23 113.56 -4.33 1.55e+00 4.16e-01 7.79e+00 angle pdb=" N THR E 44 " pdb=" CA THR E 44 " pdb=" C THR E 44 " ideal model delta sigma weight residual 109.23 113.51 -4.28 1.55e+00 4.16e-01 7.63e+00 angle pdb=" N THR J 44 " pdb=" CA THR J 44 " pdb=" C THR J 44 " ideal model delta sigma weight residual 109.23 113.51 -4.28 1.55e+00 4.16e-01 7.61e+00 angle pdb=" N THR C 44 " pdb=" CA THR C 44 " pdb=" C THR C 44 " ideal model delta sigma weight residual 109.23 113.50 -4.27 1.55e+00 4.16e-01 7.61e+00 angle pdb=" N THR G 44 " pdb=" CA THR G 44 " pdb=" C THR G 44 " ideal model delta sigma weight residual 109.23 113.50 -4.27 1.55e+00 4.16e-01 7.60e+00 ... (remaining 6625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 2500 16.71 - 33.41: 300 33.41 - 50.12: 20 50.12 - 66.82: 10 66.82 - 83.53: 10 Dihedral angle restraints: 2840 sinusoidal: 900 harmonic: 1940 Sorted by residual: dihedral pdb=" CA GLY G 73 " pdb=" C GLY G 73 " pdb=" N VAL G 74 " pdb=" CA VAL G 74 " ideal model delta harmonic sigma weight residual 180.00 148.94 31.06 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA GLY B 73 " pdb=" C GLY B 73 " pdb=" N VAL B 74 " pdb=" CA VAL B 74 " ideal model delta harmonic sigma weight residual 180.00 148.99 31.01 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLY F 73 " pdb=" C GLY F 73 " pdb=" N VAL F 74 " pdb=" CA VAL F 74 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 2837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 428 0.040 - 0.079: 174 0.079 - 0.119: 200 0.119 - 0.159: 48 0.159 - 0.199: 20 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB THR H 44 " pdb=" CA THR H 44 " pdb=" OG1 THR H 44 " pdb=" CG2 THR H 44 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CB THR E 44 " pdb=" CA THR E 44 " pdb=" OG1 THR E 44 " pdb=" CG2 THR E 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CB THR D 44 " pdb=" CA THR D 44 " pdb=" OG1 THR D 44 " pdb=" CG2 THR D 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 867 not shown) Planarity restraints: 830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 72 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C THR C 72 " -0.024 2.00e-02 2.50e+03 pdb=" O THR C 72 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 73 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 72 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C THR E 72 " -0.024 2.00e-02 2.50e+03 pdb=" O THR E 72 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY E 73 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 72 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C THR I 72 " -0.024 2.00e-02 2.50e+03 pdb=" O THR I 72 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY I 73 " 0.008 2.00e-02 2.50e+03 ... (remaining 827 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2121 2.92 - 3.41: 4427 3.41 - 3.91: 8204 3.91 - 4.40: 9433 4.40 - 4.90: 17678 Nonbonded interactions: 41863 Sorted by model distance: nonbonded pdb=" OE1 GLN A 62 " pdb=" NE2 GLN B 62 " model vdw 2.424 3.120 nonbonded pdb=" OE1 GLN F 62 " pdb=" NE2 GLN G 62 " model vdw 2.454 3.120 nonbonded pdb=" N VAL F 74 " pdb=" O VAL G 74 " model vdw 2.479 3.120 nonbonded pdb=" N VAL A 74 " pdb=" O VAL B 74 " model vdw 2.480 3.120 nonbonded pdb=" N LYS A 58 " pdb=" O GLU B 57 " model vdw 2.483 3.120 ... (remaining 41858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 1.410 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.008 0.053 4910 Z= 0.540 Angle : 0.938 5.474 6630 Z= 0.553 Chirality : 0.069 0.199 870 Planarity : 0.004 0.014 830 Dihedral : 14.938 83.526 1620 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 4.26 % Allowed : 6.38 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.007 0.002 PHE D 94 TYR 0.021 0.005 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.502 Fit side-chains REVERT: B 80 LYS cc_start: 0.8097 (mttp) cc_final: 0.7744 (mtpt) REVERT: E 80 LYS cc_start: 0.8592 (mttp) cc_final: 0.8309 (mtpp) REVERT: F 65 ASN cc_start: 0.9013 (m-40) cc_final: 0.8790 (m-40) REVERT: J 80 LYS cc_start: 0.8250 (mttp) cc_final: 0.7879 (mtmt) outliers start: 20 outliers final: 4 residues processed: 67 average time/residue: 1.2665 time to fit residues: 88.3106 Evaluate side-chains 44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 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 = 0.4242 r_free = 0.4242 target = 0.145103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.126081 restraints weight = 5395.003| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.29 r_work: 0.3870 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4910 Z= 0.226 Angle : 0.590 6.575 6630 Z= 0.338 Chirality : 0.053 0.134 870 Planarity : 0.002 0.017 830 Dihedral : 7.782 42.152 724 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.68 % Allowed : 10.21 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 PHE 0.004 0.001 PHE D 94 TYR 0.013 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.482 Fit side-chains REVERT: B 80 LYS cc_start: 0.8224 (mttp) cc_final: 0.7778 (mtpt) REVERT: D 80 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8260 (mtpm) REVERT: E 80 LYS cc_start: 0.8637 (mttp) cc_final: 0.8112 (mtpp) REVERT: J 58 LYS cc_start: 0.7706 (ttmt) cc_final: 0.6837 (tptm) REVERT: J 83 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7911 (mt-10) outliers start: 22 outliers final: 9 residues processed: 60 average time/residue: 1.2585 time to fit residues: 78.6457 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.138102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.119559 restraints weight = 5469.820| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.21 r_work: 0.3784 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4910 Z= 0.399 Angle : 0.641 6.105 6630 Z= 0.370 Chirality : 0.054 0.143 870 Planarity : 0.003 0.009 830 Dihedral : 7.747 41.382 723 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 4.47 % Allowed : 11.28 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 50 PHE 0.007 0.001 PHE D 94 TYR 0.021 0.004 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.481 Fit side-chains REVERT: B 80 LYS cc_start: 0.8298 (mttp) cc_final: 0.7726 (mtpt) REVERT: D 24 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: E 80 LYS cc_start: 0.8700 (mttp) cc_final: 0.8028 (mtpp) REVERT: F 65 ASN cc_start: 0.9090 (m-40) cc_final: 0.8868 (m-40) REVERT: I 83 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8214 (mt-10) REVERT: J 46 GLU cc_start: 0.8161 (tp30) cc_final: 0.7850 (tm-30) REVERT: J 58 LYS cc_start: 0.7778 (ttmt) cc_final: 0.6791 (tptm) outliers start: 21 outliers final: 12 residues processed: 61 average time/residue: 1.3917 time to fit residues: 88.1354 Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 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 = 0.4208 r_free = 0.4208 target = 0.142704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.123960 restraints weight = 5429.379| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.26 r_work: 0.3840 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4910 Z= 0.225 Angle : 0.573 6.936 6630 Z= 0.328 Chirality : 0.053 0.134 870 Planarity : 0.002 0.010 830 Dihedral : 7.051 41.011 722 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.89 % Allowed : 12.77 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.004 0.001 PHE D 94 TYR 0.013 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.563 Fit side-chains REVERT: B 23 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7491 (mtpp) REVERT: B 80 LYS cc_start: 0.8141 (mttp) cc_final: 0.7599 (mtpt) REVERT: C 83 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7837 (mt-10) REVERT: D 80 LYS cc_start: 0.8628 (mtpm) cc_final: 0.8387 (mtpp) REVERT: G 58 LYS cc_start: 0.7547 (tttt) cc_final: 0.7151 (tttm) REVERT: I 83 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8154 (mt-10) REVERT: J 46 GLU cc_start: 0.8035 (tp30) cc_final: 0.7691 (tm-30) REVERT: J 58 LYS cc_start: 0.7670 (ttmt) cc_final: 0.6708 (tptm) outliers start: 23 outliers final: 16 residues processed: 61 average time/residue: 1.2901 time to fit residues: 81.9795 Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 39 optimal weight: 0.2980 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS F 65 ASN J 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.133562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.115061 restraints weight = 5643.830| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.20 r_work: 0.3734 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 4910 Z= 0.545 Angle : 0.706 6.206 6630 Z= 0.409 Chirality : 0.056 0.141 870 Planarity : 0.003 0.010 830 Dihedral : 7.799 41.948 722 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 5.74 % Allowed : 12.13 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.009 0.002 PHE D 94 TYR 0.024 0.005 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.490 Fit side-chains REVERT: B 80 LYS cc_start: 0.8295 (mttp) cc_final: 0.7697 (mtpt) REVERT: C 60 LYS cc_start: 0.7642 (mttt) cc_final: 0.7384 (mtmt) REVERT: D 80 LYS cc_start: 0.8712 (mtpm) cc_final: 0.8501 (mtpp) REVERT: E 80 LYS cc_start: 0.8760 (mttp) cc_final: 0.8149 (mtpp) REVERT: F 65 ASN cc_start: 0.9105 (m-40) cc_final: 0.8896 (m-40) REVERT: H 60 LYS cc_start: 0.7791 (mttt) cc_final: 0.7271 (mtpp) REVERT: J 46 GLU cc_start: 0.8107 (tp30) cc_final: 0.7816 (tp30) REVERT: J 58 LYS cc_start: 0.7849 (ttmt) cc_final: 0.6837 (tptm) REVERT: J 83 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8098 (mt-10) outliers start: 27 outliers final: 16 residues processed: 72 average time/residue: 1.3618 time to fit residues: 101.6071 Evaluate side-chains 69 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.0470 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.139757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.121706 restraints weight = 5801.102| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.24 r_work: 0.3846 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4910 Z= 0.181 Angle : 0.578 7.153 6630 Z= 0.331 Chirality : 0.053 0.131 870 Planarity : 0.002 0.010 830 Dihedral : 6.857 41.138 722 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.47 % Allowed : 14.04 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 50 PHE 0.003 0.001 PHE C 94 TYR 0.011 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.496 Fit side-chains REVERT: B 23 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7489 (mtpp) REVERT: B 80 LYS cc_start: 0.8164 (mttp) cc_final: 0.7741 (mtpp) REVERT: D 80 LYS cc_start: 0.8638 (mtpm) cc_final: 0.8395 (mtpp) REVERT: D 83 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7872 (mt-10) REVERT: G 24 GLN cc_start: 0.7716 (mp10) cc_final: 0.7497 (mp10) REVERT: H 60 LYS cc_start: 0.7658 (mttt) cc_final: 0.7207 (mtpp) REVERT: J 46 GLU cc_start: 0.7932 (tp30) cc_final: 0.7594 (tp30) REVERT: J 58 LYS cc_start: 0.7774 (ttmt) cc_final: 0.6794 (tptm) outliers start: 21 outliers final: 18 residues processed: 60 average time/residue: 1.3015 time to fit residues: 81.2110 Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.138037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.119207 restraints weight = 5558.497| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.25 r_work: 0.3778 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4910 Z= 0.350 Angle : 0.617 6.967 6630 Z= 0.357 Chirality : 0.054 0.140 870 Planarity : 0.002 0.009 830 Dihedral : 7.099 39.875 722 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 4.68 % Allowed : 15.11 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.006 0.001 PHE D 94 TYR 0.016 0.003 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.532 Fit side-chains REVERT: B 80 LYS cc_start: 0.8267 (mttp) cc_final: 0.7818 (mtpt) REVERT: E 80 LYS cc_start: 0.8619 (mttp) cc_final: 0.8153 (mtpp) REVERT: G 24 GLN cc_start: 0.7789 (mp10) cc_final: 0.7558 (mp10) REVERT: H 60 LYS cc_start: 0.7761 (mttt) cc_final: 0.7293 (mtpp) REVERT: J 46 GLU cc_start: 0.8023 (tp30) cc_final: 0.7720 (tp30) REVERT: J 58 LYS cc_start: 0.7734 (ttmt) cc_final: 0.6767 (tptp) outliers start: 22 outliers final: 18 residues processed: 61 average time/residue: 1.3447 time to fit residues: 85.2761 Evaluate side-chains 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 60 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 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 = 0.4263 r_free = 0.4263 target = 0.147487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.130719 restraints weight = 5848.029| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.14 r_work: 0.3872 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4910 Z= 0.191 Angle : 0.563 6.985 6630 Z= 0.324 Chirality : 0.053 0.135 870 Planarity : 0.002 0.010 830 Dihedral : 6.675 40.160 722 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 4.47 % Allowed : 15.74 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 50 PHE 0.003 0.001 PHE D 94 TYR 0.010 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.512 Fit side-chains REVERT: B 80 LYS cc_start: 0.8180 (mttp) cc_final: 0.7566 (mtpp) REVERT: G 24 GLN cc_start: 0.7820 (mp10) cc_final: 0.7585 (mp10) REVERT: G 58 LYS cc_start: 0.7641 (tttt) cc_final: 0.7344 (tttm) REVERT: H 60 LYS cc_start: 0.7623 (mttt) cc_final: 0.7192 (mtpp) REVERT: J 46 GLU cc_start: 0.7937 (tp30) cc_final: 0.7577 (tp30) REVERT: J 58 LYS cc_start: 0.7720 (ttmt) cc_final: 0.6766 (tptm) outliers start: 21 outliers final: 16 residues processed: 57 average time/residue: 1.2268 time to fit residues: 73.1664 Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 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 = 0.4092 r_free = 0.4092 target = 0.134176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.115516 restraints weight = 5578.833| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.21 r_work: 0.3738 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 4910 Z= 0.505 Angle : 0.694 6.341 6630 Z= 0.402 Chirality : 0.056 0.152 870 Planarity : 0.003 0.015 830 Dihedral : 7.525 40.491 722 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer: Outliers : 5.11 % Allowed : 15.74 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.009 0.002 PHE D 94 TYR 0.022 0.004 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.487 Fit side-chains REVERT: B 80 LYS cc_start: 0.8103 (mttp) cc_final: 0.7644 (mtpt) REVERT: C 60 LYS cc_start: 0.7646 (mttt) cc_final: 0.7402 (mtmt) REVERT: C 83 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8074 (mt-10) REVERT: E 80 LYS cc_start: 0.8667 (mttp) cc_final: 0.8206 (mtpp) REVERT: G 24 GLN cc_start: 0.7855 (mp10) cc_final: 0.7623 (mp10) REVERT: G 58 LYS cc_start: 0.7640 (tttt) cc_final: 0.7359 (tttm) REVERT: H 60 LYS cc_start: 0.7802 (mttt) cc_final: 0.7341 (mtpp) REVERT: J 46 GLU cc_start: 0.8021 (tp30) cc_final: 0.7737 (tp30) REVERT: J 58 LYS cc_start: 0.7776 (ttmt) cc_final: 0.6788 (tptp) outliers start: 24 outliers final: 15 residues processed: 68 average time/residue: 1.4584 time to fit residues: 102.6487 Evaluate side-chains 67 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 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 = 0.4245 r_free = 0.4245 target = 0.145019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.128203 restraints weight = 5883.634| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.16 r_work: 0.3848 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4910 Z= 0.208 Angle : 0.595 6.156 6630 Z= 0.341 Chirality : 0.053 0.136 870 Planarity : 0.002 0.010 830 Dihedral : 6.870 41.645 722 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.62 % Allowed : 17.02 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.003 0.001 PHE C 94 TYR 0.011 0.002 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.609 Fit side-chains REVERT: B 80 LYS cc_start: 0.8030 (mttp) cc_final: 0.7529 (mtpp) REVERT: G 24 GLN cc_start: 0.7921 (mp10) cc_final: 0.7710 (mp10) REVERT: G 58 LYS cc_start: 0.7650 (tttt) cc_final: 0.7370 (tttm) REVERT: H 60 LYS cc_start: 0.7632 (mttt) cc_final: 0.7182 (mtpp) REVERT: I 61 GLU cc_start: 0.8167 (mp0) cc_final: 0.7841 (mp0) REVERT: J 46 GLU cc_start: 0.7866 (tp30) cc_final: 0.7551 (tp30) REVERT: J 58 LYS cc_start: 0.7726 (ttmt) cc_final: 0.6757 (tptm) REVERT: J 61 GLU cc_start: 0.8372 (mp0) cc_final: 0.7710 (mp0) outliers start: 17 outliers final: 13 residues processed: 55 average time/residue: 1.3616 time to fit residues: 77.8559 Evaluate side-chains 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.134537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.117243 restraints weight = 5694.409| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.20 r_work: 0.3811 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4910 Z= 0.302 Angle : 0.614 5.800 6630 Z= 0.353 Chirality : 0.053 0.137 870 Planarity : 0.002 0.009 830 Dihedral : 6.968 40.231 722 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 4.04 % Allowed : 16.81 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.005 0.001 PHE D 94 TYR 0.014 0.003 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3153.73 seconds wall clock time: 56 minutes 36.74 seconds (3396.74 seconds total)