Starting phenix.real_space_refine on Tue Mar 3 13:05:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rt0_4994/03_2026/6rt0_4994.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rt0_4994/03_2026/6rt0_4994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rt0_4994/03_2026/6rt0_4994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rt0_4994/03_2026/6rt0_4994.map" model { file = "/net/cci-nas-00/data/ceres_data/6rt0_4994/03_2026/6rt0_4994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rt0_4994/03_2026/6rt0_4994.cif" } resolution = 3.1 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= 0.002 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 3065 2.51 5 N 865 2.21 5 O 995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4925 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "F" 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 Chain: "G" 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 Chain: "H" 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 Chain: "I" 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 Chain: "J" 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 Time building chain proxies: 1.35, per 1000 atoms: 0.27 Number of scatterers: 4925 At special positions: 0 Unit cell: (80.688, 126.608, 42.64, 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 995 8.00 N 865 7.00 C 3065 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: 0.38 Conformation dependent library (CDL) restraints added in 383.6 milliseconds 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1230 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 23 removed outlier: 6.417A pdb=" N VAL A 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 23 Processing sheet with id=AA3, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.433A pdb=" N LEU A 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY D 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 49 removed outlier: 6.434A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 66 removed outlier: 6.609A pdb=" N GLU B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR C 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN A 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASN D 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR A 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.268A pdb=" N VAL A 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 75 through 79 removed outlier: 6.350A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLN C 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLN B 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 88 through 89 removed outlier: 8.383A pdb=" N ALA C 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER A 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA D 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA A 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N THR D 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR B 92 " --> pdb=" O GLY C 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 89 removed outlier: 8.383A pdb=" N ALA C 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER A 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA D 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA A 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N THR D 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA D 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 19 through 23 removed outlier: 6.497A pdb=" N ALA F 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLU G 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA F 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR G 22 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS F 21 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL G 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA I 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA G 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N GLU I 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA G 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N THR I 22 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS G 21 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL I 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA J 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLU J 20 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA I 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR J 22 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LYS I 21 " --> pdb=" O THR J 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 37 through 41 removed outlier: 6.502A pdb=" N LEU F 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLY G 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL F 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU G 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLY I 41 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL G 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLY J 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 47 through 49 Processing sheet with id=AB4, first strand: chain 'H' and resid 61 through 66 removed outlier: 6.394A pdb=" N GLN F 62 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN G 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR F 64 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN G 62 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASN I 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR G 64 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN I 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASN J 65 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR I 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 69 through 71 removed outlier: 6.793A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL G 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL I 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 75 through 79 removed outlier: 6.449A pdb=" N ALA F 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLN H 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR G 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA I 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL G 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR I 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA J 78 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL I 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 88 through 93 removed outlier: 6.320A pdb=" N ILE F 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ALA H 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA F 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLY H 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR F 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER G 87 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ALA I 90 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA G 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER I 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ALA J 90 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 53 through 55 removed outlier: 6.444A pdb=" N THR G 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 96 hydrogen bonds defined for protein. 285 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: 0.70 Time building geometry restraints manager: 0.52 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: 875 1.29 - 1.36: 785 1.36 - 1.43: 260 1.43 - 1.51: 1036 1.51 - 1.58: 1979 Bond restraints: 4935 Sorted by residual: bond pdb=" CA LYS A 97 " pdb=" CB LYS A 97 " ideal model delta sigma weight residual 1.530 1.491 0.039 2.00e-02 2.50e+03 3.77e+00 bond pdb=" CB GLU C 46 " pdb=" CG GLU C 46 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.62e+00 bond pdb=" CA LYS D 97 " pdb=" CB LYS D 97 " ideal model delta sigma weight residual 1.530 1.499 0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" CA GLY A 47 " pdb=" C GLY A 47 " ideal model delta sigma weight residual 1.519 1.529 -0.010 7.00e-03 2.04e+04 2.23e+00 bond pdb=" CA LYS B 97 " pdb=" CB LYS B 97 " ideal model delta sigma weight residual 1.530 1.502 0.028 2.00e-02 2.50e+03 1.97e+00 ... (remaining 4930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 6135 1.63 - 3.27: 438 3.27 - 4.90: 67 4.90 - 6.53: 23 6.53 - 8.16: 2 Bond angle restraints: 6665 Sorted by residual: angle pdb=" CA GLU C 46 " pdb=" CB GLU C 46 " pdb=" CG GLU C 46 " ideal model delta sigma weight residual 114.10 122.26 -8.16 2.00e+00 2.50e-01 1.67e+01 angle pdb=" C THR A 22 " pdb=" N LYS A 23 " pdb=" CA LYS A 23 " ideal model delta sigma weight residual 121.94 115.84 6.10 1.76e+00 3.23e-01 1.20e+01 angle pdb=" C THR D 22 " pdb=" N LYS D 23 " pdb=" CA LYS D 23 " ideal model delta sigma weight residual 122.33 116.64 5.69 1.68e+00 3.54e-01 1.15e+01 angle pdb=" CB GLU C 46 " pdb=" CG GLU C 46 " pdb=" CD GLU C 46 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.70e+00 3.46e-01 1.09e+01 angle pdb=" N GLU G 83 " pdb=" CA GLU G 83 " pdb=" C GLU G 83 " ideal model delta sigma weight residual 111.71 116.01 -4.30 1.34e+00 5.57e-01 1.03e+01 ... (remaining 6660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 2559 17.43 - 34.85: 250 34.85 - 52.27: 37 52.27 - 69.70: 7 69.70 - 87.12: 2 Dihedral angle restraints: 2855 sinusoidal: 900 harmonic: 1955 Sorted by residual: dihedral pdb=" CA GLY I 73 " pdb=" C GLY I 73 " pdb=" N VAL I 74 " pdb=" CA VAL I 74 " ideal model delta harmonic sigma weight residual 180.00 152.49 27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLY E 84 " pdb=" C GLY E 84 " pdb=" N ALA E 85 " pdb=" CA ALA E 85 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 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 180.00 153.64 26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 2852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 336 0.030 - 0.059: 237 0.059 - 0.088: 132 0.088 - 0.118: 120 0.118 - 0.147: 50 Chirality restraints: 875 Sorted by residual: chirality pdb=" CA ILE H 88 " pdb=" N ILE H 88 " pdb=" C ILE H 88 " pdb=" CB ILE H 88 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA VAL E 70 " pdb=" N VAL E 70 " pdb=" C VAL E 70 " pdb=" CB VAL E 70 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA LYS D 23 " pdb=" N LYS D 23 " pdb=" C LYS D 23 " pdb=" CB LYS D 23 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 872 not shown) Planarity restraints: 835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 72 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C THR G 72 " -0.038 2.00e-02 2.50e+03 pdb=" O THR G 72 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY G 73 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 72 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C THR B 72 " -0.038 2.00e-02 2.50e+03 pdb=" O THR B 72 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY B 73 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 72 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C THR F 72 " -0.034 2.00e-02 2.50e+03 pdb=" O THR F 72 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY F 73 " 0.012 2.00e-02 2.50e+03 ... (remaining 832 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 1913 2.91 - 3.41: 3889 3.41 - 3.91: 7720 3.91 - 4.40: 7881 4.40 - 4.90: 16278 Nonbonded interactions: 37681 Sorted by model distance: nonbonded pdb=" NZ LYS G 45 " pdb=" OE2 GLU G 46 " model vdw 2.415 3.120 nonbonded pdb=" O THR C 75 " pdb=" OG1 THR C 75 " model vdw 2.417 3.040 nonbonded pdb=" N VAL G 74 " pdb=" O VAL I 74 " model vdw 2.428 3.120 nonbonded pdb=" OE1 GLN A 24 " pdb=" NE2 GLN B 24 " model vdw 2.439 3.120 nonbonded pdb=" NE2 GLN F 62 " pdb=" OE1 GLN H 62 " model vdw 2.445 3.120 ... (remaining 37676 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 14 through 96) selection = (chain 'B' and resid 14 through 96) selection = (chain 'C' and resid 14 through 96) selection = (chain 'D' and resid 14 through 96) selection = (chain 'E' and resid 14 through 96) selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 1.420 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.450 Find NCS groups from input model: 0.100 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.006 0.057 4935 Z= 0.299 Angle : 0.974 8.165 6665 Z= 0.585 Chirality : 0.062 0.147 875 Planarity : 0.004 0.022 835 Dihedral : 14.226 87.119 1625 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 1.06 % Allowed : 9.15 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.27), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.005 TYR F 39 PHE 0.016 0.002 PHE C 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 4935) covalent geometry : angle 0.97415 ( 6665) hydrogen bonds : bond 0.15657 ( 85) hydrogen bonds : angle 6.75333 ( 285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.181 Fit side-chains REVERT: B 46 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7184 (tp30) REVERT: B 58 LYS cc_start: 0.7357 (ttmt) cc_final: 0.6543 (tptt) REVERT: B 80 LYS cc_start: 0.8228 (mttp) cc_final: 0.7670 (mtpp) REVERT: D 80 LYS cc_start: 0.8353 (mttp) cc_final: 0.8058 (mttt) REVERT: F 58 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7207 (tptm) REVERT: G 24 GLN cc_start: 0.7398 (mp10) cc_final: 0.7057 (tm-30) outliers start: 5 outliers final: 0 residues processed: 83 average time/residue: 0.1393 time to fit residues: 13.4717 Evaluate side-chains 71 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.122186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.102034 restraints weight = 6364.907| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.27 r_work: 0.3615 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4935 Z= 0.179 Angle : 0.687 7.615 6665 Z= 0.393 Chirality : 0.054 0.136 875 Planarity : 0.002 0.016 835 Dihedral : 7.182 26.968 725 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.64 % Allowed : 13.62 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR F 39 PHE 0.003 0.001 PHE I 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 4935) covalent geometry : angle 0.68743 ( 6665) hydrogen bonds : bond 0.03860 ( 85) hydrogen bonds : angle 4.77391 ( 285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.134 Fit side-chains REVERT: A 20 GLU cc_start: 0.7667 (mp0) cc_final: 0.7395 (mm-30) REVERT: B 46 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7375 (tp30) REVERT: B 58 LYS cc_start: 0.7306 (ttmt) cc_final: 0.6258 (tptt) REVERT: C 24 GLN cc_start: 0.7565 (mp10) cc_final: 0.7036 (tm-30) REVERT: E 58 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7053 (tptm) REVERT: F 58 LYS cc_start: 0.7818 (ttmt) cc_final: 0.6917 (tptm) REVERT: G 24 GLN cc_start: 0.7474 (mp10) cc_final: 0.6821 (tm-30) REVERT: H 60 LYS cc_start: 0.7711 (mttt) cc_final: 0.7441 (mttm) REVERT: I 20 GLU cc_start: 0.8206 (mp0) cc_final: 0.7972 (mp0) REVERT: I 43 LYS cc_start: 0.7653 (tttt) cc_final: 0.7364 (tttm) outliers start: 3 outliers final: 1 residues processed: 83 average time/residue: 0.1105 time to fit residues: 10.7935 Evaluate side-chains 79 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.116186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096431 restraints weight = 6557.697| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.24 r_work: 0.3517 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 4935 Z= 0.351 Angle : 0.828 7.207 6665 Z= 0.481 Chirality : 0.059 0.150 875 Planarity : 0.003 0.010 835 Dihedral : 7.785 26.662 725 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.39 % Favored : 85.61 % Rotamer: Outliers : 1.91 % Allowed : 18.09 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.004 TYR J 39 PHE 0.007 0.002 PHE B 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00817 ( 4935) covalent geometry : angle 0.82847 ( 6665) hydrogen bonds : bond 0.05607 ( 85) hydrogen bonds : angle 4.88747 ( 285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.189 Fit side-chains REVERT: B 46 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7518 (tp30) REVERT: B 58 LYS cc_start: 0.7352 (ttmt) cc_final: 0.6310 (tptt) REVERT: C 24 GLN cc_start: 0.7594 (mp10) cc_final: 0.7021 (tm-30) REVERT: D 80 LYS cc_start: 0.8418 (mttp) cc_final: 0.8133 (mttt) REVERT: E 58 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7209 (tptm) REVERT: F 58 LYS cc_start: 0.7794 (ttmt) cc_final: 0.6857 (tptm) REVERT: G 24 GLN cc_start: 0.7571 (mp10) cc_final: 0.6887 (tm-30) REVERT: I 20 GLU cc_start: 0.8333 (mp0) cc_final: 0.8074 (mp0) REVERT: I 43 LYS cc_start: 0.7701 (tttt) cc_final: 0.7388 (tttm) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.1156 time to fit residues: 12.0917 Evaluate side-chains 87 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.118297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.098545 restraints weight = 6473.359| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.25 r_work: 0.3554 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4935 Z= 0.225 Angle : 0.733 7.247 6665 Z= 0.421 Chirality : 0.055 0.148 875 Planarity : 0.002 0.010 835 Dihedral : 7.208 26.731 725 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 2.13 % Allowed : 20.21 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR F 39 PHE 0.003 0.001 PHE I 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 4935) covalent geometry : angle 0.73276 ( 6665) hydrogen bonds : bond 0.04320 ( 85) hydrogen bonds : angle 4.66761 ( 285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.177 Fit side-chains REVERT: B 46 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7461 (tp30) REVERT: B 58 LYS cc_start: 0.7377 (ttmt) cc_final: 0.6351 (tptt) REVERT: B 80 LYS cc_start: 0.8244 (mttp) cc_final: 0.7748 (mtpp) REVERT: C 24 GLN cc_start: 0.7644 (mp10) cc_final: 0.6954 (tm-30) REVERT: E 58 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7087 (tptm) REVERT: F 58 LYS cc_start: 0.7770 (ttmt) cc_final: 0.6832 (tptm) REVERT: G 24 GLN cc_start: 0.7678 (mp10) cc_final: 0.7466 (mp10) REVERT: I 20 GLU cc_start: 0.8291 (mp0) cc_final: 0.8002 (mp0) REVERT: I 43 LYS cc_start: 0.7642 (tttt) cc_final: 0.7321 (tttm) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.1298 time to fit residues: 13.0616 Evaluate side-chains 86 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.118377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.098611 restraints weight = 6527.107| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.27 r_work: 0.3559 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 4935 Z= 0.208 Angle : 0.701 7.084 6665 Z= 0.402 Chirality : 0.055 0.148 875 Planarity : 0.002 0.010 835 Dihedral : 7.020 25.830 725 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.66 % Favored : 87.34 % Rotamer: Outliers : 3.19 % Allowed : 19.57 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR F 39 PHE 0.004 0.001 PHE J 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4935) covalent geometry : angle 0.70086 ( 6665) hydrogen bonds : bond 0.04025 ( 85) hydrogen bonds : angle 4.49649 ( 285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.142 Fit side-chains REVERT: B 46 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7423 (tp30) REVERT: B 58 LYS cc_start: 0.7377 (ttmt) cc_final: 0.6339 (tptt) REVERT: B 80 LYS cc_start: 0.8234 (mttp) cc_final: 0.7741 (mtpp) REVERT: C 24 GLN cc_start: 0.7623 (mp10) cc_final: 0.6931 (tm-30) REVERT: E 58 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7083 (tptm) REVERT: F 58 LYS cc_start: 0.7757 (ttmt) cc_final: 0.6805 (tptm) REVERT: G 24 GLN cc_start: 0.7706 (mp10) cc_final: 0.7481 (mp10) REVERT: I 20 GLU cc_start: 0.8282 (mp0) cc_final: 0.7984 (mp0) REVERT: I 43 LYS cc_start: 0.7614 (tttt) cc_final: 0.7337 (tttm) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.1110 time to fit residues: 11.5319 Evaluate side-chains 90 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.120219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.101086 restraints weight = 6455.164| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.11 r_work: 0.3533 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 4935 Z= 0.318 Angle : 0.803 7.242 6665 Z= 0.467 Chirality : 0.058 0.154 875 Planarity : 0.003 0.011 835 Dihedral : 7.545 25.730 725 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 2.98 % Allowed : 20.21 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.004 TYR J 39 PHE 0.005 0.001 PHE B 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00735 ( 4935) covalent geometry : angle 0.80338 ( 6665) hydrogen bonds : bond 0.05110 ( 85) hydrogen bonds : angle 4.71595 ( 285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.129 Fit side-chains REVERT: B 58 LYS cc_start: 0.7512 (ttmt) cc_final: 0.6545 (tptt) REVERT: D 80 LYS cc_start: 0.8481 (mttp) cc_final: 0.8240 (mttt) REVERT: E 58 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7295 (tptm) REVERT: F 58 LYS cc_start: 0.7888 (ttmt) cc_final: 0.6976 (tptm) REVERT: I 43 LYS cc_start: 0.7739 (tttt) cc_final: 0.7490 (tttm) outliers start: 14 outliers final: 13 residues processed: 86 average time/residue: 0.1141 time to fit residues: 11.6695 Evaluate side-chains 90 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.129091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.108533 restraints weight = 6155.237| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.15 r_work: 0.3669 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4935 Z= 0.108 Angle : 0.620 7.390 6665 Z= 0.350 Chirality : 0.053 0.142 875 Planarity : 0.002 0.010 835 Dihedral : 6.265 25.036 725 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 1.28 % Allowed : 22.77 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.003 0.001 PHE J 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4935) covalent geometry : angle 0.62002 ( 6665) hydrogen bonds : bond 0.02325 ( 85) hydrogen bonds : angle 4.14735 ( 285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.167 Fit side-chains REVERT: A 20 GLU cc_start: 0.7591 (mp0) cc_final: 0.7313 (mm-30) REVERT: B 23 LYS cc_start: 0.8046 (ptmt) cc_final: 0.7824 (ptmm) REVERT: B 46 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7453 (tp30) REVERT: B 58 LYS cc_start: 0.7413 (ttmt) cc_final: 0.6416 (tptt) REVERT: E 58 LYS cc_start: 0.7896 (ttmt) cc_final: 0.7098 (tptm) REVERT: F 43 LYS cc_start: 0.7435 (tttt) cc_final: 0.7230 (mtpt) REVERT: F 58 LYS cc_start: 0.7785 (ttmt) cc_final: 0.6913 (tptm) REVERT: I 20 GLU cc_start: 0.8191 (mp0) cc_final: 0.7880 (mp0) REVERT: I 43 LYS cc_start: 0.7627 (tttt) cc_final: 0.7300 (tttm) REVERT: J 83 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8603 (mt-10) outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 0.1243 time to fit residues: 11.4927 Evaluate side-chains 79 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain G residue 58 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.122738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.102417 restraints weight = 6404.756| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.14 r_work: 0.3575 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 4935 Z= 0.254 Angle : 0.733 7.119 6665 Z= 0.424 Chirality : 0.055 0.150 875 Planarity : 0.002 0.009 835 Dihedral : 7.085 24.582 725 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 2.34 % Allowed : 22.77 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR J 39 PHE 0.005 0.001 PHE B 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 4935) covalent geometry : angle 0.73292 ( 6665) hydrogen bonds : bond 0.04505 ( 85) hydrogen bonds : angle 4.47308 ( 285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.185 Fit side-chains REVERT: B 24 GLN cc_start: 0.7511 (mt0) cc_final: 0.6535 (pp30) REVERT: B 58 LYS cc_start: 0.7476 (ttmt) cc_final: 0.6463 (tptt) REVERT: E 58 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7249 (tptm) REVERT: F 58 LYS cc_start: 0.7762 (ttmt) cc_final: 0.6828 (tptm) REVERT: I 43 LYS cc_start: 0.7667 (tttt) cc_final: 0.7417 (tttm) outliers start: 11 outliers final: 11 residues processed: 81 average time/residue: 0.1155 time to fit residues: 11.1143 Evaluate side-chains 87 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 0.0170 chunk 13 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.103150 restraints weight = 6318.614| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.14 r_work: 0.3580 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 4935 Z= 0.238 Angle : 0.727 7.276 6665 Z= 0.421 Chirality : 0.056 0.151 875 Planarity : 0.002 0.010 835 Dihedral : 7.122 26.050 725 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 2.34 % Allowed : 22.77 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR J 39 PHE 0.005 0.001 PHE I 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 4935) covalent geometry : angle 0.72743 ( 6665) hydrogen bonds : bond 0.04349 ( 85) hydrogen bonds : angle 4.48167 ( 285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.211 Fit side-chains REVERT: B 46 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7543 (tp30) REVERT: B 58 LYS cc_start: 0.7469 (ttmt) cc_final: 0.6467 (tptt) REVERT: B 80 LYS cc_start: 0.8307 (mttp) cc_final: 0.7838 (mtpp) REVERT: E 58 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7253 (tptm) REVERT: F 58 LYS cc_start: 0.7735 (ttmt) cc_final: 0.6821 (tptm) REVERT: H 83 GLU cc_start: 0.8039 (mp0) cc_final: 0.6971 (mp0) REVERT: I 43 LYS cc_start: 0.7688 (tttt) cc_final: 0.7438 (tttm) outliers start: 11 outliers final: 11 residues processed: 80 average time/residue: 0.1238 time to fit residues: 11.7363 Evaluate side-chains 86 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 0.0060 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.125377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.104811 restraints weight = 6281.460| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.16 r_work: 0.3611 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4935 Z= 0.164 Angle : 0.659 7.133 6665 Z= 0.378 Chirality : 0.054 0.145 875 Planarity : 0.002 0.010 835 Dihedral : 6.646 24.906 725 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 2.55 % Allowed : 22.77 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR F 39 PHE 0.005 0.001 PHE I 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4935) covalent geometry : angle 0.65912 ( 6665) hydrogen bonds : bond 0.03422 ( 85) hydrogen bonds : angle 4.26058 ( 285) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.174 Fit side-chains REVERT: B 24 GLN cc_start: 0.7479 (mt0) cc_final: 0.6744 (pp30) REVERT: B 46 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7507 (tp30) REVERT: B 58 LYS cc_start: 0.7478 (ttmt) cc_final: 0.6472 (tptt) REVERT: E 58 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7133 (tptm) REVERT: F 58 LYS cc_start: 0.7757 (ttmt) cc_final: 0.6853 (tptm) REVERT: H 83 GLU cc_start: 0.8034 (mp0) cc_final: 0.7629 (mp0) REVERT: I 43 LYS cc_start: 0.7636 (tttt) cc_final: 0.7382 (tttm) outliers start: 12 outliers final: 12 residues processed: 79 average time/residue: 0.1179 time to fit residues: 11.0667 Evaluate side-chains 85 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 24 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.127372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.106684 restraints weight = 6244.958| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.17 r_work: 0.3651 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4935 Z= 0.134 Angle : 0.624 7.068 6665 Z= 0.356 Chirality : 0.053 0.143 875 Planarity : 0.002 0.010 835 Dihedral : 6.350 25.038 725 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 2.55 % Allowed : 22.77 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR F 39 PHE 0.004 0.001 PHE I 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4935) covalent geometry : angle 0.62412 ( 6665) hydrogen bonds : bond 0.02931 ( 85) hydrogen bonds : angle 4.10334 ( 285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1313.54 seconds wall clock time: 23 minutes 5.06 seconds (1385.06 seconds total)