Starting phenix.real_space_refine on Tue Feb 11 08:13:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rt0_4994/02_2025/6rt0_4994.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rt0_4994/02_2025/6rt0_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_4994/02_2025/6rt0_4994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rt0_4994/02_2025/6rt0_4994.map" model { file = "/net/cci-nas-00/data/ceres_data/6rt0_4994/02_2025/6rt0_4994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rt0_4994/02_2025/6rt0_4994.cif" } resolution = 3.1 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 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.63, per 1000 atoms: 0.74 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: 1.40 Conformation dependent library (CDL) restraints added in 652.5 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: 0.97 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: 1.35 Time building geometry restraints manager: 1.49 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: 0.01 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: 0.020 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.370 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- 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= 0.448 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 (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: -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 HIS 0.003 0.001 HIS A 50 PHE 0.016 0.002 PHE C 94 TYR 0.021 0.005 TYR F 39 *********************** 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 : 0.501 Fit side-chains REVERT: B 46 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7183 (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: 0.3028 time to fit residues: 29.1544 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 : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.121434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.101333 restraints weight = 6344.518| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.24 r_work: 0.3604 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1298 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= 0.303 Angle : 0.710 7.597 6665 Z= 0.407 Chirality : 0.054 0.137 875 Planarity : 0.002 0.014 835 Dihedral : 7.333 26.949 725 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.64 % Allowed : 13.83 % Favored : 85.53 % 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: -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 HIS 0.002 0.001 HIS A 50 PHE 0.004 0.001 PHE I 94 TYR 0.015 0.003 TYR F 39 *********************** 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 84 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.409 Fit side-chains REVERT: B 46 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7401 (tp30) REVERT: B 58 LYS cc_start: 0.7303 (ttmt) cc_final: 0.6262 (tptt) REVERT: B 80 LYS cc_start: 0.8216 (mttp) cc_final: 0.7766 (mtpp) REVERT: C 24 GLN cc_start: 0.7554 (mp10) cc_final: 0.7033 (tm-30) REVERT: E 58 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7062 (tptm) REVERT: F 58 LYS cc_start: 0.7842 (ttmt) cc_final: 0.6941 (tptm) REVERT: G 24 GLN cc_start: 0.7491 (mp10) cc_final: 0.6837 (tm-30) REVERT: I 20 GLU cc_start: 0.8217 (mp0) cc_final: 0.7976 (mp0) REVERT: I 43 LYS cc_start: 0.7649 (tttt) cc_final: 0.7305 (tttm) outliers start: 3 outliers final: 1 residues processed: 82 average time/residue: 0.2725 time to fit residues: 26.3124 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 : 0.539 ------------------------------------------------------------------------------- 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 67 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.117200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.097316 restraints weight = 6422.485| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.24 r_work: 0.3539 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.007 0.032 4935 Z= 0.452 Angle : 0.777 7.189 6665 Z= 0.449 Chirality : 0.056 0.147 875 Planarity : 0.003 0.010 835 Dihedral : 7.593 26.732 725 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 1.70 % Allowed : 18.51 % 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: -4.07 (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 HIS 0.002 0.001 HIS A 50 PHE 0.005 0.001 PHE B 94 TYR 0.019 0.004 TYR J 39 *********************** 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 90 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.552 Fit side-chains REVERT: B 46 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7514 (tp30) REVERT: B 58 LYS cc_start: 0.7350 (ttmt) cc_final: 0.6325 (tptt) REVERT: C 24 GLN cc_start: 0.7594 (mp10) cc_final: 0.7020 (tm-30) REVERT: E 58 LYS cc_start: 0.7893 (ttmt) cc_final: 0.7201 (tptm) REVERT: F 58 LYS cc_start: 0.7774 (ttmt) cc_final: 0.6834 (tptm) REVERT: G 24 GLN cc_start: 0.7531 (mp10) cc_final: 0.6873 (tm-30) REVERT: I 20 GLU cc_start: 0.8307 (mp0) cc_final: 0.8048 (mp0) REVERT: I 43 LYS cc_start: 0.7684 (tttt) cc_final: 0.7358 (tttm) REVERT: I 83 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8625 (mt-10) outliers start: 8 outliers final: 6 residues processed: 87 average time/residue: 0.2538 time to fit residues: 26.2831 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 : 0.492 ------------------------------------------------------------------------------- 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 20 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.119350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.099388 restraints weight = 6570.852| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.29 r_work: 0.3576 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4935 Z= 0.297 Angle : 0.691 7.247 6665 Z= 0.396 Chirality : 0.054 0.144 875 Planarity : 0.002 0.010 835 Dihedral : 7.019 26.259 725 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.70 % Allowed : 20.00 % Favored : 78.30 % 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: -3.99 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE I 94 TYR 0.014 0.003 TYR F 39 *********************** 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 86 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.528 Fit side-chains REVERT: A 20 GLU cc_start: 0.7678 (mp0) cc_final: 0.7379 (mm-30) REVERT: B 46 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7449 (tp30) REVERT: B 58 LYS cc_start: 0.7364 (ttmt) cc_final: 0.6340 (tptt) REVERT: C 24 GLN cc_start: 0.7590 (mp10) cc_final: 0.6953 (tm-30) REVERT: E 58 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7096 (tptm) REVERT: F 58 LYS cc_start: 0.7766 (ttmt) cc_final: 0.6864 (tptm) REVERT: I 20 GLU cc_start: 0.8257 (mp0) cc_final: 0.7978 (mp0) REVERT: I 43 LYS cc_start: 0.7618 (tttt) cc_final: 0.7283 (tttm) REVERT: I 83 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8563 (mt-10) outliers start: 8 outliers final: 7 residues processed: 83 average time/residue: 0.2630 time to fit residues: 25.9653 Evaluate side-chains 84 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 F residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 0.0050 chunk 56 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.6600 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.117630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.097954 restraints weight = 6591.506| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.27 r_work: 0.3548 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1851 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= 0.360 Angle : 0.713 7.096 6665 Z= 0.411 Chirality : 0.055 0.147 875 Planarity : 0.002 0.010 835 Dihedral : 7.126 26.038 725 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 2.77 % Allowed : 20.21 % Favored : 77.02 % 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: -4.04 (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 HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE B 94 TYR 0.015 0.003 TYR J 39 *********************** 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 91 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.571 Fit side-chains REVERT: B 46 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7460 (tp30) REVERT: B 58 LYS cc_start: 0.7378 (ttmt) cc_final: 0.6364 (tptt) REVERT: C 24 GLN cc_start: 0.7599 (mp10) cc_final: 0.6963 (tm-30) REVERT: E 58 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7086 (tptm) REVERT: F 58 LYS cc_start: 0.7735 (ttmt) cc_final: 0.6781 (tptm) REVERT: I 20 GLU cc_start: 0.8309 (mp0) cc_final: 0.8010 (mp0) REVERT: I 43 LYS cc_start: 0.7612 (tttt) cc_final: 0.7329 (tttm) outliers start: 13 outliers final: 11 residues processed: 87 average time/residue: 0.2520 time to fit residues: 26.1384 Evaluate side-chains 89 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 31 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.118836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099138 restraints weight = 6574.409| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.28 r_work: 0.3563 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1930 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= 0.300 Angle : 0.691 7.155 6665 Z= 0.397 Chirality : 0.054 0.147 875 Planarity : 0.002 0.010 835 Dihedral : 6.903 25.943 725 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 2.77 % Allowed : 20.43 % 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 (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: -3.94 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE J 94 TYR 0.013 0.003 TYR F 39 *********************** 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 88 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.489 Fit side-chains REVERT: B 46 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7425 (tp30) REVERT: B 58 LYS cc_start: 0.7413 (ttmt) cc_final: 0.6372 (tptt) REVERT: C 24 GLN cc_start: 0.7558 (mp10) cc_final: 0.6906 (tm-30) REVERT: E 58 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7084 (tptm) REVERT: F 58 LYS cc_start: 0.7746 (ttmt) cc_final: 0.6812 (tptm) REVERT: I 20 GLU cc_start: 0.8257 (mp0) cc_final: 0.7951 (mp0) REVERT: I 43 LYS cc_start: 0.7583 (tttt) cc_final: 0.7306 (tttm) outliers start: 13 outliers final: 12 residues processed: 83 average time/residue: 0.2535 time to fit residues: 24.9725 Evaluate side-chains 86 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 32 optimal weight: 0.0370 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8864 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.129404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.108899 restraints weight = 6067.076| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.15 r_work: 0.3683 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4935 Z= 0.150 Angle : 0.593 7.015 6665 Z= 0.336 Chirality : 0.053 0.137 875 Planarity : 0.001 0.009 835 Dihedral : 6.130 24.136 725 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 1.49 % Allowed : 21.70 % 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 (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: -3.70 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.002 0.000 PHE I 94 TYR 0.009 0.002 TYR F 39 *********************** 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: 7 poor density : 76 time to evaluate : 0.499 Fit side-chains REVERT: A 20 GLU cc_start: 0.7567 (mp0) cc_final: 0.7301 (mm-30) REVERT: B 23 LYS cc_start: 0.8030 (ptmt) cc_final: 0.7808 (ptmm) REVERT: B 58 LYS cc_start: 0.7470 (ttmt) cc_final: 0.6482 (tptt) REVERT: C 24 GLN cc_start: 0.7428 (mp10) cc_final: 0.6911 (tm-30) REVERT: E 58 LYS cc_start: 0.7856 (ttmt) cc_final: 0.7026 (tptm) REVERT: F 58 LYS cc_start: 0.7769 (ttmt) cc_final: 0.6902 (tptm) REVERT: I 20 GLU cc_start: 0.8196 (mp0) cc_final: 0.7893 (mp0) REVERT: I 43 LYS cc_start: 0.7660 (tttt) cc_final: 0.7408 (ttmt) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.2673 time to fit residues: 25.1876 Evaluate side-chains 77 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 92 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 0 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.122581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.102253 restraints weight = 6381.145| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.15 r_work: 0.3552 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4935 Z= 0.441 Angle : 0.752 7.078 6665 Z= 0.436 Chirality : 0.056 0.149 875 Planarity : 0.003 0.014 835 Dihedral : 7.171 25.218 725 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer: Outliers : 2.77 % Allowed : 21.06 % Favored : 76.17 % 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: -3.95 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.005 0.001 PHE B 94 TYR 0.018 0.004 TYR J 39 *********************** 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 93 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.571 Fit side-chains REVERT: B 58 LYS cc_start: 0.7510 (ttmt) cc_final: 0.6523 (tptt) REVERT: C 24 GLN cc_start: 0.7577 (mp10) cc_final: 0.6929 (tm-30) REVERT: E 58 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7277 (tptm) REVERT: F 58 LYS cc_start: 0.7780 (ttmt) cc_final: 0.6869 (tptm) REVERT: H 83 GLU cc_start: 0.8088 (mp0) cc_final: 0.7098 (mp0) REVERT: I 43 LYS cc_start: 0.7721 (tttt) cc_final: 0.7472 (tttm) outliers start: 13 outliers final: 12 residues processed: 87 average time/residue: 0.2455 time to fit residues: 25.5397 Evaluate side-chains 91 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 0.0000 chunk 1 optimal weight: 4.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.123315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.102823 restraints weight = 6297.685| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.17 r_work: 0.3576 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2072 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= 0.377 Angle : 0.736 7.193 6665 Z= 0.424 Chirality : 0.056 0.150 875 Planarity : 0.002 0.013 835 Dihedral : 7.113 25.761 725 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 2.34 % Allowed : 21.91 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.01 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.003 0.001 PHE B 94 TYR 0.015 0.003 TYR J 39 *********************** 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 87 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.543 Fit side-chains REVERT: B 58 LYS cc_start: 0.7515 (ttmt) cc_final: 0.6529 (tptt) REVERT: E 58 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7250 (tptm) REVERT: F 58 LYS cc_start: 0.7797 (ttmt) cc_final: 0.6892 (tptm) REVERT: H 83 GLU cc_start: 0.8085 (mp0) cc_final: 0.7046 (mp0) REVERT: I 43 LYS cc_start: 0.7670 (tttt) cc_final: 0.7418 (tttm) outliers start: 11 outliers final: 10 residues processed: 82 average time/residue: 0.2691 time to fit residues: 26.1856 Evaluate side-chains 86 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 0.0000 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.125846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.105332 restraints weight = 6255.406| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.15 r_work: 0.3624 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4935 Z= 0.252 Angle : 0.671 7.117 6665 Z= 0.382 Chirality : 0.054 0.145 875 Planarity : 0.002 0.014 835 Dihedral : 6.624 24.993 725 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 1.70 % Allowed : 22.34 % 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 (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: -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 HIS 0.002 0.001 HIS F 50 PHE 0.002 0.001 PHE J 94 TYR 0.012 0.002 TYR F 39 ********************** 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 81 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.511 Fit side-chains REVERT: B 58 LYS cc_start: 0.7478 (ttmt) cc_final: 0.6469 (tptt) REVERT: E 58 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7140 (tptm) REVERT: F 58 LYS cc_start: 0.7748 (ttmt) cc_final: 0.6863 (tptm) REVERT: H 83 GLU cc_start: 0.8044 (mp0) cc_final: 0.7629 (mp0) REVERT: I 43 LYS cc_start: 0.7623 (tttt) cc_final: 0.7362 (tttm) outliers start: 8 outliers final: 8 residues processed: 78 average time/residue: 0.2647 time to fit residues: 24.4570 Evaluate side-chains 81 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.0030 chunk 28 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.5712 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.126503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.105967 restraints weight = 6248.990| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.16 r_work: 0.3636 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4935 Z= 0.234 Angle : 0.649 7.084 6665 Z= 0.370 Chirality : 0.053 0.144 875 Planarity : 0.002 0.014 835 Dihedral : 6.479 25.102 725 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 2.13 % Allowed : 22.13 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.78 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.003 0.001 PHE J 94 TYR 0.011 0.002 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2723.06 seconds wall clock time: 48 minutes 55.88 seconds (2935.88 seconds total)