Starting phenix.real_space_refine on Wed Aug 5 18:54:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30yw_58153/08_2026/30yw_58153.cif Found real_map, /net/cci-nas-00/data/ceres_data/30yw_58153/08_2026/30yw_58153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30yw_58153/08_2026/30yw_58153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30yw_58153/08_2026/30yw_58153.map" model { file = "/net/cci-nas-00/data/ceres_data/30yw_58153/08_2026/30yw_58153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30yw_58153/08_2026/30yw_58153.cif" } resolution = 2.8 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= 0.002 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 6993 2.51 5 N 1892 2.21 5 O 2208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11111 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 883 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 883 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 883 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 883 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 883 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 883 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 968 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 968 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 973 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "J" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 968 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 968 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 968 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.02, per 1000 atoms: 0.27 Number of scatterers: 11111 At special positions: 0 Unit cell: (103.197, 96.485, 91.451, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 2208 8.00 N 1892 7.00 C 6993 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: 0.95 Conformation dependent library (CDL) restraints added in 400.7 milliseconds 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 16.5% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'G' and resid 3 through 13 Processing helix chain 'G' and resid 28 through 34 removed outlier: 3.926A pdb=" N ASN G 33 " --> pdb=" O GLY G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 92 Processing helix chain 'H' and resid 3 through 13 Processing helix chain 'H' and resid 28 through 34 removed outlier: 3.812A pdb=" N ASN H 33 " --> pdb=" O GLY H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 92 Processing helix chain 'I' and resid 3 through 13 Processing helix chain 'I' and resid 28 through 34 removed outlier: 3.918A pdb=" N ASN I 33 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 91 Processing helix chain 'J' and resid 3 through 13 Processing helix chain 'J' and resid 28 through 34 removed outlier: 3.906A pdb=" N ASN J 33 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 92 Processing helix chain 'K' and resid 3 through 13 Processing helix chain 'K' and resid 28 through 34 removed outlier: 3.949A pdb=" N ASN K 33 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 92 Processing helix chain 'L' and resid 3 through 13 Processing helix chain 'L' and resid 28 through 34 removed outlier: 3.903A pdb=" N ASN L 33 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 92 removed outlier: 3.540A pdb=" N ASN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 19 removed outlier: 5.897A pdb=" N GLU A 18 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA A 36 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N TYR A 42 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ARG A 69 " --> pdb=" O TYR A 42 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL A 44 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 67 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 46 " --> pdb=" O ASP A 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 57 through 69 current: chain 'A' and resid 87 through 95 removed outlier: 8.681A pdb=" N TYR A 88 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N THR A 112 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE A 90 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS A 110 " --> pdb=" O ILE A 90 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 104 through 116 current: chain 'B' and resid 30 through 54 removed outlier: 8.691A pdb=" N TYR B 42 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ARG B 69 " --> pdb=" O TYR B 42 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL B 44 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 67 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 46 " --> pdb=" O ASP B 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 57 through 69 current: chain 'B' and resid 87 through 94 removed outlier: 8.657A pdb=" N TYR B 88 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N THR B 112 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE B 90 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS B 110 " --> pdb=" O ILE B 90 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 104 through 116 current: chain 'C' and resid 34 through 54 removed outlier: 8.637A pdb=" N TYR C 42 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ARG C 69 " --> pdb=" O TYR C 42 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL C 44 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 67 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 46 " --> pdb=" O ASP C 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 69 current: chain 'C' and resid 87 through 95 removed outlier: 9.059A pdb=" N GLN C 87 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N THR C 112 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR C 108 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL C 93 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE C 106 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE C 104 " --> pdb=" O PRO C 95 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 104 through 116 current: chain 'D' and resid 34 through 54 removed outlier: 8.514A pdb=" N TYR D 42 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG D 69 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL D 44 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL D 67 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR D 46 " --> pdb=" O ASP D 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 69 current: chain 'D' and resid 87 through 95 removed outlier: 8.747A pdb=" N TYR D 88 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR D 112 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE D 90 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS D 110 " --> pdb=" O ILE D 90 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 104 through 116 current: chain 'E' and resid 32 through 54 removed outlier: 8.545A pdb=" N TYR E 42 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ARG E 69 " --> pdb=" O TYR E 42 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL E 44 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL E 67 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 46 " --> pdb=" O ASP E 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 69 current: chain 'E' and resid 87 through 95 removed outlier: 8.805A pdb=" N GLN E 87 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N THR E 112 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR E 108 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL E 93 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE E 106 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE E 104 " --> pdb=" O PRO E 95 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 104 through 116 current: chain 'F' and resid 30 through 53 removed outlier: 8.577A pdb=" N TYR F 42 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ARG F 69 " --> pdb=" O TYR F 42 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL F 44 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL F 67 " --> pdb=" O VAL F 44 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 69 current: chain 'F' and resid 87 through 94 removed outlier: 8.699A pdb=" N TYR F 88 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR F 112 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE F 90 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS F 110 " --> pdb=" O ILE F 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 23 Processing sheet with id=AA4, first strand: chain 'D' and resid 22 through 23 Processing sheet with id=AA5, first strand: chain 'G' and resid 21 through 24 removed outlier: 7.262A pdb=" N LEU G 41 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU G 68 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR G 43 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE G 66 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN G 45 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL G 64 " --> pdb=" O ASN G 45 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN G 47 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN G 62 " --> pdb=" O ASN G 47 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE G 60 " --> pdb=" O PRO G 49 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR G 51 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER G 58 " --> pdb=" O THR G 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 56 through 69 current: chain 'G' and resid 111 through 122 Processing sheet with id=AA6, first strand: chain 'H' and resid 21 through 24 removed outlier: 5.848A pdb=" N CYS H 40 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE H 69 " --> pdb=" O CYS H 40 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL H 42 " --> pdb=" O ARG H 67 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ARG H 67 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU H 44 " --> pdb=" O GLU H 65 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU H 65 " --> pdb=" O GLU H 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU H 46 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR H 52 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 69 current: chain 'H' and resid 111 through 122 Processing sheet with id=AA7, first strand: chain 'I' and resid 21 through 24 removed outlier: 7.139A pdb=" N LEU I 41 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU I 68 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR I 43 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE I 66 " --> pdb=" O THR I 43 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASN I 45 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL I 64 " --> pdb=" O ASN I 45 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN I 47 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLN I 62 " --> pdb=" O ASN I 47 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE I 60 " --> pdb=" O PRO I 49 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR I 51 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER I 58 " --> pdb=" O THR I 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 56 through 69 current: chain 'I' and resid 111 through 122 Processing sheet with id=AA8, first strand: chain 'J' and resid 21 through 24 removed outlier: 6.543A pdb=" N GLY J 63 " --> pdb=" O ASN J 45 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN J 47 " --> pdb=" O HIS J 61 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS J 61 " --> pdb=" O ASN J 47 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLU J 59 " --> pdb=" O PRO J 49 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR J 51 " --> pdb=" O PHE J 57 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE J 57 " --> pdb=" O THR J 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 69 current: chain 'J' and resid 111 through 122 Processing sheet with id=AA9, first strand: chain 'K' and resid 21 through 24 removed outlier: 6.594A pdb=" N GLY K 63 " --> pdb=" O ASN K 45 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN K 47 " --> pdb=" O HIS K 61 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS K 61 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU K 59 " --> pdb=" O PRO K 49 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR K 51 " --> pdb=" O PHE K 57 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE K 57 " --> pdb=" O THR K 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 69 current: chain 'K' and resid 111 through 122 Processing sheet with id=AB1, first strand: chain 'L' and resid 21 through 24 removed outlier: 7.230A pdb=" N LEU L 41 " --> pdb=" O LEU L 68 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU L 68 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR L 43 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE L 66 " --> pdb=" O THR L 43 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASN L 45 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL L 64 " --> pdb=" O ASN L 45 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN L 47 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN L 62 " --> pdb=" O ASN L 47 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE L 60 " --> pdb=" O PRO L 49 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR L 51 " --> pdb=" O SER L 58 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER L 58 " --> pdb=" O THR L 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 56 through 69 current: chain 'L' and resid 111 through 122 272 hydrogen bonds defined for protein. 684 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: 1.56 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3752 1.34 - 1.46: 2305 1.46 - 1.58: 5283 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 11364 Sorted by residual: bond pdb=" N PHE D 5 " pdb=" CA PHE D 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N SER H 2 " pdb=" CA SER H 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N SER I 2 " pdb=" CA SER I 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N SER K 2 " pdb=" CA SER K 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N SER L 2 " pdb=" CA SER L 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 11359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 15033 1.24 - 2.49: 356 2.49 - 3.73: 80 3.73 - 4.97: 17 4.97 - 6.21: 2 Bond angle restraints: 15488 Sorted by residual: angle pdb=" CA PRO E 25 " pdb=" N PRO E 25 " pdb=" CD PRO E 25 " ideal model delta sigma weight residual 112.00 107.57 4.43 1.40e+00 5.10e-01 1.00e+01 angle pdb=" N PRO E 25 " pdb=" CD PRO E 25 " pdb=" CG PRO E 25 " ideal model delta sigma weight residual 103.20 98.96 4.24 1.50e+00 4.44e-01 7.98e+00 angle pdb=" CB PRO E 25 " pdb=" CG PRO E 25 " pdb=" CD PRO E 25 " ideal model delta sigma weight residual 106.10 99.89 6.21 3.20e+00 9.77e-02 3.77e+00 angle pdb=" N PHE K 25 " pdb=" CA PHE K 25 " pdb=" C PHE K 25 " ideal model delta sigma weight residual 110.80 114.82 -4.02 2.13e+00 2.20e-01 3.56e+00 angle pdb=" N PHE L 25 " pdb=" CA PHE L 25 " pdb=" C PHE L 25 " ideal model delta sigma weight residual 110.80 114.78 -3.98 2.13e+00 2.20e-01 3.49e+00 ... (remaining 15483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6174 17.91 - 35.82: 473 35.82 - 53.73: 48 53.73 - 71.65: 10 71.65 - 89.56: 17 Dihedral angle restraints: 6722 sinusoidal: 2606 harmonic: 4116 Sorted by residual: dihedral pdb=" CA ASP I 79 " pdb=" CB ASP I 79 " pdb=" CG ASP I 79 " pdb=" OD1 ASP I 79 " ideal model delta sinusoidal sigma weight residual -30.00 -87.18 57.18 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB GLU A 31 " pdb=" CG GLU A 31 " pdb=" CD GLU A 31 " pdb=" OE1 GLU A 31 " ideal model delta sinusoidal sigma weight residual 0.00 -88.41 88.41 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA VAL J 26 " pdb=" C VAL J 26 " pdb=" N ILE J 27 " pdb=" CA ILE J 27 " ideal model delta harmonic sigma weight residual 180.00 164.03 15.97 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 6719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 926 0.029 - 0.057: 528 0.057 - 0.086: 119 0.086 - 0.115: 107 0.115 - 0.143: 48 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA ILE L 27 " pdb=" N ILE L 27 " pdb=" C ILE L 27 " pdb=" CB ILE L 27 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE G 19 " pdb=" N ILE G 19 " pdb=" C ILE G 19 " pdb=" CB ILE G 19 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE G 27 " pdb=" N ILE G 27 " pdb=" C ILE G 27 " pdb=" CB ILE G 27 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1725 not shown) Planarity restraints: 2053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 76 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO D 77 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 77 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 77 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 76 " 0.038 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO C 77 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 77 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 77 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 76 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO F 77 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO F 77 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 77 " -0.029 5.00e-02 4.00e+02 ... (remaining 2050 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 117 2.63 - 3.20: 10047 3.20 - 3.76: 16144 3.76 - 4.33: 24195 4.33 - 4.90: 40458 Nonbonded interactions: 90961 Sorted by model distance: nonbonded pdb=" OH TYR F 42 " pdb=" OD1 ASP F 82 " model vdw 2.059 3.040 nonbonded pdb=" OD1 ASP B 71 " pdb=" OG SER B 73 " model vdw 2.060 3.040 nonbonded pdb=" OD1 ASP A 71 " pdb=" OG SER A 73 " model vdw 2.073 3.040 nonbonded pdb=" OD1 ASP C 71 " pdb=" OG SER C 73 " model vdw 2.074 3.040 nonbonded pdb=" OD2 ASP K 36 " pdb=" OG SER K 71 " model vdw 2.078 3.040 ... (remaining 90956 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = (chain 'I' and (resid 2 through 90 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 123)) selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 15.520 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.770 Find NCS groups from input model: 0.200 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.003 0.037 11364 Z= 0.129 Angle : 0.503 6.214 15488 Z= 0.273 Chirality : 0.045 0.143 1728 Planarity : 0.005 0.069 2053 Dihedral : 13.184 89.557 4058 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.53 (0.23), residues: 1386 helix: 0.79 (0.33), residues: 282 sheet: -0.36 (0.19), residues: 744 loop : -0.87 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 29 TYR 0.014 0.001 TYR A 53 PHE 0.013 0.001 PHE K 25 TRP 0.015 0.001 TRP H 18 HIS 0.002 0.001 HIS F 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (11364) covalent geometry : angle 0.50322 / 0.27 (15488) hydrogen bonds : bond 0.21683 / 14.64 ( 272) hydrogen bonds : angle 7.99700 / 5.52 ( 684) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7403 (tp30) cc_final: 0.7026 (tp30) REVERT: D 115 LYS cc_start: 0.6906 (mttm) cc_final: 0.6589 (mttp) REVERT: E 49 MET cc_start: 0.8703 (mtp) cc_final: 0.8477 (mtp) REVERT: F 54 GLN cc_start: 0.7755 (mt0) cc_final: 0.7472 (mm110) REVERT: H 75 ASN cc_start: 0.8323 (p0) cc_final: 0.7896 (p0) REVERT: J 107 ASP cc_start: 0.8485 (m-30) cc_final: 0.8219 (m-30) REVERT: K 75 ASN cc_start: 0.8159 (p0) cc_final: 0.7855 (p0) REVERT: L 75 ASN cc_start: 0.8092 (p0) cc_final: 0.7517 (p0) REVERT: L 95 PHE cc_start: 0.6987 (m-10) cc_final: 0.6599 (m-80) outliers start: 0 outliers final: 1 residues processed: 343 average time/residue: 0.4337 time to fit residues: 163.1027 Evaluate side-chains 268 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 GLN B 50 ASN B 87 GLN E 54 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 ASN G 110 GLN J 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108608 restraints weight = 17656.678| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.79 r_work: 0.3266 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11364 Z= 0.153 Angle : 0.567 5.818 15488 Z= 0.312 Chirality : 0.047 0.154 1728 Planarity : 0.006 0.067 2053 Dihedral : 4.443 39.807 1508 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.18 % Allowed : 11.02 % Favored : 85.80 % 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: -0.33 (0.23), residues: 1386 helix: 0.94 (0.33), residues: 282 sheet: -0.31 (0.18), residues: 768 loop : -0.59 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 47 TYR 0.009 0.001 TYR C 88 PHE 0.014 0.002 PHE L 57 TRP 0.012 0.002 TRP L 18 HIS 0.004 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (11364) covalent geometry : angle 0.56738 / 0.31 (15488) hydrogen bonds : bond 0.04394 / 2.99 ( 272) hydrogen bonds : angle 5.38850 / 3.68 ( 684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 0.411 Fit side-chains REVERT: B 49 MET cc_start: 0.9026 (mtp) cc_final: 0.8787 (mtp) REVERT: D 71 ASP cc_start: 0.8863 (t0) cc_final: 0.8466 (t0) REVERT: D 81 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: D 91 VAL cc_start: 0.8187 (t) cc_final: 0.7855 (t) REVERT: D 114 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7832 (ttp-110) REVERT: E 18 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8730 (mt-10) REVERT: E 49 MET cc_start: 0.8909 (mtp) cc_final: 0.8501 (mtp) REVERT: F 54 GLN cc_start: 0.7953 (mt0) cc_final: 0.7344 (mm110) REVERT: J 107 ASP cc_start: 0.8530 (m-30) cc_final: 0.8209 (m-30) REVERT: K 62 GLN cc_start: 0.8297 (mt0) cc_final: 0.7909 (mt0) REVERT: K 75 ASN cc_start: 0.8335 (p0) cc_final: 0.8026 (p0) REVERT: L 95 PHE cc_start: 0.7279 (m-10) cc_final: 0.6930 (m-80) outliers start: 39 outliers final: 18 residues processed: 293 average time/residue: 0.3778 time to fit residues: 121.8728 Evaluate side-chains 261 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 241 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 35 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 103 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 GLN B 50 ASN D 54 GLN E 50 ASN E 54 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN J 47 ASN L 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109717 restraints weight = 17703.928| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.78 r_work: 0.3286 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11364 Z= 0.111 Angle : 0.516 5.991 15488 Z= 0.285 Chirality : 0.045 0.146 1728 Planarity : 0.005 0.062 2053 Dihedral : 4.079 19.956 1506 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.78 % Allowed : 14.53 % Favored : 82.69 % 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: -0.23 (0.24), residues: 1386 helix: 1.12 (0.33), residues: 282 sheet: -0.25 (0.18), residues: 768 loop : -0.65 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.009 0.001 TYR H 103 PHE 0.010 0.001 PHE L 57 TRP 0.006 0.001 TRP L 18 HIS 0.001 0.000 HIS H 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11364) covalent geometry : angle 0.51593 / 0.28 (15488) hydrogen bonds : bond 0.03599 / 2.44 ( 272) hydrogen bonds : angle 4.98979 / 3.39 ( 684) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 0.293 Fit side-chains REVERT: B 6 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7935 (pttt) REVERT: B 49 MET cc_start: 0.8965 (mtp) cc_final: 0.8759 (mtp) REVERT: B 71 ASP cc_start: 0.8849 (t70) cc_final: 0.8589 (t0) REVERT: D 23 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8026 (tt) REVERT: D 71 ASP cc_start: 0.8890 (t0) cc_final: 0.8425 (t0) REVERT: E 6 LYS cc_start: 0.8406 (ptmt) cc_final: 0.8103 (pttt) REVERT: E 18 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8581 (mt-10) REVERT: E 49 MET cc_start: 0.8906 (mtp) cc_final: 0.8520 (mtp) REVERT: E 65 ASP cc_start: 0.8324 (t70) cc_final: 0.7969 (t0) REVERT: F 54 GLN cc_start: 0.7906 (mt0) cc_final: 0.7293 (mm110) REVERT: I 59 GLU cc_start: 0.7965 (tt0) cc_final: 0.7482 (tt0) REVERT: J 107 ASP cc_start: 0.8538 (m-30) cc_final: 0.8200 (m-30) REVERT: K 62 GLN cc_start: 0.8319 (mt0) cc_final: 0.7953 (mt0) REVERT: L 95 PHE cc_start: 0.7197 (m-10) cc_final: 0.6903 (m-80) outliers start: 34 outliers final: 19 residues processed: 270 average time/residue: 0.3784 time to fit residues: 111.9493 Evaluate side-chains 256 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain K residue 104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 128 optimal weight: 0.0570 chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 GLN D 54 GLN E 54 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN I 62 GLN L 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108940 restraints weight = 17762.789| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.81 r_work: 0.3274 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11364 Z= 0.121 Angle : 0.523 5.868 15488 Z= 0.289 Chirality : 0.046 0.152 1728 Planarity : 0.005 0.063 2053 Dihedral : 4.039 19.309 1506 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.10 % Allowed : 15.84 % Favored : 81.06 % 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: -0.19 (0.24), residues: 1386 helix: 1.21 (0.33), residues: 282 sheet: -0.21 (0.18), residues: 768 loop : -0.70 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 67 TYR 0.010 0.001 TYR D 53 PHE 0.010 0.001 PHE G 25 TRP 0.006 0.001 TRP K 94 HIS 0.002 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11364) covalent geometry : angle 0.52306 / 0.29 (15488) hydrogen bonds : bond 0.03389 / 2.30 ( 272) hydrogen bonds : angle 4.80119 / 3.26 ( 684) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 0.442 Fit side-chains REVERT: B 6 LYS cc_start: 0.8277 (ptmt) cc_final: 0.7991 (pttt) REVERT: B 49 MET cc_start: 0.8975 (mtp) cc_final: 0.8710 (mtp) REVERT: B 71 ASP cc_start: 0.8853 (t70) cc_final: 0.8621 (t0) REVERT: D 71 ASP cc_start: 0.8994 (t70) cc_final: 0.8478 (t0) REVERT: E 6 LYS cc_start: 0.8350 (ptmt) cc_final: 0.8128 (pttt) REVERT: E 18 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8524 (mt-10) REVERT: E 49 MET cc_start: 0.8960 (mtp) cc_final: 0.8551 (mtp) REVERT: E 65 ASP cc_start: 0.8352 (t70) cc_final: 0.7993 (t0) REVERT: F 49 MET cc_start: 0.8886 (mtp) cc_final: 0.8617 (mtp) REVERT: F 54 GLN cc_start: 0.7901 (mt0) cc_final: 0.7319 (mm110) REVERT: H 75 ASN cc_start: 0.8353 (p0) cc_final: 0.7851 (p0) REVERT: I 59 GLU cc_start: 0.7882 (tt0) cc_final: 0.7483 (tt0) REVERT: K 62 GLN cc_start: 0.8394 (mt0) cc_final: 0.8114 (mt0) REVERT: L 46 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: L 95 PHE cc_start: 0.7423 (m-10) cc_final: 0.7164 (m-80) outliers start: 38 outliers final: 18 residues processed: 274 average time/residue: 0.4324 time to fit residues: 129.9357 Evaluate side-chains 257 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 38 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 GLN E 50 ASN E 54 GLN E 83 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN L 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104718 restraints weight = 17827.073| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.80 r_work: 0.3213 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11364 Z= 0.185 Angle : 0.582 6.276 15488 Z= 0.320 Chirality : 0.048 0.158 1728 Planarity : 0.006 0.066 2053 Dihedral : 4.318 19.602 1506 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.00 % Allowed : 16.24 % Favored : 79.76 % 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: -0.56 (0.23), residues: 1386 helix: 1.23 (0.34), residues: 246 sheet: -0.33 (0.18), residues: 768 loop : -1.24 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 67 TYR 0.015 0.001 TYR D 53 PHE 0.014 0.002 PHE G 25 TRP 0.009 0.001 TRP I 94 HIS 0.003 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (11364) covalent geometry : angle 0.58189 / 0.32 (15488) hydrogen bonds : bond 0.03901 / 2.67 ( 272) hydrogen bonds : angle 4.91635 / 3.34 ( 684) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 0.471 Fit side-chains REVERT: B 6 LYS cc_start: 0.8306 (ptmt) cc_final: 0.8061 (pttt) REVERT: B 49 MET cc_start: 0.9016 (mtp) cc_final: 0.8729 (mtp) REVERT: B 61 GLN cc_start: 0.8526 (mt0) cc_final: 0.8189 (mm-40) REVERT: B 71 ASP cc_start: 0.8991 (t70) cc_final: 0.8788 (t0) REVERT: D 114 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7946 (ttp-110) REVERT: E 6 LYS cc_start: 0.8398 (ptmt) cc_final: 0.8168 (pttt) REVERT: E 18 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: E 49 MET cc_start: 0.9004 (mtp) cc_final: 0.8588 (mtp) REVERT: E 82 ASP cc_start: 0.8684 (p0) cc_final: 0.8472 (p0) REVERT: F 54 GLN cc_start: 0.7946 (mt0) cc_final: 0.7324 (mm110) REVERT: H 46 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: H 75 ASN cc_start: 0.8444 (p0) cc_final: 0.7979 (p0) REVERT: I 59 GLU cc_start: 0.7955 (tt0) cc_final: 0.7511 (tt0) outliers start: 49 outliers final: 21 residues processed: 282 average time/residue: 0.4552 time to fit residues: 140.6127 Evaluate side-chains 260 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 136 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 ASN B 54 GLN E 50 ASN E 54 GLN E 83 ASN F 50 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN G 62 GLN H 62 GLN K 62 GLN L 15 ASN L 62 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107561 restraints weight = 17588.662| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.77 r_work: 0.3263 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11364 Z= 0.160 Angle : 0.567 6.022 15488 Z= 0.312 Chirality : 0.047 0.157 1728 Planarity : 0.006 0.066 2053 Dihedral : 4.301 19.873 1506 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.67 % Allowed : 19.02 % Favored : 77.31 % 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: -0.57 (0.23), residues: 1386 helix: 1.29 (0.34), residues: 246 sheet: -0.37 (0.18), residues: 768 loop : -1.23 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 67 TYR 0.015 0.001 TYR D 53 PHE 0.013 0.001 PHE G 25 TRP 0.008 0.001 TRP K 94 HIS 0.003 0.001 HIS K 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11364) covalent geometry : angle 0.56685 / 0.31 (15488) hydrogen bonds : bond 0.03640 / 2.49 ( 272) hydrogen bonds : angle 4.86002 / 3.29 ( 684) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.563 Fit side-chains REVERT: B 6 LYS cc_start: 0.8307 (ptmt) cc_final: 0.8064 (pttt) REVERT: B 49 MET cc_start: 0.9017 (mtp) cc_final: 0.8727 (mtp) REVERT: B 61 GLN cc_start: 0.8591 (mt0) cc_final: 0.8342 (mm-40) REVERT: D 23 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8014 (tt) REVERT: E 6 LYS cc_start: 0.8472 (ptmt) cc_final: 0.8246 (pttt) REVERT: E 18 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8501 (mt-10) REVERT: E 49 MET cc_start: 0.9012 (mtp) cc_final: 0.8608 (mtp) REVERT: E 65 ASP cc_start: 0.8393 (t70) cc_final: 0.8024 (t0) REVERT: E 82 ASP cc_start: 0.8733 (p0) cc_final: 0.8524 (p0) REVERT: F 18 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8719 (mt-10) REVERT: F 54 GLN cc_start: 0.8025 (mt0) cc_final: 0.7405 (mm110) REVERT: G 46 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: H 46 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7302 (pm20) REVERT: H 75 ASN cc_start: 0.8441 (p0) cc_final: 0.7993 (p0) outliers start: 45 outliers final: 24 residues processed: 281 average time/residue: 0.4426 time to fit residues: 136.1928 Evaluate side-chains 274 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 GLN C 83 ASN E 50 ASN E 54 GLN E 83 ASN F 50 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN L 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106948 restraints weight = 17446.717| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.76 r_work: 0.3255 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11364 Z= 0.168 Angle : 0.581 6.500 15488 Z= 0.320 Chirality : 0.047 0.153 1728 Planarity : 0.006 0.066 2053 Dihedral : 4.310 19.720 1506 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.59 % Allowed : 19.43 % Favored : 76.98 % 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: -0.59 (0.23), residues: 1386 helix: 1.24 (0.34), residues: 246 sheet: -0.39 (0.18), residues: 768 loop : -1.22 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 67 TYR 0.017 0.001 TYR D 53 PHE 0.014 0.002 PHE B 34 TRP 0.008 0.001 TRP K 94 HIS 0.003 0.001 HIS K 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (11364) covalent geometry : angle 0.58075 / 0.32 (15488) hydrogen bonds : bond 0.03669 / 2.51 ( 272) hydrogen bonds : angle 4.83931 / 3.28 ( 684) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 0.438 Fit side-chains REVERT: B 6 LYS cc_start: 0.8287 (ptmt) cc_final: 0.8058 (pttt) REVERT: B 49 MET cc_start: 0.8994 (mtp) cc_final: 0.8688 (mtp) REVERT: B 61 GLN cc_start: 0.8557 (mt0) cc_final: 0.8352 (mm-40) REVERT: D 23 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8021 (tt) REVERT: E 6 LYS cc_start: 0.8501 (ptmt) cc_final: 0.8217 (pttt) REVERT: E 18 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8493 (mt-10) REVERT: E 49 MET cc_start: 0.9043 (mtp) cc_final: 0.8631 (mtp) REVERT: E 65 ASP cc_start: 0.8391 (t70) cc_final: 0.8006 (t0) REVERT: E 82 ASP cc_start: 0.8601 (p0) cc_final: 0.8383 (p0) REVERT: E 115 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7326 (tptt) REVERT: F 18 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8667 (mt-10) REVERT: F 49 MET cc_start: 0.9001 (mtp) cc_final: 0.8793 (mtp) REVERT: F 54 GLN cc_start: 0.8045 (mt0) cc_final: 0.7401 (mm110) REVERT: H 46 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: H 75 ASN cc_start: 0.8461 (p0) cc_final: 0.8012 (p0) REVERT: K 46 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7907 (pt0) outliers start: 44 outliers final: 25 residues processed: 272 average time/residue: 0.4551 time to fit residues: 135.9475 Evaluate side-chains 268 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 GLN C 83 ASN E 50 ASN E 54 GLN E 83 ASN F 83 ASN G 62 GLN H 62 GLN K 62 GLN L 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105989 restraints weight = 17490.260| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.77 r_work: 0.3243 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11364 Z= 0.187 Angle : 0.597 6.571 15488 Z= 0.329 Chirality : 0.048 0.155 1728 Planarity : 0.006 0.067 2053 Dihedral : 4.412 19.912 1506 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.84 % Allowed : 19.92 % Favored : 76.24 % 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: -0.67 (0.23), residues: 1386 helix: 1.16 (0.33), residues: 246 sheet: -0.42 (0.19), residues: 744 loop : -1.25 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 67 TYR 0.018 0.001 TYR D 53 PHE 0.013 0.002 PHE G 25 TRP 0.008 0.001 TRP K 94 HIS 0.003 0.001 HIS K 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (11364) covalent geometry : angle 0.59669 / 0.33 (15488) hydrogen bonds : bond 0.03799 / 2.61 ( 272) hydrogen bonds : angle 4.87121 / 3.30 ( 684) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 0.450 Fit side-chains REVERT: B 6 LYS cc_start: 0.8322 (ptmt) cc_final: 0.8106 (pttt) REVERT: B 49 MET cc_start: 0.9015 (mtp) cc_final: 0.8700 (mtp) REVERT: D 23 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8017 (tt) REVERT: D 81 GLN cc_start: 0.8049 (mt0) cc_final: 0.7797 (mt0) REVERT: E 18 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8487 (mt-10) REVERT: E 49 MET cc_start: 0.9045 (mtp) cc_final: 0.8644 (mtp) REVERT: E 65 ASP cc_start: 0.8413 (t70) cc_final: 0.8052 (t0) REVERT: E 82 ASP cc_start: 0.8741 (p0) cc_final: 0.8523 (p0) REVERT: E 115 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7638 (mptt) REVERT: F 18 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8654 (mt-10) REVERT: F 49 MET cc_start: 0.9024 (mtp) cc_final: 0.8794 (mtp) REVERT: F 54 GLN cc_start: 0.8076 (mt0) cc_final: 0.7430 (mm110) REVERT: H 46 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7328 (pm20) REVERT: H 60 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7698 (pt) outliers start: 47 outliers final: 29 residues processed: 274 average time/residue: 0.4259 time to fit residues: 128.8374 Evaluate side-chains 272 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 ASN B 54 GLN C 83 ASN E 50 ASN E 54 GLN E 83 ASN F 50 ASN F 83 ASN G 15 ASN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN K 62 GLN L 62 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103672 restraints weight = 17550.619| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.75 r_work: 0.3196 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 11364 Z= 0.270 Angle : 0.663 7.026 15488 Z= 0.364 Chirality : 0.051 0.169 1728 Planarity : 0.007 0.070 2053 Dihedral : 4.685 20.255 1506 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.67 % Allowed : 20.16 % Favored : 76.16 % 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: -0.63 (0.23), residues: 1386 helix: 0.53 (0.32), residues: 282 sheet: -0.58 (0.19), residues: 708 loop : -0.40 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 67 TYR 0.025 0.002 TYR D 53 PHE 0.015 0.002 PHE G 25 TRP 0.012 0.002 TRP I 94 HIS 0.005 0.001 HIS K 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.27 (11364) covalent geometry : angle 0.66292 / 0.36 (15488) hydrogen bonds : bond 0.04292 / 2.96 ( 272) hydrogen bonds : angle 5.07140 / 3.46 ( 684) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7755 (ttp-110) REVERT: B 6 LYS cc_start: 0.8333 (ptmt) cc_final: 0.8115 (pttt) REVERT: B 49 MET cc_start: 0.9020 (mtp) cc_final: 0.8763 (mtp) REVERT: D 23 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8000 (tt) REVERT: D 81 GLN cc_start: 0.8165 (mt0) cc_final: 0.7941 (mt0) REVERT: E 18 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8522 (mt-10) REVERT: E 49 MET cc_start: 0.9059 (mtp) cc_final: 0.8661 (mtp) REVERT: E 115 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7682 (mptt) REVERT: F 18 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8612 (mt-10) REVERT: F 54 GLN cc_start: 0.8153 (mt0) cc_final: 0.7489 (mm110) REVERT: H 46 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: H 60 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7727 (pt) outliers start: 45 outliers final: 30 residues processed: 272 average time/residue: 0.4203 time to fit residues: 125.4223 Evaluate side-chains 272 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 58 optimal weight: 7.9990 chunk 42 optimal weight: 0.0770 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 0.0010 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.6150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 GLN C 83 ASN E 50 ASN E 54 GLN F 83 ASN G 62 GLN H 62 GLN J 62 GLN K 62 GLN L 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108842 restraints weight = 17519.502| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.76 r_work: 0.3280 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11364 Z= 0.118 Angle : 0.571 6.335 15488 Z= 0.317 Chirality : 0.046 0.145 1728 Planarity : 0.006 0.065 2053 Dihedral : 4.336 19.815 1506 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.04 % Allowed : 22.53 % Favored : 75.43 % 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: -0.64 (0.23), residues: 1386 helix: 1.35 (0.34), residues: 246 sheet: -0.48 (0.18), residues: 768 loop : -1.19 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 67 TYR 0.014 0.001 TYR F 53 PHE 0.013 0.001 PHE A 80 TRP 0.008 0.001 TRP A 41 HIS 0.001 0.000 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (11364) covalent geometry : angle 0.57137 / 0.32 (15488) hydrogen bonds : bond 0.03335 / 2.26 ( 272) hydrogen bonds : angle 4.86191 / 3.29 ( 684) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: B 6 LYS cc_start: 0.8300 (ptmt) cc_final: 0.8081 (pttt) REVERT: B 49 MET cc_start: 0.8942 (mtp) cc_final: 0.8568 (mtp) REVERT: D 23 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7902 (tt) REVERT: E 18 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8428 (mt-10) REVERT: E 49 MET cc_start: 0.9021 (mtp) cc_final: 0.8613 (mtp) REVERT: E 65 ASP cc_start: 0.8285 (t0) cc_final: 0.8041 (t0) REVERT: F 54 GLN cc_start: 0.8142 (mt0) cc_final: 0.7408 (mm110) outliers start: 25 outliers final: 17 residues processed: 267 average time/residue: 0.4149 time to fit residues: 122.2840 Evaluate side-chains 256 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 237 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain K residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 28 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 GLN B 83 ASN C 83 ASN E 54 GLN E 83 ASN F 83 ASN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN L 62 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106164 restraints weight = 17912.805| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.79 r_work: 0.3231 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11364 Z= 0.131 Angle : 0.575 6.428 15488 Z= 0.318 Chirality : 0.046 0.151 1728 Planarity : 0.006 0.065 2053 Dihedral : 4.218 18.771 1506 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.04 % Allowed : 22.37 % Favored : 75.59 % 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: -0.56 (0.23), residues: 1386 helix: 1.46 (0.34), residues: 246 sheet: -0.43 (0.18), residues: 768 loop : -1.19 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 67 TYR 0.014 0.001 TYR A 53 PHE 0.013 0.001 PHE B 80 TRP 0.006 0.001 TRP A 41 HIS 0.002 0.000 HIS J 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11364) covalent geometry : angle 0.57549 / 0.32 (15488) hydrogen bonds : bond 0.03292 / 2.24 ( 272) hydrogen bonds : angle 4.74843 / 3.21 ( 684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3443.60 seconds wall clock time: 59 minutes 34.51 seconds (3574.51 seconds total)