Starting phenix.real_space_refine on Fri Aug 22 15:46:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obp_70295/08_2025/9obp_70295_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obp_70295/08_2025/9obp_70295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9obp_70295/08_2025/9obp_70295_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obp_70295/08_2025/9obp_70295_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9obp_70295/08_2025/9obp_70295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obp_70295/08_2025/9obp_70295.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 3310 2.51 5 N 930 2.21 5 O 1070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5310 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 599 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "B" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 599 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "C" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 599 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "D" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 599 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "E" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 599 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "H" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "I" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.48, per 1000 atoms: 0.28 Number of scatterers: 5310 At special positions: 0 Unit cell: (102.3, 110.67, 47.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1070 8.00 N 930 7.00 C 3310 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 194.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1330 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 63.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 6.334A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA B 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ALA D 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA E 18 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA D 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.650A pdb=" N LYS A 32 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS B 32 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS C 32 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS D 32 " --> pdb=" O THR E 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.274A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 56 removed outlier: 7.149A pdb=" N GLU A 46 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY B 47 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 52 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA B 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A 54 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA A 56 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU B 57 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU B 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY C 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA C 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR B 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA B 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU C 57 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS B 58 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 60 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL D 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N HIS D 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY C 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU D 46 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY E 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL D 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA E 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR D 54 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL E 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA D 56 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU E 57 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.479A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU B 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY C 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA C 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR B 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA B 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU C 57 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS B 58 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 60 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU D 61 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS C 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL D 63 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN D 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.382A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N THR B 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR C 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL B 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR D 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL C 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA D 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR E 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL D 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 75 through 82 removed outlier: 6.989A pdb=" N THR A 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N GLN C 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N ALA B 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N THR C 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LYS B 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN D 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N ALA C 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N THR D 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS C 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR D 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL E 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 88 through 96 removed outlier: 7.019A pdb=" N ALA B 90 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 91 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY A 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA C 90 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 91 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR C 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY B 93 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA C 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N THR D 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N ALA C 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE D 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY C 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LYS D 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 90 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA D 91 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR E 92 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY D 93 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 88 through 96 removed outlier: 7.019A pdb=" N ALA B 90 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 91 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY A 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA C 90 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 91 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR C 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY B 93 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA C 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N THR D 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N ALA C 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE D 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY C 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LYS D 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LYS E 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL D 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 38 through 42 removed outlier: 6.298A pdb=" N LEU F 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY G 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL F 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU G 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLY H 41 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL G 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL H 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 57 removed outlier: 6.840A pdb=" N VAL G 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL F 49 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N HIS G 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY F 51 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL H 48 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL G 49 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N HIS H 50 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY G 51 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL I 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL H 49 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N HIS I 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY H 51 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL J 48 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL I 49 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS J 50 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY I 51 " --> pdb=" O HIS J 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 60 through 63 removed outlier: 6.756A pdb=" N LYS F 60 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL G 63 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN F 62 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS G 60 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL H 63 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN G 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ASN H 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS H 60 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL I 63 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN H 62 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN I 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR H 64 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS I 60 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL J 63 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN I 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASN J 65 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR I 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 69 through 71 removed outlier: 6.307A pdb=" N ALA F 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA G 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA I 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 75 through 82 removed outlier: 6.684A pdb=" N THR G 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA H 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL G 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LYS H 80 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN G 79 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL H 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR G 81 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR H 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ALA I 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL H 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N LYS I 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN H 79 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL I 82 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR H 81 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR I 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA J 78 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL I 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYS J 80 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN I 79 " --> pdb=" O LYS J 80 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL J 82 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR I 81 " --> pdb=" O VAL J 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 94 through 96 removed outlier: 6.553A pdb=" N VAL F 95 " --> pdb=" O LYS G 96 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL G 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL H 95 " --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL I 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 88 through 90 removed outlier: 6.982A pdb=" N ALA I 89 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 2 through 4 138 hydrogen bonds defined for protein. 414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.66 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 950 1.29 - 1.36: 835 1.36 - 1.42: 170 1.42 - 1.49: 920 1.49 - 1.55: 2450 Bond restraints: 5325 Sorted by residual: bond pdb=" CB GLN D 99 " pdb=" CG GLN D 99 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CB GLN C 99 " pdb=" CG GLN C 99 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CA GLY D 31 " pdb=" C GLY D 31 " ideal model delta sigma weight residual 1.516 1.522 -0.006 8.10e-03 1.52e+04 6.34e-01 bond pdb=" CA LYS A 43 " pdb=" C LYS A 43 " ideal model delta sigma weight residual 1.525 1.536 -0.011 1.40e-02 5.10e+03 5.91e-01 bond pdb=" CA GLY B 31 " pdb=" C GLY B 31 " ideal model delta sigma weight residual 1.516 1.522 -0.006 8.10e-03 1.52e+04 5.73e-01 ... (remaining 5320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 6931 1.27 - 2.55: 225 2.55 - 3.82: 21 3.82 - 5.09: 6 5.09 - 6.37: 2 Bond angle restraints: 7185 Sorted by residual: angle pdb=" CB GLN D 99 " pdb=" CG GLN D 99 " pdb=" CD GLN D 99 " ideal model delta sigma weight residual 112.60 117.21 -4.61 1.70e+00 3.46e-01 7.36e+00 angle pdb=" N GLY J 93 " pdb=" CA GLY J 93 " pdb=" C GLY J 93 " ideal model delta sigma weight residual 113.18 119.55 -6.37 2.37e+00 1.78e-01 7.22e+00 angle pdb=" CB GLN C 99 " pdb=" CG GLN C 99 " pdb=" CD GLN C 99 " ideal model delta sigma weight residual 112.60 117.01 -4.41 1.70e+00 3.46e-01 6.73e+00 angle pdb=" N GLU E 61 " pdb=" CA GLU E 61 " pdb=" C GLU E 61 " ideal model delta sigma weight residual 108.79 112.59 -3.80 1.53e+00 4.27e-01 6.18e+00 angle pdb=" CA GLN C 99 " pdb=" CB GLN C 99 " pdb=" CG GLN C 99 " ideal model delta sigma weight residual 114.10 118.70 -4.60 2.00e+00 2.50e-01 5.30e+00 ... (remaining 7180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 2698 17.47 - 34.93: 302 34.93 - 52.40: 106 52.40 - 69.86: 33 69.86 - 87.33: 6 Dihedral angle restraints: 3145 sinusoidal: 1045 harmonic: 2100 Sorted by residual: dihedral pdb=" CA THR J 92 " pdb=" C THR J 92 " pdb=" N GLY J 93 " pdb=" CA GLY J 93 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LYS D 45 " pdb=" C LYS D 45 " pdb=" N GLU D 46 " pdb=" CA GLU D 46 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLN E 62 " pdb=" C GLN E 62 " pdb=" N VAL E 63 " pdb=" CA VAL E 63 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 3142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 560 0.037 - 0.074: 207 0.074 - 0.111: 116 0.111 - 0.147: 51 0.147 - 0.184: 1 Chirality restraints: 935 Sorted by residual: chirality pdb=" CA VAL I 95 " pdb=" N VAL I 95 " pdb=" C VAL I 95 " pdb=" CB VAL I 95 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CA VAL F 95 " pdb=" N VAL F 95 " pdb=" C VAL F 95 " pdb=" CB VAL F 95 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA VAL H 95 " pdb=" N VAL H 95 " pdb=" C VAL H 95 " pdb=" CB VAL H 95 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 932 not shown) Planarity restraints: 900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 66 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" C VAL G 66 " 0.018 2.00e-02 2.50e+03 pdb=" O VAL G 66 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY G 67 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 72 " 0.005 2.00e-02 2.50e+03 9.81e-03 9.63e-01 pdb=" C THR I 72 " -0.017 2.00e-02 2.50e+03 pdb=" O THR I 72 " 0.006 2.00e-02 2.50e+03 pdb=" N GLY I 73 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 72 " 0.005 2.00e-02 2.50e+03 9.07e-03 8.22e-01 pdb=" C THR H 72 " -0.016 2.00e-02 2.50e+03 pdb=" O THR H 72 " 0.006 2.00e-02 2.50e+03 pdb=" N GLY H 73 " 0.005 2.00e-02 2.50e+03 ... (remaining 897 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.96: 4 1.96 - 2.70: 77 2.70 - 3.43: 6758 3.43 - 4.17: 12987 4.17 - 4.90: 23529 Nonbonded interactions: 43355 Sorted by model distance: nonbonded pdb=" CZ PHE I 94 " pdb=" O ALA J 91 " model vdw 1.228 3.340 nonbonded pdb=" CE2 PHE I 94 " pdb=" O ALA J 91 " model vdw 1.431 3.340 nonbonded pdb=" CD1 PHE F 94 " pdb=" CB PHE G 94 " model vdw 1.650 3.740 nonbonded pdb=" CE2 PHE F 94 " pdb=" O ALA G 91 " model vdw 1.681 3.340 nonbonded pdb=" CE1 PHE F 94 " pdb=" CB PHE G 94 " model vdw 2.009 3.740 ... (remaining 43350 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' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.500 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.004 0.262 5326 Z= 0.379 Angle : 0.539 6.366 7185 Z= 0.321 Chirality : 0.053 0.184 935 Planarity : 0.002 0.010 900 Dihedral : 18.214 87.331 1815 Min Nonbonded Distance : 1.228 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 30.58 % Favored : 69.42 % 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 aren not related in a simple way. whole: -1.82 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR B 39 PHE 0.009 0.002 PHE C 94 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 5325) covalent geometry : angle 0.53920 ( 7185) hydrogen bonds : bond 0.14806 ( 119) hydrogen bonds : angle 7.79633 ( 414) Misc. bond : bond 0.26204 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.234 Fit side-chains REVERT: C 38 LEU cc_start: 0.8440 (mp) cc_final: 0.7913 (tt) REVERT: F 60 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7695 (ptmt) REVERT: F 97 LYS cc_start: 0.7781 (mttt) cc_final: 0.6999 (mptt) REVERT: G 60 LYS cc_start: 0.8212 (ptpt) cc_final: 0.7811 (ptmt) REVERT: G 62 GLN cc_start: 0.8084 (tt0) cc_final: 0.7834 (tm-30) REVERT: H 60 LYS cc_start: 0.8195 (ptpt) cc_final: 0.7560 (ptmt) REVERT: I 60 LYS cc_start: 0.8224 (ptpt) cc_final: 0.7760 (ptmt) REVERT: J 60 LYS cc_start: 0.8068 (tttm) cc_final: 0.7676 (mptp) REVERT: J 97 LYS cc_start: 0.8027 (mttt) cc_final: 0.6562 (pmtt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.5660 time to fit residues: 63.5059 Evaluate side-chains 101 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN I 65 ASN J 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.163402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.138299 restraints weight = 5371.226| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.77 r_work: 0.3923 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5326 Z= 0.189 Angle : 0.605 17.453 7185 Z= 0.330 Chirality : 0.053 0.149 935 Planarity : 0.002 0.021 900 Dihedral : 5.610 23.967 770 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 8.65 % Allowed : 24.23 % Favored : 67.12 % 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 aren not related in a simple way. whole: -1.86 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.009 0.003 PHE A 94 HIS 0.007 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5325) covalent geometry : angle 0.60523 ( 7185) hydrogen bonds : bond 0.02936 ( 119) hydrogen bonds : angle 5.14614 ( 414) Misc. bond : bond 0.00715 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 0.207 Fit side-chains REVERT: A 28 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: C 38 LEU cc_start: 0.8354 (mp) cc_final: 0.7861 (tt) REVERT: D 57 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.5839 (mt-10) REVERT: F 60 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7637 (ptpt) REVERT: F 65 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7681 (p0) REVERT: F 83 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6276 (mt-10) REVERT: F 97 LYS cc_start: 0.7953 (mttt) cc_final: 0.6998 (tptt) REVERT: G 60 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7679 (ptmt) REVERT: G 62 GLN cc_start: 0.8141 (tt0) cc_final: 0.7817 (tm-30) REVERT: G 94 PHE cc_start: 0.5852 (OUTLIER) cc_final: 0.5362 (t80) REVERT: H 60 LYS cc_start: 0.8180 (ptpt) cc_final: 0.7467 (ptmt) REVERT: I 60 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7729 (ptmt) REVERT: J 60 LYS cc_start: 0.8382 (tttm) cc_final: 0.7765 (mptt) REVERT: J 97 LYS cc_start: 0.8110 (mttt) cc_final: 0.6695 (pmtt) outliers start: 45 outliers final: 24 residues processed: 125 average time/residue: 0.5921 time to fit residues: 76.5945 Evaluate side-chains 126 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 0.0270 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.165024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.140063 restraints weight = 5270.978| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.77 r_work: 0.3945 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5326 Z= 0.149 Angle : 0.527 7.739 7185 Z= 0.297 Chirality : 0.052 0.144 935 Planarity : 0.002 0.016 900 Dihedral : 5.375 23.433 770 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 8.08 % Allowed : 23.65 % Favored : 68.27 % 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 aren not related in a simple way. whole: -1.82 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR B 39 PHE 0.008 0.002 PHE D 94 HIS 0.006 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5325) covalent geometry : angle 0.52681 ( 7185) hydrogen bonds : bond 0.02496 ( 119) hydrogen bonds : angle 4.83361 ( 414) Misc. bond : bond 0.00260 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.152 Fit side-chains REVERT: A 28 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: C 38 LEU cc_start: 0.8397 (mp) cc_final: 0.7919 (tt) REVERT: C 83 GLU cc_start: 0.7678 (mp0) cc_final: 0.7466 (mp0) REVERT: D 57 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5783 (mt-10) REVERT: D 83 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: E 100 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6575 (mp) REVERT: F 60 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7630 (ptpt) REVERT: F 97 LYS cc_start: 0.7885 (mttt) cc_final: 0.6933 (tptt) REVERT: G 60 LYS cc_start: 0.8183 (ptpt) cc_final: 0.7664 (ptmt) REVERT: G 62 GLN cc_start: 0.8142 (tt0) cc_final: 0.7836 (tm-30) REVERT: G 94 PHE cc_start: 0.5816 (OUTLIER) cc_final: 0.5397 (t80) REVERT: H 60 LYS cc_start: 0.8205 (ptpt) cc_final: 0.7476 (ptmt) REVERT: I 60 LYS cc_start: 0.8261 (ptpt) cc_final: 0.7688 (ptmt) REVERT: I 94 PHE cc_start: 0.5722 (OUTLIER) cc_final: 0.4729 (t80) REVERT: J 60 LYS cc_start: 0.8290 (tttm) cc_final: 0.7728 (mptp) REVERT: J 97 LYS cc_start: 0.8087 (mttt) cc_final: 0.6677 (pmtt) outliers start: 42 outliers final: 26 residues processed: 122 average time/residue: 0.6032 time to fit residues: 76.0874 Evaluate side-chains 131 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 65 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 0.0000 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.158140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.133287 restraints weight = 5352.038| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.76 r_work: 0.3842 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 5326 Z= 0.325 Angle : 0.692 8.540 7185 Z= 0.395 Chirality : 0.056 0.149 935 Planarity : 0.003 0.015 900 Dihedral : 6.415 26.593 770 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 10.00 % Allowed : 21.73 % Favored : 68.27 % 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 aren not related in a simple way. whole: -2.05 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR D 39 PHE 0.013 0.004 PHE I 94 HIS 0.009 0.003 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00695 ( 5325) covalent geometry : angle 0.69185 ( 7185) hydrogen bonds : bond 0.03169 ( 119) hydrogen bonds : angle 5.05285 ( 414) Misc. bond : bond 0.00312 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 103 time to evaluate : 0.215 Fit side-chains REVERT: D 57 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5768 (mt-10) REVERT: D 83 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: E 38 LEU cc_start: 0.8676 (mp) cc_final: 0.8234 (tt) REVERT: E 83 GLU cc_start: 0.7247 (mp0) cc_final: 0.6959 (mp0) REVERT: E 100 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6746 (mp) REVERT: F 60 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7592 (ptpt) REVERT: F 65 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7808 (p0) REVERT: F 83 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6650 (mm-30) REVERT: F 97 LYS cc_start: 0.7954 (mttt) cc_final: 0.6989 (tptt) REVERT: G 60 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7556 (ptmt) REVERT: G 62 GLN cc_start: 0.8162 (tt0) cc_final: 0.7804 (tm-30) REVERT: G 94 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.5403 (t80) REVERT: H 58 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8452 (mttt) REVERT: H 60 LYS cc_start: 0.8209 (ptpt) cc_final: 0.7499 (ptmt) REVERT: H 65 ASN cc_start: 0.8151 (p0) cc_final: 0.7845 (p0) REVERT: I 58 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8461 (mttt) REVERT: I 60 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7630 (ptmt) REVERT: I 62 GLN cc_start: 0.8321 (tt0) cc_final: 0.7849 (tp40) REVERT: I 94 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.4899 (t80) REVERT: J 60 LYS cc_start: 0.8490 (tttm) cc_final: 0.7887 (mptp) REVERT: J 97 LYS cc_start: 0.8140 (mttt) cc_final: 0.6702 (pmtt) outliers start: 52 outliers final: 32 residues processed: 134 average time/residue: 0.6049 time to fit residues: 83.9121 Evaluate side-chains 144 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 67 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN I 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.159557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.134616 restraints weight = 5513.286| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.79 r_work: 0.3873 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5326 Z= 0.254 Angle : 0.626 8.600 7185 Z= 0.358 Chirality : 0.055 0.152 935 Planarity : 0.003 0.012 900 Dihedral : 6.112 26.215 770 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 11.15 % Allowed : 20.58 % Favored : 68.27 % 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 aren not related in a simple way. whole: -2.08 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR D 39 PHE 0.012 0.003 PHE D 94 HIS 0.008 0.003 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 5325) covalent geometry : angle 0.62571 ( 7185) hydrogen bonds : bond 0.02808 ( 119) hydrogen bonds : angle 4.88226 ( 414) Misc. bond : bond 0.00226 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 101 time to evaluate : 0.138 Fit side-chains REVERT: A 32 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7545 (mtmt) REVERT: C 83 GLU cc_start: 0.7724 (mp0) cc_final: 0.7489 (mp0) REVERT: D 57 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5685 (mt-10) REVERT: D 83 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: E 38 LEU cc_start: 0.8659 (mp) cc_final: 0.8234 (tt) REVERT: E 83 GLU cc_start: 0.7250 (mp0) cc_final: 0.6900 (mp0) REVERT: E 100 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6920 (mp) REVERT: F 60 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7612 (ptpt) REVERT: F 65 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7776 (p0) REVERT: F 83 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6628 (mm-30) REVERT: F 97 LYS cc_start: 0.7897 (mttt) cc_final: 0.6936 (tptt) REVERT: G 60 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7619 (ptmt) REVERT: G 62 GLN cc_start: 0.8191 (tt0) cc_final: 0.7879 (tm-30) REVERT: G 83 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6975 (mt-10) REVERT: G 94 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5459 (t80) REVERT: H 60 LYS cc_start: 0.8197 (ptpt) cc_final: 0.7507 (ptmt) REVERT: I 38 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8407 (mp) REVERT: I 58 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8454 (mttt) REVERT: I 60 LYS cc_start: 0.8218 (ptpt) cc_final: 0.7655 (ptmt) REVERT: I 94 PHE cc_start: 0.5807 (OUTLIER) cc_final: 0.4771 (t80) REVERT: J 60 LYS cc_start: 0.8466 (tttm) cc_final: 0.7881 (mptp) REVERT: J 97 LYS cc_start: 0.8121 (mttt) cc_final: 0.6705 (pmtt) outliers start: 58 outliers final: 33 residues processed: 140 average time/residue: 0.5651 time to fit residues: 81.9317 Evaluate side-chains 144 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.161927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.137192 restraints weight = 5402.366| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.77 r_work: 0.3894 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5326 Z= 0.188 Angle : 0.573 7.909 7185 Z= 0.325 Chirality : 0.053 0.148 935 Planarity : 0.002 0.022 900 Dihedral : 5.826 25.321 770 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 9.23 % Allowed : 22.88 % Favored : 67.88 % 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 aren not related in a simple way. whole: -2.02 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.010 0.003 PHE D 94 HIS 0.007 0.003 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 5325) covalent geometry : angle 0.57250 ( 7185) hydrogen bonds : bond 0.02450 ( 119) hydrogen bonds : angle 4.73897 ( 414) Misc. bond : bond 0.00449 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.161 Fit side-chains REVERT: A 32 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7519 (mtmt) REVERT: C 38 LEU cc_start: 0.8387 (mp) cc_final: 0.7915 (tt) REVERT: C 83 GLU cc_start: 0.7658 (mp0) cc_final: 0.7449 (mp0) REVERT: D 57 GLU cc_start: 0.6139 (OUTLIER) cc_final: 0.5639 (mt-10) REVERT: D 83 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: E 20 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: E 38 LEU cc_start: 0.8634 (mp) cc_final: 0.8208 (tt) REVERT: F 60 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7578 (ptpt) REVERT: F 97 LYS cc_start: 0.7901 (mttt) cc_final: 0.6932 (tptt) REVERT: G 60 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7600 (ptmt) REVERT: G 62 GLN cc_start: 0.8168 (tt0) cc_final: 0.7862 (tm-30) REVERT: G 94 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5642 (t80) REVERT: H 58 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8445 (mttt) REVERT: H 60 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7465 (ptmt) REVERT: I 38 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8391 (mp) REVERT: I 60 LYS cc_start: 0.8245 (ptpt) cc_final: 0.7656 (ptmt) REVERT: I 94 PHE cc_start: 0.5808 (OUTLIER) cc_final: 0.4791 (t80) REVERT: J 60 LYS cc_start: 0.8373 (tttm) cc_final: 0.7803 (mptp) REVERT: J 97 LYS cc_start: 0.8094 (mttt) cc_final: 0.6668 (pmtt) outliers start: 48 outliers final: 29 residues processed: 130 average time/residue: 0.5885 time to fit residues: 79.1376 Evaluate side-chains 137 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 26 optimal weight: 0.0040 chunk 5 optimal weight: 0.0570 chunk 58 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 overall best weight: 0.3510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN F 50 HIS I 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.172018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.147717 restraints weight = 5291.072| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.75 r_work: 0.4035 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5326 Z= 0.079 Angle : 0.453 6.732 7185 Z= 0.259 Chirality : 0.051 0.138 935 Planarity : 0.001 0.008 900 Dihedral : 4.893 21.119 770 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.04 % Allowed : 28.85 % Favored : 67.12 % 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 aren not related in a simple way. whole: -1.77 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR D 39 PHE 0.007 0.001 PHE D 94 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00163 ( 5325) covalent geometry : angle 0.45304 ( 7185) hydrogen bonds : bond 0.01762 ( 119) hydrogen bonds : angle 4.34700 ( 414) Misc. bond : bond 0.00160 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.222 Fit side-chains REVERT: A 32 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7523 (mtmt) REVERT: C 38 LEU cc_start: 0.8307 (mp) cc_final: 0.7812 (tt) REVERT: D 57 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5576 (mt-10) REVERT: E 20 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: F 60 LYS cc_start: 0.8158 (ptpt) cc_final: 0.7662 (ptmt) REVERT: F 97 LYS cc_start: 0.7847 (mttt) cc_final: 0.6999 (mptt) REVERT: G 60 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7691 (ptmt) REVERT: G 62 GLN cc_start: 0.8127 (tt0) cc_final: 0.7858 (tm-30) REVERT: G 94 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.5360 (t80) REVERT: H 58 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8407 (mttt) REVERT: H 60 LYS cc_start: 0.8183 (ptpt) cc_final: 0.7563 (ptmt) REVERT: I 38 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8289 (mp) REVERT: I 60 LYS cc_start: 0.8017 (ptpt) cc_final: 0.7503 (ptmt) REVERT: I 94 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.4676 (t80) REVERT: J 60 LYS cc_start: 0.8181 (tttm) cc_final: 0.7593 (mptp) REVERT: J 97 LYS cc_start: 0.8035 (mttt) cc_final: 0.6610 (pmtt) outliers start: 21 outliers final: 8 residues processed: 113 average time/residue: 0.5549 time to fit residues: 64.9764 Evaluate side-chains 112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 94 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.161605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.137079 restraints weight = 5394.036| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.77 r_work: 0.3908 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5326 Z= 0.205 Angle : 0.571 6.750 7185 Z= 0.325 Chirality : 0.053 0.144 935 Planarity : 0.002 0.018 900 Dihedral : 5.699 23.723 770 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 6.54 % Allowed : 26.54 % Favored : 66.92 % 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 aren not related in a simple way. whole: -1.87 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.011 0.003 PHE D 94 HIS 0.007 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 5325) covalent geometry : angle 0.57085 ( 7185) hydrogen bonds : bond 0.02427 ( 119) hydrogen bonds : angle 4.66858 ( 414) Misc. bond : bond 0.00427 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.179 Fit side-chains REVERT: A 32 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7521 (mtmt) REVERT: C 38 LEU cc_start: 0.8414 (mp) cc_final: 0.7921 (tt) REVERT: C 83 GLU cc_start: 0.7674 (mp0) cc_final: 0.7473 (mp0) REVERT: D 57 GLU cc_start: 0.6147 (OUTLIER) cc_final: 0.5643 (mt-10) REVERT: E 20 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: E 38 LEU cc_start: 0.8676 (mp) cc_final: 0.8238 (tt) REVERT: F 60 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7584 (ptmt) REVERT: F 65 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7769 (p0) REVERT: F 97 LYS cc_start: 0.7955 (mttt) cc_final: 0.7056 (mptt) REVERT: G 60 LYS cc_start: 0.8164 (ptpt) cc_final: 0.7622 (ptmt) REVERT: G 62 GLN cc_start: 0.8175 (tt0) cc_final: 0.7858 (tm-30) REVERT: G 94 PHE cc_start: 0.6039 (OUTLIER) cc_final: 0.5494 (t80) REVERT: H 58 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8439 (mttt) REVERT: H 60 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7509 (ptmt) REVERT: I 38 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8350 (mp) REVERT: I 60 LYS cc_start: 0.8247 (ptpt) cc_final: 0.7654 (ptmt) REVERT: I 94 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.4766 (t80) REVERT: J 60 LYS cc_start: 0.8400 (tttm) cc_final: 0.7814 (mptp) REVERT: J 97 LYS cc_start: 0.8134 (mttt) cc_final: 0.6740 (pmtt) outliers start: 34 outliers final: 16 residues processed: 130 average time/residue: 0.5410 time to fit residues: 72.8386 Evaluate side-chains 132 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 61 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.162519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.137902 restraints weight = 5432.685| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.76 r_work: 0.3917 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5326 Z= 0.198 Angle : 0.582 7.070 7185 Z= 0.328 Chirality : 0.054 0.148 935 Planarity : 0.002 0.027 900 Dihedral : 5.743 24.022 770 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 7.50 % Allowed : 24.81 % Favored : 67.69 % 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 aren not related in a simple way. whole: -1.91 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.010 0.003 PHE D 94 HIS 0.008 0.003 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 5325) covalent geometry : angle 0.58193 ( 7185) hydrogen bonds : bond 0.02390 ( 119) hydrogen bonds : angle 4.65722 ( 414) Misc. bond : bond 0.00537 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.213 Fit side-chains REVERT: A 32 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7507 (mtmt) REVERT: A 83 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: C 38 LEU cc_start: 0.8384 (mp) cc_final: 0.7906 (tt) REVERT: C 83 GLU cc_start: 0.7701 (mp0) cc_final: 0.7477 (mp0) REVERT: D 57 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5634 (mt-10) REVERT: E 20 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: E 38 LEU cc_start: 0.8605 (mp) cc_final: 0.8190 (tt) REVERT: F 60 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7601 (ptmt) REVERT: F 65 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7727 (p0) REVERT: F 97 LYS cc_start: 0.7910 (mttt) cc_final: 0.6947 (tptt) REVERT: G 60 LYS cc_start: 0.8155 (ptpt) cc_final: 0.7615 (ptmt) REVERT: G 62 GLN cc_start: 0.8175 (tt0) cc_final: 0.7853 (tm-30) REVERT: G 94 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.5503 (t80) REVERT: H 58 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8446 (mttt) REVERT: H 60 LYS cc_start: 0.8174 (ptpt) cc_final: 0.7525 (ptmt) REVERT: I 38 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8379 (mp) REVERT: I 60 LYS cc_start: 0.8267 (ptpt) cc_final: 0.7683 (ptmt) REVERT: I 94 PHE cc_start: 0.5722 (OUTLIER) cc_final: 0.4707 (t80) REVERT: J 60 LYS cc_start: 0.8394 (tttm) cc_final: 0.7806 (mptp) REVERT: J 97 LYS cc_start: 0.8121 (mttt) cc_final: 0.6713 (pmtt) outliers start: 39 outliers final: 22 residues processed: 123 average time/residue: 0.5408 time to fit residues: 68.8086 Evaluate side-chains 136 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 61 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.156779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.132028 restraints weight = 5508.477| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.78 r_work: 0.3840 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 5326 Z= 0.402 Angle : 0.798 12.661 7185 Z= 0.449 Chirality : 0.060 0.213 935 Planarity : 0.004 0.043 900 Dihedral : 6.827 30.644 770 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 8.08 % Allowed : 24.04 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.28), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR D 39 PHE 0.015 0.004 PHE I 94 HIS 0.011 0.004 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00862 ( 5325) covalent geometry : angle 0.79814 ( 7185) hydrogen bonds : bond 0.03233 ( 119) hydrogen bonds : angle 5.02405 ( 414) Misc. bond : bond 0.01017 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 0.158 Fit side-chains REVERT: A 32 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7532 (mtmt) REVERT: C 42 SER cc_start: 0.8845 (m) cc_final: 0.8606 (p) REVERT: D 57 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5691 (mt-10) REVERT: E 20 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: E 38 LEU cc_start: 0.8760 (mp) cc_final: 0.8296 (tt) REVERT: F 60 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7678 (ptpt) REVERT: F 65 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7853 (p0) REVERT: F 83 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6597 (mm-30) REVERT: F 97 LYS cc_start: 0.8011 (mttt) cc_final: 0.7150 (mptt) REVERT: G 60 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7612 (ptmt) REVERT: G 62 GLN cc_start: 0.8257 (tt0) cc_final: 0.7858 (tm-30) REVERT: G 83 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7044 (mt-10) REVERT: G 94 PHE cc_start: 0.5869 (OUTLIER) cc_final: 0.5332 (t80) REVERT: H 58 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8473 (mttt) REVERT: H 60 LYS cc_start: 0.8201 (ptpt) cc_final: 0.7542 (ptmt) REVERT: H 65 ASN cc_start: 0.8209 (p0) cc_final: 0.7971 (p0) REVERT: I 60 LYS cc_start: 0.8323 (ptpt) cc_final: 0.7706 (ptmt) REVERT: I 62 GLN cc_start: 0.8337 (tt0) cc_final: 0.7920 (tp40) REVERT: I 94 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.4969 (t80) REVERT: J 60 LYS cc_start: 0.8522 (tttm) cc_final: 0.8002 (mptp) REVERT: J 97 LYS cc_start: 0.8135 (mttt) cc_final: 0.6769 (pmtt) outliers start: 42 outliers final: 26 residues processed: 137 average time/residue: 0.5927 time to fit residues: 84.1893 Evaluate side-chains 142 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.0060 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.166914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.142389 restraints weight = 5369.329| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.78 r_work: 0.3974 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5326 Z= 0.112 Angle : 0.520 6.939 7185 Z= 0.293 Chirality : 0.052 0.143 935 Planarity : 0.002 0.012 900 Dihedral : 5.342 22.966 770 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.62 % Allowed : 27.69 % Favored : 67.69 % 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 aren not related in a simple way. whole: -1.94 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR B 39 PHE 0.009 0.002 PHE D 94 HIS 0.005 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 5325) covalent geometry : angle 0.51965 ( 7185) hydrogen bonds : bond 0.02031 ( 119) hydrogen bonds : angle 4.49971 ( 414) Misc. bond : bond 0.00260 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2313.02 seconds wall clock time: 40 minutes 0.59 seconds (2400.59 seconds total)