Starting phenix.real_space_refine on Thu Jul 24 05:15:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obp_70295/07_2025/9obp_70295_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obp_70295/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9obp_70295/07_2025/9obp_70295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obp_70295/07_2025/9obp_70295.map" model { file = "/net/cci-nas-00/data/ceres_data/9obp_70295/07_2025/9obp_70295_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obp_70295/07_2025/9obp_70295_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.41, per 1000 atoms: 0.83 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: 1.48 Conformation dependent library (CDL) restraints added in 769.5 milliseconds 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: 0.85 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: 1.38 Time building geometry restraints manager: 1.61 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: 0.01 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.650 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.003 0.001 HIS H 50 PHE 0.009 0.002 PHE C 94 TYR 0.008 0.001 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.14806 ( 119) hydrogen bonds : angle 7.79633 ( 414) covalent geometry : bond 0.00225 ( 5325) covalent geometry : angle 0.53920 ( 7185) 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 : 0.510 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: 1.3349 time to fit residues: 149.4167 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 : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 40 optimal weight: 0.0870 chunk 63 optimal weight: 7.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- 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** J 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.158922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.133991 restraints weight = 5338.018| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.76 r_work: 0.3866 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 5326 Z= 0.307 Angle : 0.722 18.598 7185 Z= 0.398 Chirality : 0.057 0.155 935 Planarity : 0.003 0.026 900 Dihedral : 6.321 26.488 770 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 9.23 % Allowed : 23.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS H 50 PHE 0.011 0.003 PHE D 94 TYR 0.012 0.003 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 119) hydrogen bonds : angle 5.36060 ( 414) covalent geometry : bond 0.00657 ( 5325) covalent geometry : angle 0.72191 ( 7185) Misc. bond : bond 0.00683 ( 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 150 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.543 Fit side-chains REVERT: D 57 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5786 (mt-10) REVERT: E 100 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6657 (mp) REVERT: F 60 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7631 (ptpt) REVERT: F 65 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7757 (p0) REVERT: F 83 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6430 (mt-10) REVERT: F 97 LYS cc_start: 0.7956 (mttt) cc_final: 0.6997 (tptt) REVERT: G 60 LYS cc_start: 0.8234 (ptpt) cc_final: 0.7641 (ptmt) REVERT: G 62 GLN cc_start: 0.8143 (tt0) cc_final: 0.7799 (tm-30) REVERT: H 57 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: H 60 LYS cc_start: 0.8274 (ptpt) cc_final: 0.7747 (ptpp) REVERT: I 58 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8435 (mttt) REVERT: I 60 LYS cc_start: 0.8309 (ptpt) cc_final: 0.7705 (ptmt) REVERT: J 60 LYS cc_start: 0.8494 (tttm) cc_final: 0.7914 (mptt) REVERT: J 97 LYS cc_start: 0.8201 (mttt) cc_final: 0.6856 (pmtt) outliers start: 48 outliers final: 29 residues processed: 132 average time/residue: 1.3542 time to fit residues: 185.0682 Evaluate side-chains 133 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 G residue 38 LEU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 75 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 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 49 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.164180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.139264 restraints weight = 5306.974| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.77 r_work: 0.3935 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1265 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= 0.154 Angle : 0.532 8.060 7185 Z= 0.303 Chirality : 0.052 0.145 935 Planarity : 0.002 0.016 900 Dihedral : 5.535 24.615 770 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 9.04 % Allowed : 22.31 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (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 HIS 0.007 0.002 HIS J 50 PHE 0.009 0.002 PHE I 94 TYR 0.009 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02514 ( 119) hydrogen bonds : angle 4.85704 ( 414) covalent geometry : bond 0.00324 ( 5325) covalent geometry : angle 0.53241 ( 7185) 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 150 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 103 time to evaluate : 0.480 Fit side-chains REVERT: C 38 LEU cc_start: 0.8411 (mp) cc_final: 0.7945 (tt) REVERT: D 57 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5680 (mt-10) REVERT: F 60 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7583 (ptpt) REVERT: F 97 LYS cc_start: 0.7859 (mttt) cc_final: 0.6893 (tptt) REVERT: G 60 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7640 (ptmt) REVERT: G 62 GLN cc_start: 0.8145 (tt0) cc_final: 0.7842 (tm-30) REVERT: G 94 PHE cc_start: 0.6010 (OUTLIER) cc_final: 0.5524 (t80) REVERT: H 60 LYS cc_start: 0.8225 (ptpt) cc_final: 0.7519 (ptmt) REVERT: I 60 LYS cc_start: 0.8281 (ptpt) cc_final: 0.7701 (ptmt) REVERT: I 94 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.4680 (t80) REVERT: J 60 LYS cc_start: 0.8309 (tttm) cc_final: 0.7741 (mptt) REVERT: J 97 LYS cc_start: 0.8078 (mttt) cc_final: 0.6657 (pmtt) outliers start: 47 outliers final: 27 residues processed: 131 average time/residue: 1.3481 time to fit residues: 182.9523 Evaluate side-chains 131 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 38 LEU 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 81 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 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 51 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 26 optimal weight: 0.0370 overall best weight: 1.2864 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.163372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.138542 restraints weight = 5389.445| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.78 r_work: 0.3925 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5326 Z= 0.159 Angle : 0.533 7.685 7185 Z= 0.306 Chirality : 0.052 0.145 935 Planarity : 0.002 0.010 900 Dihedral : 5.512 24.173 770 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 8.65 % Allowed : 23.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 50 PHE 0.009 0.002 PHE D 94 TYR 0.010 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02377 ( 119) hydrogen bonds : angle 4.73254 ( 414) covalent geometry : bond 0.00337 ( 5325) covalent geometry : angle 0.53321 ( 7185) Misc. bond : bond 0.00179 ( 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 149 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 0.514 Fit side-chains REVERT: A 28 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: C 38 LEU cc_start: 0.8404 (mp) cc_final: 0.7919 (tt) REVERT: D 57 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5706 (mt-10) REVERT: E 57 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6819 (mt-10) REVERT: F 60 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7589 (ptpt) REVERT: F 97 LYS cc_start: 0.7922 (mttt) cc_final: 0.6946 (tptt) REVERT: G 60 LYS cc_start: 0.8138 (ptpt) cc_final: 0.7588 (ptmt) REVERT: G 62 GLN cc_start: 0.8152 (tt0) cc_final: 0.7838 (tm-30) REVERT: G 94 PHE cc_start: 0.6025 (OUTLIER) cc_final: 0.5532 (t80) REVERT: H 60 LYS cc_start: 0.8180 (ptpt) cc_final: 0.7505 (ptmt) REVERT: I 60 LYS cc_start: 0.8262 (ptpt) cc_final: 0.7684 (ptmt) REVERT: I 94 PHE cc_start: 0.5809 (OUTLIER) cc_final: 0.4766 (t80) REVERT: J 60 LYS cc_start: 0.8332 (tttm) cc_final: 0.7741 (mptt) REVERT: J 97 LYS cc_start: 0.8120 (mttt) cc_final: 0.6689 (pmtt) outliers start: 45 outliers final: 32 residues processed: 128 average time/residue: 1.3449 time to fit residues: 178.3359 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 : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 28 GLU 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 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 35 GLU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 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 75 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 38 LEU 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 59 THR 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 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 18 optimal weight: 4.9990 chunk 69 optimal weight: 0.0570 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 2.7704 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.157874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.133218 restraints weight = 5413.468| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.77 r_work: 0.3841 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5326 Z= 0.301 Angle : 0.667 8.235 7185 Z= 0.384 Chirality : 0.056 0.150 935 Planarity : 0.003 0.014 900 Dihedral : 6.303 26.272 770 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 10.77 % Allowed : 21.73 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.28), 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 HIS 0.008 0.003 HIS H 50 PHE 0.012 0.003 PHE D 94 TYR 0.012 0.003 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03024 ( 119) hydrogen bonds : angle 4.98809 ( 414) covalent geometry : bond 0.00643 ( 5325) covalent geometry : angle 0.66709 ( 7185) Misc. bond : bond 0.00245 ( 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 157 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 101 time to evaluate : 0.617 Fit side-chains REVERT: A 32 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7524 (mtmt) REVERT: D 57 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5659 (mt-10) REVERT: E 20 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: E 38 LEU cc_start: 0.8686 (mp) cc_final: 0.8240 (tt) REVERT: E 57 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6859 (mt-10) REVERT: E 100 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6857 (mp) REVERT: F 60 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7603 (ptpt) REVERT: F 65 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7790 (p0) REVERT: F 83 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6656 (mm-30) REVERT: F 97 LYS cc_start: 0.7928 (mttt) cc_final: 0.7037 (mptt) REVERT: G 60 LYS cc_start: 0.8174 (ptpt) cc_final: 0.7563 (ptmt) REVERT: G 62 GLN cc_start: 0.8169 (tt0) cc_final: 0.7819 (tm-30) REVERT: G 94 PHE cc_start: 0.5947 (OUTLIER) cc_final: 0.5381 (t80) REVERT: H 58 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8422 (mttt) REVERT: H 60 LYS cc_start: 0.8206 (ptpt) cc_final: 0.7496 (ptmt) REVERT: H 65 ASN cc_start: 0.8173 (p0) cc_final: 0.7916 (p0) REVERT: I 58 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8464 (mttt) REVERT: I 60 LYS cc_start: 0.8251 (ptpt) cc_final: 0.7616 (ptmt) REVERT: I 94 PHE cc_start: 0.5883 (OUTLIER) cc_final: 0.4883 (t80) REVERT: J 60 LYS cc_start: 0.8500 (tttm) cc_final: 0.7897 (mptt) REVERT: J 97 LYS cc_start: 0.8194 (mttt) cc_final: 0.6806 (pmtt) outliers start: 56 outliers final: 34 residues processed: 136 average time/residue: 1.2960 time to fit residues: 182.9637 Evaluate side-chains 145 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 99 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 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 E residue 20 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 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 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 38 LEU 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 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 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 61 GLU 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 58 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.158566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.133833 restraints weight = 5397.223| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.77 r_work: 0.3850 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5326 Z= 0.278 Angle : 0.648 8.457 7185 Z= 0.372 Chirality : 0.055 0.153 935 Planarity : 0.003 0.013 900 Dihedral : 6.293 26.822 770 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 10.96 % Allowed : 21.73 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS J 50 PHE 0.012 0.003 PHE D 94 TYR 0.011 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02891 ( 119) hydrogen bonds : angle 4.88874 ( 414) covalent geometry : bond 0.00593 ( 5325) covalent geometry : angle 0.64809 ( 7185) Misc. bond : bond 0.00200 ( 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 158 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 101 time to evaluate : 0.535 Fit side-chains REVERT: A 32 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7536 (mtmt) REVERT: A 57 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6161 (mp0) REVERT: D 57 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5647 (mt-10) REVERT: D 83 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: E 20 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: E 38 LEU cc_start: 0.8660 (mp) cc_final: 0.8224 (tt) REVERT: E 57 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6808 (mt-10) REVERT: E 83 GLU cc_start: 0.7272 (mp0) cc_final: 0.6971 (mp0) REVERT: F 60 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7606 (ptpt) REVERT: F 65 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7784 (p0) REVERT: F 83 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6649 (mm-30) REVERT: F 97 LYS cc_start: 0.7905 (mttt) cc_final: 0.6935 (tptt) REVERT: G 60 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7592 (ptmt) REVERT: G 62 GLN cc_start: 0.8185 (tt0) cc_final: 0.7857 (tm-30) REVERT: G 94 PHE cc_start: 0.5976 (OUTLIER) cc_final: 0.5444 (t80) REVERT: H 58 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8421 (mttt) REVERT: H 60 LYS cc_start: 0.8184 (ptpt) cc_final: 0.7523 (ptmt) REVERT: I 58 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8457 (mttt) REVERT: I 60 LYS cc_start: 0.8213 (ptpt) cc_final: 0.7587 (ptmt) REVERT: I 94 PHE cc_start: 0.5900 (OUTLIER) cc_final: 0.4889 (t80) REVERT: J 60 LYS cc_start: 0.8441 (tttm) cc_final: 0.7868 (mptt) REVERT: J 97 LYS cc_start: 0.8167 (mttt) cc_final: 0.6763 (pmtt) outliers start: 57 outliers final: 36 residues processed: 135 average time/residue: 1.3951 time to fit residues: 194.9147 Evaluate side-chains 148 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 23 LYS 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 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 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 57 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 75 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 38 LEU 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 75 THR 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 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 61 GLU 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 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 67 optimal weight: 0.0070 chunk 54 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.169047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.144797 restraints weight = 5265.356| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.75 r_work: 0.4008 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5326 Z= 0.094 Angle : 0.473 7.304 7185 Z= 0.270 Chirality : 0.052 0.140 935 Planarity : 0.002 0.014 900 Dihedral : 5.106 23.602 770 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.15 % Allowed : 26.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (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 HIS 0.005 0.002 HIS J 50 PHE 0.008 0.002 PHE D 94 TYR 0.008 0.001 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.01928 ( 119) hydrogen bonds : angle 4.46837 ( 414) covalent geometry : bond 0.00195 ( 5325) covalent geometry : angle 0.47308 ( 7185) Misc. bond : bond 0.00192 ( 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 140 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.593 Fit side-chains REVERT: A 32 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7519 (mtmt) REVERT: C 38 LEU cc_start: 0.8401 (mp) cc_final: 0.7937 (tt) REVERT: D 57 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5582 (mt-10) REVERT: D 83 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: E 20 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: E 83 GLU cc_start: 0.7299 (mp0) cc_final: 0.7089 (mp0) REVERT: F 60 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7665 (ptmt) REVERT: F 97 LYS cc_start: 0.7849 (mttt) cc_final: 0.6980 (mptt) REVERT: G 60 LYS cc_start: 0.8192 (ptpt) cc_final: 0.7655 (ptmt) REVERT: G 62 GLN cc_start: 0.8119 (tt0) cc_final: 0.7855 (tm-30) REVERT: G 94 PHE cc_start: 0.5818 (OUTLIER) cc_final: 0.5444 (t80) REVERT: H 58 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8424 (mttt) REVERT: H 60 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7492 (ptmt) REVERT: I 60 LYS cc_start: 0.8093 (ptpt) cc_final: 0.7570 (ptmt) REVERT: I 94 PHE cc_start: 0.5653 (OUTLIER) cc_final: 0.4601 (t80) REVERT: J 60 LYS cc_start: 0.8247 (tttm) cc_final: 0.7668 (mptp) REVERT: J 97 LYS cc_start: 0.8060 (mttt) cc_final: 0.6610 (pmtt) outliers start: 32 outliers final: 14 residues processed: 123 average time/residue: 1.3299 time to fit residues: 169.5881 Evaluate side-chains 124 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 42 SER 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 44 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.0060 chunk 2 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.0402 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.160343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135876 restraints weight = 5350.652| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.76 r_work: 0.3889 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5326 Z= 0.232 Angle : 0.608 7.338 7185 Z= 0.345 Chirality : 0.054 0.147 935 Planarity : 0.003 0.026 900 Dihedral : 5.940 25.651 770 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 7.69 % Allowed : 25.77 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS H 50 PHE 0.011 0.003 PHE D 94 TYR 0.010 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02577 ( 119) hydrogen bonds : angle 4.77565 ( 414) covalent geometry : bond 0.00495 ( 5325) covalent geometry : angle 0.60783 ( 7185) Misc. bond : bond 0.00584 ( 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: 40 poor density : 106 time to evaluate : 0.570 Fit side-chains REVERT: A 32 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7505 (mtmt) REVERT: A 83 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7557 (tp30) REVERT: C 38 LEU cc_start: 0.8420 (mp) cc_final: 0.7928 (tt) REVERT: D 28 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: D 57 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5612 (mt-10) REVERT: D 83 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: E 20 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: E 38 LEU cc_start: 0.8624 (mp) cc_final: 0.8207 (tt) REVERT: F 60 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7582 (ptpt) REVERT: F 65 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7794 (p0) REVERT: F 97 LYS cc_start: 0.7942 (mttt) cc_final: 0.7057 (mptt) REVERT: G 60 LYS cc_start: 0.8192 (ptpt) cc_final: 0.7608 (ptmt) REVERT: G 62 GLN cc_start: 0.8220 (tt0) cc_final: 0.7865 (tm-30) REVERT: G 94 PHE cc_start: 0.6015 (OUTLIER) cc_final: 0.5446 (t80) REVERT: H 58 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8439 (mttt) REVERT: H 60 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7497 (ptmt) REVERT: I 60 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7599 (ptmt) REVERT: I 62 GLN cc_start: 0.8252 (tt0) cc_final: 0.7836 (tp40) REVERT: I 94 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.4818 (t80) REVERT: J 60 LYS cc_start: 0.8445 (tttm) cc_final: 0.7830 (mptt) REVERT: J 97 LYS cc_start: 0.8153 (mttt) cc_final: 0.6780 (pmtt) outliers start: 40 outliers final: 23 residues processed: 126 average time/residue: 1.3555 time to fit residues: 176.8428 Evaluate side-chains 138 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 C residue 35 GLU Chi-restraints excluded: chain D residue 28 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 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 G residue 38 LEU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 45 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.168524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.144230 restraints weight = 5319.469| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.77 r_work: 0.3997 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5326 Z= 0.100 Angle : 0.476 6.635 7185 Z= 0.272 Chirality : 0.051 0.138 935 Planarity : 0.002 0.009 900 Dihedral : 5.126 24.775 770 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.77 % Allowed : 27.69 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.29), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 50 PHE 0.008 0.002 PHE D 94 TYR 0.009 0.001 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.01928 ( 119) hydrogen bonds : angle 4.44459 ( 414) covalent geometry : bond 0.00210 ( 5325) covalent geometry : angle 0.47590 ( 7185) Misc. bond : bond 0.00207 ( 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 134 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.634 Fit side-chains REVERT: A 32 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7571 (mtmt) REVERT: C 38 LEU cc_start: 0.8380 (mp) cc_final: 0.7884 (tt) REVERT: D 57 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5567 (mt-10) REVERT: E 20 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: F 60 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7598 (ptmt) REVERT: F 97 LYS cc_start: 0.7856 (mttt) cc_final: 0.7002 (mptt) REVERT: G 60 LYS cc_start: 0.8196 (ptpt) cc_final: 0.7656 (ptmt) REVERT: G 62 GLN cc_start: 0.8156 (tt0) cc_final: 0.7887 (tm-30) REVERT: G 94 PHE cc_start: 0.5822 (OUTLIER) cc_final: 0.5437 (t80) REVERT: H 58 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8390 (mttt) REVERT: H 60 LYS cc_start: 0.8145 (ptpt) cc_final: 0.7495 (ptmt) REVERT: I 60 LYS cc_start: 0.8101 (ptpt) cc_final: 0.7588 (ptmt) REVERT: I 94 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.4734 (t80) REVERT: J 60 LYS cc_start: 0.8283 (tttm) cc_final: 0.7679 (mptp) REVERT: J 97 LYS cc_start: 0.8089 (mttt) cc_final: 0.6668 (pmtt) outliers start: 30 outliers final: 18 residues processed: 114 average time/residue: 1.3958 time to fit residues: 164.9756 Evaluate side-chains 127 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 74 VAL 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 20 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.160793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.136443 restraints weight = 5405.249| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.75 r_work: 0.3898 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5326 Z= 0.224 Angle : 0.599 6.735 7185 Z= 0.340 Chirality : 0.054 0.144 935 Planarity : 0.003 0.024 900 Dihedral : 5.874 26.284 770 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.58 % Allowed : 27.69 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.008 0.003 HIS H 50 PHE 0.011 0.003 PHE D 94 TYR 0.011 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02528 ( 119) hydrogen bonds : angle 4.72558 ( 414) covalent geometry : bond 0.00479 ( 5325) covalent geometry : angle 0.59852 ( 7185) Misc. bond : bond 0.00533 ( 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 135 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.555 Fit side-chains REVERT: A 32 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7496 (mtmt) REVERT: C 38 LEU cc_start: 0.8419 (mp) cc_final: 0.7935 (tt) REVERT: D 57 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5620 (mt-10) REVERT: E 20 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: E 38 LEU cc_start: 0.8687 (mp) cc_final: 0.8261 (tt) REVERT: F 60 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7595 (ptmt) REVERT: F 65 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7778 (p0) REVERT: F 97 LYS cc_start: 0.7953 (mttt) cc_final: 0.7073 (mptt) REVERT: G 60 LYS cc_start: 0.8168 (ptpt) cc_final: 0.7605 (ptmt) REVERT: G 62 GLN cc_start: 0.8213 (tt0) cc_final: 0.7891 (tm-30) REVERT: G 94 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5533 (t80) REVERT: H 58 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8428 (mttt) REVERT: H 60 LYS cc_start: 0.8165 (ptpt) cc_final: 0.7548 (ptmt) REVERT: I 60 LYS cc_start: 0.8198 (ptpt) cc_final: 0.7590 (ptmt) REVERT: I 62 GLN cc_start: 0.8211 (tt0) cc_final: 0.7786 (tp40) REVERT: I 94 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.4830 (t80) REVERT: J 60 LYS cc_start: 0.8416 (tttm) cc_final: 0.7837 (mptp) REVERT: J 97 LYS cc_start: 0.8154 (mttt) cc_final: 0.6791 (pmtt) outliers start: 29 outliers final: 18 residues processed: 120 average time/residue: 1.3519 time to fit residues: 168.1227 Evaluate side-chains 132 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 20 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.158200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.133868 restraints weight = 5472.493| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.75 r_work: 0.3846 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 5326 Z= 0.306 Angle : 0.695 8.384 7185 Z= 0.394 Chirality : 0.057 0.153 935 Planarity : 0.003 0.028 900 Dihedral : 6.379 27.446 770 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 7.50 % Allowed : 26.15 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.009 0.003 HIS H 50 PHE 0.012 0.004 PHE I 94 TYR 0.012 0.003 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 119) hydrogen bonds : angle 4.90991 ( 414) covalent geometry : bond 0.00654 ( 5325) covalent geometry : angle 0.69461 ( 7185) Misc. bond : bond 0.00666 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5161.89 seconds wall clock time: 88 minutes 34.60 seconds (5314.60 seconds total)