Starting phenix.real_space_refine on Mon Aug 25 12:44:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikk_60657/08_2025/9ikk_60657_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikk_60657/08_2025/9ikk_60657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ikk_60657/08_2025/9ikk_60657_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikk_60657/08_2025/9ikk_60657_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ikk_60657/08_2025/9ikk_60657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikk_60657/08_2025/9ikk_60657.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 17776 2.51 5 N 4640 2.21 5 O 5968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28480 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "C" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "D" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "E" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "F" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "G" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "H" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "I" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "J" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "K" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "L" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "M" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "N" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "O" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain: "P" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1780 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Time building chain proxies: 6.46, per 1000 atoms: 0.23 Number of scatterers: 28480 At special positions: 0 Unit cell: (93.3215, 93.3215, 297.531, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 5968 8.00 N 4640 7.00 C 17776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 64 sheets defined 10.5% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.711A pdb=" N LEU A 98 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.711A pdb=" N LEU B 98 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'C' and resid 34 through 41 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.710A pdb=" N LEU C 98 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.625A pdb=" N ALA D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.710A pdb=" N LEU D 98 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'E' and resid 34 through 41 Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.711A pdb=" N LEU E 98 " --> pdb=" O ILE E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 216 Processing helix chain 'F' and resid 34 through 41 Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA F 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 98 removed outlier: 3.711A pdb=" N LEU F 98 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 216 Processing helix chain 'G' and resid 34 through 41 Processing helix chain 'G' and resid 67 through 72 removed outlier: 3.625A pdb=" N ALA G 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 98 removed outlier: 3.711A pdb=" N LEU G 98 " --> pdb=" O ILE G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 216 Processing helix chain 'H' and resid 34 through 41 Processing helix chain 'H' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 98 removed outlier: 3.711A pdb=" N LEU H 98 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 216 Processing helix chain 'I' and resid 34 through 41 Processing helix chain 'I' and resid 67 through 72 removed outlier: 3.625A pdb=" N ALA I 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 98 removed outlier: 3.710A pdb=" N LEU I 98 " --> pdb=" O ILE I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 216 Processing helix chain 'J' and resid 34 through 41 Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA J 72 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 98 removed outlier: 3.710A pdb=" N LEU J 98 " --> pdb=" O ILE J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 216 Processing helix chain 'K' and resid 34 through 41 Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA K 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 98 removed outlier: 3.710A pdb=" N LEU K 98 " --> pdb=" O ILE K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 216 Processing helix chain 'L' and resid 34 through 41 Processing helix chain 'L' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA L 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 98 removed outlier: 3.711A pdb=" N LEU L 98 " --> pdb=" O ILE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 216 Processing helix chain 'M' and resid 34 through 41 Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.625A pdb=" N ALA M 72 " --> pdb=" O ALA M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 98 removed outlier: 3.711A pdb=" N LEU M 98 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 216 Processing helix chain 'N' and resid 34 through 41 Processing helix chain 'N' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA N 72 " --> pdb=" O ALA N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 98 removed outlier: 3.710A pdb=" N LEU N 98 " --> pdb=" O ILE N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 216 Processing helix chain 'O' and resid 34 through 41 Processing helix chain 'O' and resid 67 through 72 removed outlier: 3.625A pdb=" N ALA O 72 " --> pdb=" O ALA O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 98 removed outlier: 3.711A pdb=" N LEU O 98 " --> pdb=" O ILE O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 216 Processing helix chain 'P' and resid 34 through 41 Processing helix chain 'P' and resid 67 through 72 removed outlier: 3.624A pdb=" N ALA P 72 " --> pdb=" O ALA P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 98 removed outlier: 3.710A pdb=" N LEU P 98 " --> pdb=" O ILE P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 216 Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 32 removed outlier: 8.186A pdb=" N VAL E 28 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR A 9 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE E 30 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 11 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE E 32 " --> pdb=" O THR A 11 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP A 13 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 4 " --> pdb=" O MET E 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 27 through 32 removed outlier: 8.186A pdb=" N VAL E 28 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR A 9 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE E 30 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 11 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE E 32 " --> pdb=" O THR A 11 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP A 13 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 4 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL E 225 " --> pdb=" O MET E 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 24 removed outlier: 6.908A pdb=" N GLY A 46 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 185 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 48 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 65 Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 81 removed outlier: 6.467A pdb=" N VAL A 225 " --> pdb=" O MET A 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.606A pdb=" N ILE A 90 " --> pdb=" O TYR A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 27 through 32 removed outlier: 8.181A pdb=" N VAL F 28 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR B 9 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE F 30 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 11 " --> pdb=" O PHE F 30 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE F 32 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP B 13 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER B 4 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET F 234 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 27 through 32 removed outlier: 8.181A pdb=" N VAL F 28 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR B 9 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE F 30 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 11 " --> pdb=" O PHE F 30 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE F 32 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP B 13 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER B 4 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET F 234 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL F 225 " --> pdb=" O MET F 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 24 removed outlier: 6.907A pdb=" N GLY B 46 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE B 185 " --> pdb=" O GLY B 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 48 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 58 through 65 Processing sheet with id=AB2, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.468A pdb=" N VAL B 225 " --> pdb=" O MET B 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 89 through 90 removed outlier: 3.605A pdb=" N ILE B 90 " --> pdb=" O TYR B 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 27 through 32 removed outlier: 8.157A pdb=" N VAL G 28 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR C 9 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE G 30 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR C 11 " --> pdb=" O PHE G 30 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE G 32 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP C 13 " --> pdb=" O PHE G 32 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER C 4 " --> pdb=" O MET G 234 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 27 through 32 removed outlier: 8.157A pdb=" N VAL G 28 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR C 9 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE G 30 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR C 11 " --> pdb=" O PHE G 30 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE G 32 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP C 13 " --> pdb=" O PHE G 32 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER C 4 " --> pdb=" O MET G 234 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL G 225 " --> pdb=" O MET G 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 18 through 24 removed outlier: 6.908A pdb=" N GLY C 46 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE C 185 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 48 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 58 through 65 Processing sheet with id=AB8, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.468A pdb=" N VAL C 225 " --> pdb=" O MET C 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 89 through 90 removed outlier: 3.605A pdb=" N ILE C 90 " --> pdb=" O TYR C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 27 through 32 removed outlier: 8.108A pdb=" N VAL H 28 " --> pdb=" O ASN D 7 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR D 9 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE H 30 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR D 11 " --> pdb=" O PHE H 30 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE H 32 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP D 13 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER D 4 " --> pdb=" O MET H 234 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 27 through 32 removed outlier: 8.108A pdb=" N VAL H 28 " --> pdb=" O ASN D 7 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR D 9 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE H 30 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR D 11 " --> pdb=" O PHE H 30 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE H 32 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP D 13 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER D 4 " --> pdb=" O MET H 234 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL H 225 " --> pdb=" O MET H 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 18 through 24 removed outlier: 6.907A pdb=" N GLY D 46 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE D 185 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 48 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 58 through 65 Processing sheet with id=AC5, first strand: chain 'D' and resid 77 through 81 removed outlier: 6.468A pdb=" N VAL D 225 " --> pdb=" O MET D 79 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 89 through 90 removed outlier: 3.605A pdb=" N ILE D 90 " --> pdb=" O TYR D 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 27 through 32 removed outlier: 8.213A pdb=" N VAL I 28 " --> pdb=" O ASN E 7 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR E 9 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE I 30 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR E 11 " --> pdb=" O PHE I 30 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N PHE I 32 " --> pdb=" O THR E 11 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASP E 13 " --> pdb=" O PHE I 32 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER E 4 " --> pdb=" O MET I 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET I 234 " --> pdb=" O SER E 4 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 27 through 32 removed outlier: 8.213A pdb=" N VAL I 28 " --> pdb=" O ASN E 7 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR E 9 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE I 30 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR E 11 " --> pdb=" O PHE I 30 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N PHE I 32 " --> pdb=" O THR E 11 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASP E 13 " --> pdb=" O PHE I 32 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER E 4 " --> pdb=" O MET I 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET I 234 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL I 225 " --> pdb=" O MET I 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 18 through 24 removed outlier: 6.907A pdb=" N GLY E 46 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE E 185 " --> pdb=" O GLY E 46 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 48 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 89 through 90 removed outlier: 3.606A pdb=" N ILE E 90 " --> pdb=" O TYR E 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'J' and resid 27 through 32 removed outlier: 8.175A pdb=" N VAL J 28 " --> pdb=" O ASN F 7 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR F 9 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE J 30 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR F 11 " --> pdb=" O PHE J 30 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE J 32 " --> pdb=" O THR F 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP F 13 " --> pdb=" O PHE J 32 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 4 " --> pdb=" O MET J 234 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 27 through 32 removed outlier: 8.175A pdb=" N VAL J 28 " --> pdb=" O ASN F 7 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR F 9 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE J 30 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR F 11 " --> pdb=" O PHE J 30 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE J 32 " --> pdb=" O THR F 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP F 13 " --> pdb=" O PHE J 32 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 4 " --> pdb=" O MET J 234 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL J 225 " --> pdb=" O MET J 79 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 18 through 24 removed outlier: 6.908A pdb=" N GLY F 46 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE F 185 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL F 48 " --> pdb=" O ILE F 183 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 89 through 90 removed outlier: 3.606A pdb=" N ILE F 90 " --> pdb=" O TYR F 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 27 through 32 removed outlier: 8.164A pdb=" N VAL K 28 " --> pdb=" O ASN G 7 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR G 9 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE K 30 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR G 11 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE K 32 " --> pdb=" O THR G 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP G 13 " --> pdb=" O PHE K 32 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER G 4 " --> pdb=" O MET K 234 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET K 234 " --> pdb=" O SER G 4 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 27 through 32 removed outlier: 8.164A pdb=" N VAL K 28 " --> pdb=" O ASN G 7 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR G 9 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE K 30 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR G 11 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE K 32 " --> pdb=" O THR G 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP G 13 " --> pdb=" O PHE K 32 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER G 4 " --> pdb=" O MET K 234 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET K 234 " --> pdb=" O SER G 4 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL K 225 " --> pdb=" O MET K 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 18 through 24 removed outlier: 6.908A pdb=" N GLY G 46 " --> pdb=" O PHE G 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE G 185 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 48 " --> pdb=" O ILE G 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.605A pdb=" N ILE G 90 " --> pdb=" O TYR G 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'L' and resid 27 through 32 removed outlier: 8.142A pdb=" N VAL L 28 " --> pdb=" O ASN H 7 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N THR H 9 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE L 30 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR H 11 " --> pdb=" O PHE L 30 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE L 32 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP H 13 " --> pdb=" O PHE L 32 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER H 4 " --> pdb=" O MET L 234 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET L 234 " --> pdb=" O SER H 4 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 27 through 32 removed outlier: 8.142A pdb=" N VAL L 28 " --> pdb=" O ASN H 7 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N THR H 9 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE L 30 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR H 11 " --> pdb=" O PHE L 30 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE L 32 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP H 13 " --> pdb=" O PHE L 32 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER H 4 " --> pdb=" O MET L 234 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET L 234 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL L 225 " --> pdb=" O MET L 79 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 18 through 24 removed outlier: 6.908A pdb=" N GLY H 46 " --> pdb=" O PHE H 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE H 185 " --> pdb=" O GLY H 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL H 48 " --> pdb=" O ILE H 183 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 89 through 90 removed outlier: 3.605A pdb=" N ILE H 90 " --> pdb=" O TYR H 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'M' and resid 27 through 32 removed outlier: 8.102A pdb=" N VAL M 28 " --> pdb=" O ASN I 7 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR I 9 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE M 30 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR I 11 " --> pdb=" O PHE M 30 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE M 32 " --> pdb=" O THR I 11 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP I 13 " --> pdb=" O PHE M 32 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER I 4 " --> pdb=" O MET M 234 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 27 through 32 removed outlier: 8.102A pdb=" N VAL M 28 " --> pdb=" O ASN I 7 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR I 9 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE M 30 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR I 11 " --> pdb=" O PHE M 30 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE M 32 " --> pdb=" O THR I 11 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP I 13 " --> pdb=" O PHE M 32 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER I 4 " --> pdb=" O MET M 234 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL M 225 " --> pdb=" O MET M 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 18 through 24 removed outlier: 6.907A pdb=" N GLY I 46 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE I 185 " --> pdb=" O GLY I 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL I 48 " --> pdb=" O ILE I 183 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 89 through 90 removed outlier: 3.606A pdb=" N ILE I 90 " --> pdb=" O TYR I 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'N' and resid 27 through 32 removed outlier: 8.215A pdb=" N VAL N 28 " --> pdb=" O ASN J 7 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR J 9 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE N 30 " --> pdb=" O THR J 9 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR J 11 " --> pdb=" O PHE N 30 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE N 32 " --> pdb=" O THR J 11 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP J 13 " --> pdb=" O PHE N 32 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER J 4 " --> pdb=" O MET N 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET N 234 " --> pdb=" O SER J 4 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 27 through 32 removed outlier: 8.215A pdb=" N VAL N 28 " --> pdb=" O ASN J 7 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR J 9 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE N 30 " --> pdb=" O THR J 9 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR J 11 " --> pdb=" O PHE N 30 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE N 32 " --> pdb=" O THR J 11 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP J 13 " --> pdb=" O PHE N 32 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER J 4 " --> pdb=" O MET N 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET N 234 " --> pdb=" O SER J 4 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL N 225 " --> pdb=" O MET N 79 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 18 through 24 removed outlier: 6.908A pdb=" N GLY J 46 " --> pdb=" O PHE J 185 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE J 185 " --> pdb=" O GLY J 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL J 48 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 89 through 90 removed outlier: 3.605A pdb=" N ILE J 90 " --> pdb=" O TYR J 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'O' and resid 27 through 32 removed outlier: 8.175A pdb=" N VAL O 28 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR K 9 " --> pdb=" O VAL O 28 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE O 30 " --> pdb=" O THR K 9 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR K 11 " --> pdb=" O PHE O 30 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE O 32 " --> pdb=" O THR K 11 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP K 13 " --> pdb=" O PHE O 32 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER K 4 " --> pdb=" O MET O 234 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 27 through 32 removed outlier: 8.175A pdb=" N VAL O 28 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR K 9 " --> pdb=" O VAL O 28 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE O 30 " --> pdb=" O THR K 9 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR K 11 " --> pdb=" O PHE O 30 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE O 32 " --> pdb=" O THR K 11 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP K 13 " --> pdb=" O PHE O 32 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER K 4 " --> pdb=" O MET O 234 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL O 225 " --> pdb=" O MET O 79 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 18 through 24 removed outlier: 6.907A pdb=" N GLY K 46 " --> pdb=" O PHE K 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE K 185 " --> pdb=" O GLY K 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL K 48 " --> pdb=" O ILE K 183 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 89 through 90 removed outlier: 3.605A pdb=" N ILE K 90 " --> pdb=" O TYR K 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'P' and resid 27 through 32 removed outlier: 8.150A pdb=" N VAL P 28 " --> pdb=" O ASN L 7 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR L 9 " --> pdb=" O VAL P 28 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE P 30 " --> pdb=" O THR L 9 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR L 11 " --> pdb=" O PHE P 30 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE P 32 " --> pdb=" O THR L 11 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP L 13 " --> pdb=" O PHE P 32 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER L 4 " --> pdb=" O MET P 234 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET P 234 " --> pdb=" O SER L 4 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 27 through 32 removed outlier: 8.150A pdb=" N VAL P 28 " --> pdb=" O ASN L 7 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR L 9 " --> pdb=" O VAL P 28 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE P 30 " --> pdb=" O THR L 9 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR L 11 " --> pdb=" O PHE P 30 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE P 32 " --> pdb=" O THR L 11 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP L 13 " --> pdb=" O PHE P 32 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER L 4 " --> pdb=" O MET P 234 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET P 234 " --> pdb=" O SER L 4 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL P 225 " --> pdb=" O MET P 79 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 18 through 24 removed outlier: 6.907A pdb=" N GLY L 46 " --> pdb=" O PHE L 185 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE L 185 " --> pdb=" O GLY L 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL L 48 " --> pdb=" O ILE L 183 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.605A pdb=" N ILE L 90 " --> pdb=" O TYR L 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'M' and resid 18 through 24 removed outlier: 6.908A pdb=" N GLY M 46 " --> pdb=" O PHE M 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE M 185 " --> pdb=" O GLY M 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL M 48 " --> pdb=" O ILE M 183 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 89 through 90 removed outlier: 3.605A pdb=" N ILE M 90 " --> pdb=" O TYR M 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'N' and resid 18 through 24 removed outlier: 6.907A pdb=" N GLY N 46 " --> pdb=" O PHE N 185 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE N 185 " --> pdb=" O GLY N 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL N 48 " --> pdb=" O ILE N 183 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 89 through 90 removed outlier: 3.606A pdb=" N ILE N 90 " --> pdb=" O TYR N 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'O' and resid 18 through 24 removed outlier: 6.908A pdb=" N GLY O 46 " --> pdb=" O PHE O 185 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE O 185 " --> pdb=" O GLY O 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL O 48 " --> pdb=" O ILE O 183 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 89 through 90 removed outlier: 3.606A pdb=" N ILE O 90 " --> pdb=" O TYR O 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'P' and resid 18 through 24 removed outlier: 6.907A pdb=" N GLY P 46 " --> pdb=" O PHE P 185 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE P 185 " --> pdb=" O GLY P 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL P 48 " --> pdb=" O ILE P 183 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 89 through 90 removed outlier: 3.606A pdb=" N ILE P 90 " --> pdb=" O TYR P 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 780 hydrogen bonds defined for protein. 2016 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: 4.79 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9680 1.34 - 1.46: 6380 1.46 - 1.58: 12868 1.58 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 29088 Sorted by residual: bond pdb=" CA ARG G 126 " pdb=" CB ARG G 126 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.33e-02 5.65e+03 1.53e+00 bond pdb=" CA ARG H 126 " pdb=" CB ARG H 126 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.33e-02 5.65e+03 1.49e+00 bond pdb=" CA ARG B 126 " pdb=" CB ARG B 126 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.33e-02 5.65e+03 1.44e+00 bond pdb=" CA ARG D 126 " pdb=" CB ARG D 126 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.33e-02 5.65e+03 1.43e+00 bond pdb=" CA ARG M 126 " pdb=" CB ARG M 126 " ideal model delta sigma weight residual 1.524 1.539 -0.016 1.33e-02 5.65e+03 1.42e+00 ... (remaining 29083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 37734 1.33 - 2.66: 1458 2.66 - 3.99: 378 3.99 - 5.32: 155 5.32 - 6.64: 51 Bond angle restraints: 39776 Sorted by residual: angle pdb=" CA GLU D 26 " pdb=" CB GLU D 26 " pdb=" CG GLU D 26 " ideal model delta sigma weight residual 114.10 120.74 -6.64 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA GLU I 26 " pdb=" CB GLU I 26 " pdb=" CG GLU I 26 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU M 26 " pdb=" CB GLU M 26 " pdb=" CG GLU M 26 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU F 26 " pdb=" CB GLU F 26 " pdb=" CG GLU F 26 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU H 26 " pdb=" CB GLU H 26 " pdb=" CG GLU H 26 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 ... (remaining 39771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14993 17.93 - 35.86: 1712 35.86 - 53.79: 256 53.79 - 71.71: 63 71.71 - 89.64: 32 Dihedral angle restraints: 17056 sinusoidal: 6160 harmonic: 10896 Sorted by residual: dihedral pdb=" CA GLN M 176 " pdb=" C GLN M 176 " pdb=" N ASN M 177 " pdb=" CA ASN M 177 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLN I 176 " pdb=" C GLN I 176 " pdb=" N ASN I 177 " pdb=" CA ASN I 177 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLN K 176 " pdb=" C GLN K 176 " pdb=" N ASN K 177 " pdb=" CA ASN K 177 " ideal model delta harmonic sigma weight residual 180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 17053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2615 0.028 - 0.056: 1051 0.056 - 0.084: 382 0.084 - 0.112: 370 0.112 - 0.140: 62 Chirality restraints: 4480 Sorted by residual: chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA VAL F 80 " pdb=" N VAL F 80 " pdb=" C VAL F 80 " pdb=" CB VAL F 80 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA VAL I 80 " pdb=" N VAL I 80 " pdb=" C VAL I 80 " pdb=" CB VAL I 80 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 4477 not shown) Planarity restraints: 5360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL M 188 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO M 189 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO M 189 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO M 189 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 188 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO G 189 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 189 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 189 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL K 188 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO K 189 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO K 189 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO K 189 " 0.017 5.00e-02 4.00e+02 ... (remaining 5357 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2286 2.74 - 3.28: 29354 3.28 - 3.82: 46464 3.82 - 4.36: 55360 4.36 - 4.90: 96177 Nonbonded interactions: 229641 Sorted by model distance: nonbonded pdb=" N LEU F 2 " pdb=" OE2 GLU J 236 " model vdw 2.199 3.120 nonbonded pdb=" N LEU A 2 " pdb=" OE2 GLU E 236 " model vdw 2.273 3.120 nonbonded pdb=" ND2 ASN J 86 " pdb=" OH TYR J 220 " model vdw 2.285 3.120 nonbonded pdb=" ND2 ASN L 86 " pdb=" OH TYR L 220 " model vdw 2.285 3.120 nonbonded pdb=" ND2 ASN G 86 " pdb=" OH TYR G 220 " model vdw 2.285 3.120 ... (remaining 229636 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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 group one per residue 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: 2.730 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.800 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 29088 Z= 0.157 Angle : 0.704 6.644 39776 Z= 0.396 Chirality : 0.043 0.140 4480 Planarity : 0.004 0.030 5360 Dihedral : 15.433 89.643 10112 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.52 % Allowed : 14.90 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.13), residues: 3760 helix: -1.90 (0.32), residues: 208 sheet: 1.33 (0.19), residues: 656 loop : -1.99 (0.11), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 149 TYR 0.011 0.001 TYR I 180 PHE 0.007 0.001 PHE P 82 TRP 0.006 0.001 TRP F 76 Details of bonding type rmsd covalent geometry : bond 0.00328 (29088) covalent geometry : angle 0.70448 (39776) hydrogen bonds : bond 0.17537 ( 654) hydrogen bonds : angle 9.31428 ( 2016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 572 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 TYR cc_start: 0.7339 (m-80) cc_final: 0.7125 (m-80) REVERT: D 19 GLN cc_start: 0.8521 (mt0) cc_final: 0.8296 (mt0) REVERT: D 34 GLN cc_start: 0.8675 (mp10) cc_final: 0.8452 (mp10) REVERT: E 166 TYR cc_start: 0.8543 (p90) cc_final: 0.8284 (p90) REVERT: F 5 GLU cc_start: 0.8206 (pt0) cc_final: 0.7900 (pt0) REVERT: F 65 PHE cc_start: 0.7907 (t80) cc_final: 0.7627 (t80) REVERT: G 90 ILE cc_start: 0.8495 (tt) cc_final: 0.8228 (tp) REVERT: G 219 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7439 (mtt90) REVERT: I 219 ARG cc_start: 0.8341 (mtt180) cc_final: 0.7949 (mtt90) REVERT: J 90 ILE cc_start: 0.8059 (tt) cc_final: 0.7775 (tp) REVERT: K 84 ASP cc_start: 0.6694 (p0) cc_final: 0.6477 (p0) REVERT: K 90 ILE cc_start: 0.7620 (tt) cc_final: 0.7227 (tp) REVERT: K 208 GLU cc_start: 0.8085 (pp20) cc_final: 0.7855 (pp20) REVERT: L 25 SER cc_start: 0.8044 (m) cc_final: 0.7696 (p) REVERT: L 112 THR cc_start: 0.6982 (OUTLIER) cc_final: 0.6751 (p) REVERT: M 90 ILE cc_start: 0.7794 (tt) cc_final: 0.7435 (tp) REVERT: M 149 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7395 (mtp85) REVERT: P 12 MET cc_start: 0.7732 (ttm) cc_final: 0.6639 (ptt) outliers start: 16 outliers final: 1 residues processed: 588 average time/residue: 0.1628 time to fit residues: 152.8711 Evaluate side-chains 379 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 377 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 112 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 110 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN E 110 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN J 23 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN K 205 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 GLN L 205 ASN M 110 ASN O 110 ASN P 110 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.092288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.074811 restraints weight = 70800.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.077347 restraints weight = 34062.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079100 restraints weight = 21089.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080265 restraints weight = 15145.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081059 restraints weight = 11970.200| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 29088 Z= 0.214 Angle : 0.671 8.884 39776 Z= 0.348 Chirality : 0.047 0.166 4480 Planarity : 0.005 0.046 5360 Dihedral : 5.075 29.439 4082 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.49 % Allowed : 17.20 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.13), residues: 3760 helix: -2.17 (0.29), residues: 304 sheet: 1.08 (0.20), residues: 656 loop : -2.07 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 149 TYR 0.019 0.002 TYR F 180 PHE 0.013 0.001 PHE I 179 TRP 0.007 0.002 TRP M 58 Details of bonding type rmsd covalent geometry : bond 0.00500 (29088) covalent geometry : angle 0.67075 (39776) hydrogen bonds : bond 0.03804 ( 654) hydrogen bonds : angle 6.20785 ( 2016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 396 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8617 (tpp80) cc_final: 0.8360 (tpp80) REVERT: B 34 GLN cc_start: 0.8869 (mp10) cc_final: 0.8470 (mp10) REVERT: B 235 VAL cc_start: 0.8039 (t) cc_final: 0.7817 (m) REVERT: C 25 SER cc_start: 0.9056 (m) cc_final: 0.8838 (p) REVERT: C 166 TYR cc_start: 0.8991 (p90) cc_final: 0.8637 (p90) REVERT: D 34 GLN cc_start: 0.8756 (mp10) cc_final: 0.8456 (mp10) REVERT: F 131 GLU cc_start: 0.7903 (mp0) cc_final: 0.7557 (mp0) REVERT: G 34 GLN cc_start: 0.8498 (mp10) cc_final: 0.7826 (mp10) REVERT: G 90 ILE cc_start: 0.8417 (tt) cc_final: 0.8124 (tp) REVERT: G 176 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6888 (tp40) REVERT: G 219 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7379 (mtt90) REVERT: H 219 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7977 (mtt-85) REVERT: I 34 GLN cc_start: 0.8511 (mp10) cc_final: 0.8217 (mp10) REVERT: I 149 ARG cc_start: 0.8430 (mtp85) cc_final: 0.7472 (mtp85) REVERT: I 219 ARG cc_start: 0.8349 (mtt180) cc_final: 0.8041 (mtt180) REVERT: J 34 GLN cc_start: 0.8706 (mp10) cc_final: 0.8432 (mp10) REVERT: K 90 ILE cc_start: 0.8258 (tt) cc_final: 0.8021 (tp) REVERT: K 219 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7280 (mtt180) REVERT: L 79 MET cc_start: 0.8446 (tpt) cc_final: 0.8159 (ttm) REVERT: M 25 SER cc_start: 0.8124 (OUTLIER) cc_final: 0.7846 (p) REVERT: N 25 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7861 (p) REVERT: N 131 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7050 (mm-30) REVERT: O 25 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7980 (p) REVERT: P 25 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8169 (p) outliers start: 77 outliers final: 39 residues processed: 441 average time/residue: 0.1602 time to fit residues: 111.3889 Evaluate side-chains 378 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 334 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 79 MET Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 234 MET Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 234 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 259 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 341 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 323 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 110 ASN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 ASN M 110 ASN M 133 ASN P 102 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.089832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.072317 restraints weight = 71519.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.074766 restraints weight = 34755.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076437 restraints weight = 21784.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077553 restraints weight = 15771.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078311 restraints weight = 12582.027| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 29088 Z= 0.237 Angle : 0.669 11.228 39776 Z= 0.343 Chirality : 0.047 0.166 4480 Planarity : 0.005 0.073 5360 Dihedral : 5.196 28.088 4082 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.59 % Allowed : 17.88 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.13), residues: 3760 helix: -2.12 (0.30), residues: 304 sheet: 0.84 (0.20), residues: 656 loop : -2.11 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 215 TYR 0.017 0.002 TYR F 180 PHE 0.016 0.001 PHE K 65 TRP 0.007 0.001 TRP K 58 Details of bonding type rmsd covalent geometry : bond 0.00556 (29088) covalent geometry : angle 0.66902 (39776) hydrogen bonds : bond 0.03730 ( 654) hydrogen bonds : angle 5.81750 ( 2016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 370 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7956 (mp10) cc_final: 0.7679 (mp10) REVERT: B 81 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8052 (t) REVERT: B 235 VAL cc_start: 0.8588 (t) cc_final: 0.8295 (m) REVERT: C 25 SER cc_start: 0.9194 (m) cc_final: 0.8936 (p) REVERT: C 166 TYR cc_start: 0.9033 (p90) cc_final: 0.8767 (p90) REVERT: D 34 GLN cc_start: 0.8752 (mp10) cc_final: 0.8466 (mp10) REVERT: E 22 MET cc_start: 0.8373 (tmm) cc_final: 0.7992 (tmm) REVERT: G 90 ILE cc_start: 0.8444 (tt) cc_final: 0.8095 (tp) REVERT: G 95 ILE cc_start: 0.9124 (mm) cc_final: 0.8844 (mt) REVERT: G 219 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7348 (mtt90) REVERT: H 102 GLN cc_start: 0.8683 (tt0) cc_final: 0.8448 (tt0) REVERT: I 22 MET cc_start: 0.8598 (ttp) cc_final: 0.8369 (ttp) REVERT: I 34 GLN cc_start: 0.8617 (mp10) cc_final: 0.8191 (mp10) REVERT: I 219 ARG cc_start: 0.8404 (mtt180) cc_final: 0.7996 (mtt180) REVERT: K 12 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8773 (tmm) REVERT: K 90 ILE cc_start: 0.8774 (tt) cc_final: 0.8510 (tp) REVERT: K 95 ILE cc_start: 0.8818 (mm) cc_final: 0.8537 (mt) REVERT: K 96 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9080 (m) REVERT: K 219 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7296 (mtt180) REVERT: L 79 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8220 (mtt) REVERT: L 96 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8803 (m) REVERT: M 25 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.8048 (p) REVERT: M 79 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8198 (tpp) REVERT: M 96 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8708 (m) REVERT: N 25 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8147 (p) REVERT: N 131 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7320 (mm-30) REVERT: N 180 TYR cc_start: 0.7795 (t80) cc_final: 0.7586 (t80) REVERT: N 236 GLU cc_start: 0.6996 (pt0) cc_final: 0.6728 (pt0) REVERT: O 126 ARG cc_start: 0.7470 (ptt90) cc_final: 0.7216 (ptt90) REVERT: P 25 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8366 (p) outliers start: 111 outliers final: 64 residues processed: 449 average time/residue: 0.1674 time to fit residues: 122.3801 Evaluate side-chains 412 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 338 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 79 MET Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 79 MET Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 234 MET Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 234 MET Chi-restraints excluded: chain P residue 235 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 274 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 360 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 364 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN E 205 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 ASN ** G 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN J 133 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 155 ASN O 133 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.088045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.070684 restraints weight = 71795.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.073104 restraints weight = 35380.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074723 restraints weight = 22325.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075800 restraints weight = 16304.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.076546 restraints weight = 13074.716| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 29088 Z= 0.343 Angle : 0.768 16.322 39776 Z= 0.390 Chirality : 0.049 0.182 4480 Planarity : 0.005 0.052 5360 Dihedral : 5.680 30.287 4082 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.31 % Allowed : 18.88 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.12), residues: 3760 helix: -2.09 (0.26), residues: 400 sheet: 0.46 (0.20), residues: 656 loop : -2.34 (0.10), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 215 TYR 0.020 0.002 TYR F 180 PHE 0.023 0.002 PHE K 65 TRP 0.008 0.002 TRP L 58 Details of bonding type rmsd covalent geometry : bond 0.00797 (29088) covalent geometry : angle 0.76767 (39776) hydrogen bonds : bond 0.03893 ( 654) hydrogen bonds : angle 5.81385 ( 2016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 355 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7384 (mt-10) REVERT: A 166 TYR cc_start: 0.8341 (p90) cc_final: 0.8101 (p90) REVERT: B 81 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8045 (t) REVERT: B 235 VAL cc_start: 0.8766 (t) cc_final: 0.8531 (m) REVERT: C 25 SER cc_start: 0.9277 (m) cc_final: 0.9026 (p) REVERT: D 34 GLN cc_start: 0.8896 (mp10) cc_final: 0.8633 (mp10) REVERT: F 22 MET cc_start: 0.8456 (ttp) cc_final: 0.8119 (ttt) REVERT: F 96 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8750 (t) REVERT: G 90 ILE cc_start: 0.8542 (tt) cc_final: 0.8164 (tp) REVERT: G 95 ILE cc_start: 0.9151 (mm) cc_final: 0.8870 (mt) REVERT: H 102 GLN cc_start: 0.8825 (tt0) cc_final: 0.8577 (tt0) REVERT: H 110 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7249 (p0) REVERT: I 25 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8333 (p) REVERT: I 34 GLN cc_start: 0.8623 (mp10) cc_final: 0.8193 (mp10) REVERT: J 23 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6446 (mt0) REVERT: J 34 GLN cc_start: 0.8723 (mp10) cc_final: 0.8473 (mp10) REVERT: K 12 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8623 (ptm) REVERT: K 90 ILE cc_start: 0.8999 (tt) cc_final: 0.8799 (tp) REVERT: K 95 ILE cc_start: 0.8837 (mm) cc_final: 0.8581 (mt) REVERT: L 96 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8927 (m) REVERT: L 219 ARG cc_start: 0.8225 (mtt180) cc_final: 0.7803 (mtt180) REVERT: M 25 SER cc_start: 0.8681 (m) cc_final: 0.8429 (p) REVERT: M 79 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8198 (tpp) REVERT: M 96 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8878 (m) REVERT: N 25 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8393 (p) REVERT: N 79 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8082 (mtt) REVERT: N 131 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7684 (mm-30) REVERT: N 236 GLU cc_start: 0.7207 (pt0) cc_final: 0.6971 (pt0) REVERT: O 126 ARG cc_start: 0.7403 (ptt90) cc_final: 0.7194 (ptt90) REVERT: P 176 GLN cc_start: 0.6334 (OUTLIER) cc_final: 0.5966 (tp40) REVERT: P 219 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7536 (ptp-170) outliers start: 164 outliers final: 101 residues processed: 476 average time/residue: 0.1573 time to fit residues: 123.6257 Evaluate side-chains 447 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 333 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 215 ARG Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 23 GLN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 79 MET Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain M residue 79 MET Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 228 LEU Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 234 MET Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 234 MET Chi-restraints excluded: chain P residue 38 TYR Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 176 GLN Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 219 ARG Chi-restraints excluded: chain P residue 234 MET Chi-restraints excluded: chain P residue 235 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 26 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 228 optimal weight: 0.0870 chunk 292 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 326 optimal weight: 1.9990 chunk 320 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 352 optimal weight: 8.9990 chunk 344 optimal weight: 8.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN C 205 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 GLN G 205 ASN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073989 restraints weight = 70506.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.076461 restraints weight = 34643.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078115 restraints weight = 21770.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079242 restraints weight = 15826.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079966 restraints weight = 12610.913| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29088 Z= 0.150 Angle : 0.614 10.221 39776 Z= 0.316 Chirality : 0.045 0.155 4480 Planarity : 0.005 0.058 5360 Dihedral : 5.112 25.717 4082 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.21 % Allowed : 20.34 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.12), residues: 3760 helix: -1.28 (0.37), residues: 208 sheet: 0.24 (0.18), residues: 784 loop : -2.29 (0.10), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 143 TYR 0.018 0.001 TYR P 180 PHE 0.026 0.001 PHE C 82 TRP 0.006 0.001 TRP D 76 Details of bonding type rmsd covalent geometry : bond 0.00352 (29088) covalent geometry : angle 0.61374 (39776) hydrogen bonds : bond 0.03274 ( 654) hydrogen bonds : angle 5.49654 ( 2016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 397 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8178 (m) REVERT: B 235 VAL cc_start: 0.8651 (t) cc_final: 0.8432 (m) REVERT: C 25 SER cc_start: 0.9205 (m) cc_final: 0.8902 (p) REVERT: C 79 MET cc_start: 0.9431 (mmt) cc_final: 0.9221 (mmm) REVERT: C 112 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7495 (t) REVERT: D 34 GLN cc_start: 0.8644 (mp10) cc_final: 0.8396 (mp10) REVERT: D 202 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7865 (p0) REVERT: E 79 MET cc_start: 0.8265 (tpp) cc_final: 0.7897 (mtt) REVERT: E 129 LEU cc_start: 0.8780 (mm) cc_final: 0.8415 (tp) REVERT: F 131 GLU cc_start: 0.8334 (mp0) cc_final: 0.7850 (mp0) REVERT: F 219 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7294 (ptt-90) REVERT: G 79 MET cc_start: 0.8805 (mmt) cc_final: 0.8579 (mtp) REVERT: G 90 ILE cc_start: 0.8420 (tt) cc_final: 0.8060 (tp) REVERT: G 219 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7626 (mtt90) REVERT: I 25 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8201 (p) REVERT: I 34 GLN cc_start: 0.8634 (mp10) cc_final: 0.8212 (mp10) REVERT: I 149 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7444 (mtp85) REVERT: I 219 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7668 (mtt180) REVERT: J 205 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8211 (t0) REVERT: K 12 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8753 (tmm) REVERT: K 79 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7856 (mtt) REVERT: K 90 ILE cc_start: 0.8774 (tt) cc_final: 0.8562 (tp) REVERT: K 95 ILE cc_start: 0.8792 (mm) cc_final: 0.8505 (mt) REVERT: K 96 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.9082 (m) REVERT: K 149 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8470 (mtp85) REVERT: L 79 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8012 (mtt) REVERT: L 219 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7808 (mtt180) REVERT: L 222 TYR cc_start: 0.7498 (t80) cc_final: 0.7296 (t80) REVERT: M 96 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8835 (m) REVERT: N 131 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7661 (mm-30) REVERT: N 231 LYS cc_start: 0.8860 (tttt) cc_final: 0.8518 (ttmm) REVERT: O 139 ASP cc_start: 0.8386 (p0) cc_final: 0.7933 (p0) REVERT: P 219 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7314 (ptp-170) outliers start: 130 outliers final: 75 residues processed: 490 average time/residue: 0.1636 time to fit residues: 130.6176 Evaluate side-chains 429 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 343 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 38 TYR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 79 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain L residue 79 MET Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 234 MET Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 38 TYR Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 176 GLN Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 217 ASP Chi-restraints excluded: chain P residue 219 ARG Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 234 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 238 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 chunk 8 optimal weight: 0.3980 chunk 194 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.072132 restraints weight = 71091.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074571 restraints weight = 34855.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076213 restraints weight = 21890.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077282 restraints weight = 15895.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.078026 restraints weight = 12754.610| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 29088 Z= 0.240 Angle : 0.683 13.113 39776 Z= 0.348 Chirality : 0.046 0.195 4480 Planarity : 0.005 0.052 5360 Dihedral : 5.270 20.033 4080 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.60 % Allowed : 21.08 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.12), residues: 3760 helix: -1.29 (0.31), residues: 304 sheet: 0.16 (0.18), residues: 784 loop : -2.41 (0.10), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 219 TYR 0.017 0.002 TYR K 195 PHE 0.023 0.001 PHE K 65 TRP 0.007 0.001 TRP D 76 Details of bonding type rmsd covalent geometry : bond 0.00562 (29088) covalent geometry : angle 0.68347 (39776) hydrogen bonds : bond 0.03479 ( 654) hydrogen bonds : angle 5.48049 ( 2016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 357 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8130 (m) REVERT: B 81 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7961 (t) REVERT: B 235 VAL cc_start: 0.8834 (t) cc_final: 0.8571 (m) REVERT: C 25 SER cc_start: 0.9242 (m) cc_final: 0.8989 (p) REVERT: C 112 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7534 (t) REVERT: D 34 GLN cc_start: 0.8710 (mp10) cc_final: 0.8451 (mp10) REVERT: D 202 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7557 (p0) REVERT: E 22 MET cc_start: 0.8055 (ttp) cc_final: 0.7805 (tmm) REVERT: G 90 ILE cc_start: 0.8514 (tt) cc_final: 0.8126 (tp) REVERT: G 95 ILE cc_start: 0.9090 (mm) cc_final: 0.8863 (mt) REVERT: I 25 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8363 (p) REVERT: I 34 GLN cc_start: 0.8651 (mp10) cc_final: 0.8249 (mp10) REVERT: I 149 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7551 (mtp85) REVERT: I 219 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7761 (mtt180) REVERT: J 79 MET cc_start: 0.8754 (tpp) cc_final: 0.8531 (tpp) REVERT: K 12 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8556 (ptm) REVERT: K 79 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7859 (mtt) REVERT: K 90 ILE cc_start: 0.8913 (tt) cc_final: 0.8674 (tp) REVERT: K 95 ILE cc_start: 0.8841 (mm) cc_final: 0.8613 (mt) REVERT: K 96 THR cc_start: 0.9386 (OUTLIER) cc_final: 0.9176 (m) REVERT: K 149 ARG cc_start: 0.8813 (mtp85) cc_final: 0.8540 (mtp85) REVERT: L 219 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7821 (mtt180) REVERT: L 222 TYR cc_start: 0.7579 (t80) cc_final: 0.7374 (t80) REVERT: M 25 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8457 (p) REVERT: M 79 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7683 (mtt) REVERT: M 96 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8910 (m) REVERT: N 25 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8319 (p) REVERT: N 51 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8969 (p) REVERT: N 131 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7913 (mm-30) REVERT: O 22 MET cc_start: 0.9228 (ttt) cc_final: 0.8948 (ttt) REVERT: O 208 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7538 (tm-30) REVERT: P 176 GLN cc_start: 0.6132 (OUTLIER) cc_final: 0.5891 (tp40) REVERT: P 219 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7728 (ptp-170) outliers start: 142 outliers final: 102 residues processed: 453 average time/residue: 0.1785 time to fit residues: 131.5020 Evaluate side-chains 450 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 333 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 38 TYR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 23 GLN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 23 GLN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 79 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 79 MET Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 MET Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 234 MET Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 38 TYR Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 176 GLN Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 219 ARG Chi-restraints excluded: chain P residue 234 MET Chi-restraints excluded: chain P residue 235 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 304 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 355 optimal weight: 7.9990 chunk 308 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 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 = 0.3422 r_free = 0.3422 target = 0.089781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.072559 restraints weight = 70870.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.075012 restraints weight = 34805.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076663 restraints weight = 21809.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.077781 restraints weight = 15804.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078468 restraints weight = 12597.840| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29088 Z= 0.214 Angle : 0.664 12.168 39776 Z= 0.338 Chirality : 0.046 0.257 4480 Planarity : 0.004 0.049 5360 Dihedral : 5.233 19.673 4080 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.79 % Allowed : 21.28 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.12), residues: 3760 helix: -1.32 (0.37), residues: 208 sheet: 0.09 (0.18), residues: 784 loop : -2.35 (0.10), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 143 TYR 0.016 0.002 TYR K 195 PHE 0.021 0.001 PHE K 65 TRP 0.006 0.001 TRP D 76 Details of bonding type rmsd covalent geometry : bond 0.00500 (29088) covalent geometry : angle 0.66358 (39776) hydrogen bonds : bond 0.03409 ( 654) hydrogen bonds : angle 5.42321 ( 2016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 350 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8303 (m) REVERT: B 34 GLN cc_start: 0.9147 (mp10) cc_final: 0.8831 (mp10) REVERT: B 81 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7962 (t) REVERT: B 234 MET cc_start: 0.8747 (ttp) cc_final: 0.8535 (ppp) REVERT: C 25 SER cc_start: 0.9240 (m) cc_final: 0.8989 (p) REVERT: C 112 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7475 (t) REVERT: D 34 GLN cc_start: 0.8675 (mp10) cc_final: 0.8406 (mp10) REVERT: D 202 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7554 (p0) REVERT: E 22 MET cc_start: 0.8055 (ttp) cc_final: 0.7829 (tmm) REVERT: E 79 MET cc_start: 0.8173 (tpp) cc_final: 0.7938 (mtt) REVERT: F 131 GLU cc_start: 0.8224 (mp0) cc_final: 0.7847 (mp0) REVERT: G 79 MET cc_start: 0.8796 (mmt) cc_final: 0.8479 (mtp) REVERT: H 231 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8398 (mttt) REVERT: I 25 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8371 (p) REVERT: I 34 GLN cc_start: 0.8603 (mp10) cc_final: 0.8197 (mp10) REVERT: I 149 ARG cc_start: 0.8310 (mtp85) cc_final: 0.7514 (mtp85) REVERT: I 219 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7568 (mtt180) REVERT: J 131 GLU cc_start: 0.7980 (mp0) cc_final: 0.7710 (pt0) REVERT: K 12 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8720 (tmm) REVERT: K 79 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7726 (mtt) REVERT: K 90 ILE cc_start: 0.8894 (tt) cc_final: 0.8579 (tp) REVERT: K 95 ILE cc_start: 0.8843 (mm) cc_final: 0.8608 (mt) REVERT: K 149 ARG cc_start: 0.8820 (mtp85) cc_final: 0.8519 (mtp85) REVERT: K 219 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7114 (mtt90) REVERT: L 219 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7831 (mtt180) REVERT: L 222 TYR cc_start: 0.7513 (t80) cc_final: 0.7304 (t80) REVERT: M 25 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8456 (p) REVERT: M 96 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8785 (m) REVERT: N 25 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8347 (p) REVERT: N 131 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7985 (mm-30) REVERT: O 22 MET cc_start: 0.9202 (ttt) cc_final: 0.8802 (ttt) REVERT: P 219 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7717 (ptp-170) outliers start: 148 outliers final: 119 residues processed: 455 average time/residue: 0.1634 time to fit residues: 121.1678 Evaluate side-chains 466 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 335 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 215 ARG Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 231 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 38 TYR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain J residue 23 GLN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 23 GLN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 79 MET Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 236 GLU Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 51 SER Chi-restraints excluded: chain O residue 79 MET Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 234 MET Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 38 TYR Chi-restraints excluded: chain P residue 102 GLN Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 217 ASP Chi-restraints excluded: chain P residue 219 ARG Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 234 MET Chi-restraints excluded: chain P residue 235 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 28 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 356 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 overall best weight: 5.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN I 110 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.069215 restraints weight = 72380.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.071566 restraints weight = 36010.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.073147 restraints weight = 22778.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.074200 restraints weight = 16654.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074916 restraints weight = 13400.823| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 29088 Z= 0.328 Angle : 0.767 16.661 39776 Z= 0.388 Chirality : 0.048 0.251 4480 Planarity : 0.005 0.075 5360 Dihedral : 5.642 23.076 4080 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.28 % Allowed : 20.73 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.12), residues: 3760 helix: -1.38 (0.30), residues: 304 sheet: -0.12 (0.17), residues: 784 loop : -2.55 (0.10), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 219 TYR 0.020 0.002 TYR K 195 PHE 0.020 0.002 PHE K 65 TRP 0.008 0.002 TRP M 76 Details of bonding type rmsd covalent geometry : bond 0.00765 (29088) covalent geometry : angle 0.76707 (39776) hydrogen bonds : bond 0.03829 ( 654) hydrogen bonds : angle 5.58027 ( 2016) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 338 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8218 (m) REVERT: A 79 MET cc_start: 0.8821 (mmt) cc_final: 0.8483 (mmt) REVERT: B 34 GLN cc_start: 0.9138 (mp10) cc_final: 0.8831 (mp10) REVERT: B 79 MET cc_start: 0.9031 (mmt) cc_final: 0.8716 (mmt) REVERT: B 81 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7991 (t) REVERT: B 234 MET cc_start: 0.8773 (ttp) cc_final: 0.8558 (ppp) REVERT: C 25 SER cc_start: 0.9349 (m) cc_final: 0.9086 (p) REVERT: C 112 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7421 (t) REVERT: D 34 GLN cc_start: 0.8800 (mp10) cc_final: 0.8526 (mp10) REVERT: D 202 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7635 (p0) REVERT: E 79 MET cc_start: 0.8321 (tpp) cc_final: 0.8015 (mtt) REVERT: F 131 GLU cc_start: 0.8334 (mp0) cc_final: 0.7872 (mp0) REVERT: I 25 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8491 (p) REVERT: I 149 ARG cc_start: 0.8478 (mtp85) cc_final: 0.7614 (mtp85) REVERT: I 219 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7517 (mtt90) REVERT: K 25 SER cc_start: 0.9313 (OUTLIER) cc_final: 0.8942 (p) REVERT: K 90 ILE cc_start: 0.9063 (tt) cc_final: 0.8833 (tp) REVERT: M 25 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8477 (p) REVERT: M 79 MET cc_start: 0.8234 (mmm) cc_final: 0.7776 (mtt) REVERT: M 96 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8879 (m) REVERT: N 25 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8586 (p) REVERT: N 51 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8913 (p) REVERT: N 79 MET cc_start: 0.8648 (mmt) cc_final: 0.8405 (tpp) REVERT: N 131 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8057 (mm-30) REVERT: O 22 MET cc_start: 0.9279 (ttt) cc_final: 0.8823 (ttt) REVERT: P 176 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.5969 (tp40) outliers start: 163 outliers final: 126 residues processed: 457 average time/residue: 0.1585 time to fit residues: 118.0417 Evaluate side-chains 464 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 327 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 215 ARG Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 38 TYR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 208 GLU Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain J residue 23 GLN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 79 MET Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 23 GLN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 228 LEU Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 51 SER Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 MET Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 234 MET Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 38 TYR Chi-restraints excluded: chain P residue 102 GLN Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 176 GLN Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 217 ASP Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 234 MET Chi-restraints excluded: chain P residue 235 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 336 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN P 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.069588 restraints weight = 71103.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072065 restraints weight = 34811.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.073740 restraints weight = 21787.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.074855 restraints weight = 15737.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.075563 restraints weight = 12554.543| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 29088 Z= 0.198 Angle : 0.665 12.183 39776 Z= 0.339 Chirality : 0.045 0.219 4480 Planarity : 0.005 0.047 5360 Dihedral : 5.287 19.872 4080 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.27 % Allowed : 21.83 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.12), residues: 3760 helix: -1.31 (0.31), residues: 304 sheet: -0.12 (0.17), residues: 784 loop : -2.50 (0.10), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 149 TYR 0.016 0.001 TYR P 135 PHE 0.020 0.001 PHE K 65 TRP 0.006 0.001 TRP D 76 Details of bonding type rmsd covalent geometry : bond 0.00463 (29088) covalent geometry : angle 0.66457 (39776) hydrogen bonds : bond 0.03413 ( 654) hydrogen bonds : angle 5.44738 ( 2016) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 353 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8139 (m) REVERT: A 79 MET cc_start: 0.8812 (mmt) cc_final: 0.8540 (mmt) REVERT: B 34 GLN cc_start: 0.9107 (mp10) cc_final: 0.8801 (mp10) REVERT: B 79 MET cc_start: 0.8970 (mmt) cc_final: 0.8748 (mmt) REVERT: C 25 SER cc_start: 0.9319 (m) cc_final: 0.9016 (p) REVERT: C 112 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7536 (t) REVERT: D 34 GLN cc_start: 0.8684 (mp10) cc_final: 0.8359 (mp10) REVERT: D 202 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7518 (p0) REVERT: E 79 MET cc_start: 0.8478 (tpp) cc_final: 0.8271 (mmt) REVERT: F 131 GLU cc_start: 0.8400 (mp0) cc_final: 0.7863 (mp0) REVERT: F 201 GLU cc_start: 0.8322 (pm20) cc_final: 0.7908 (pm20) REVERT: G 79 MET cc_start: 0.8820 (mmt) cc_final: 0.8607 (mtp) REVERT: H 231 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8346 (tttt) REVERT: H 236 GLU cc_start: 0.7942 (pt0) cc_final: 0.7366 (pt0) REVERT: I 25 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8331 (p) REVERT: I 149 ARG cc_start: 0.8367 (mtp85) cc_final: 0.7535 (mtp85) REVERT: I 219 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7566 (mtt90) REVERT: J 149 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8203 (mtp85) REVERT: K 79 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8035 (mtt) REVERT: K 90 ILE cc_start: 0.8962 (tt) cc_final: 0.8708 (tp) REVERT: L 149 ARG cc_start: 0.8347 (mtp85) cc_final: 0.7770 (mtp85) REVERT: L 219 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7831 (mtt180) REVERT: M 25 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8384 (p) REVERT: M 79 MET cc_start: 0.8316 (mmm) cc_final: 0.7921 (mtt) REVERT: M 96 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8845 (m) REVERT: N 25 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8405 (p) REVERT: N 51 SER cc_start: 0.9164 (OUTLIER) cc_final: 0.8912 (p) REVERT: N 131 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8030 (mm-30) REVERT: O 22 MET cc_start: 0.9247 (ttt) cc_final: 0.8807 (ttt) REVERT: P 176 GLN cc_start: 0.5847 (OUTLIER) cc_final: 0.5637 (tp40) outliers start: 132 outliers final: 110 residues processed: 452 average time/residue: 0.1660 time to fit residues: 121.0666 Evaluate side-chains 456 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 335 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 38 TYR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 215 ARG Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 231 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 38 TYR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 79 MET Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 23 GLN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 79 MET Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 123 ASP Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 51 SER Chi-restraints excluded: chain O residue 79 MET Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 234 MET Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 38 TYR Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 176 GLN Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 217 ASP Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 234 MET Chi-restraints excluded: chain P residue 235 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 149 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 238 optimal weight: 0.0470 chunk 342 optimal weight: 0.9980 chunk 303 optimal weight: 0.2980 chunk 361 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 296 optimal weight: 0.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN D 86 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN H 155 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN J 7 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.074358 restraints weight = 70681.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.076850 restraints weight = 34655.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.078530 restraints weight = 21611.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079652 restraints weight = 15581.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.080406 restraints weight = 12362.512| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29088 Z= 0.116 Angle : 0.608 8.858 39776 Z= 0.315 Chirality : 0.044 0.199 4480 Planarity : 0.004 0.045 5360 Dihedral : 4.800 19.112 4080 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.14 % Allowed : 23.09 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.12), residues: 3760 helix: -2.60 (0.28), residues: 304 sheet: 0.23 (0.21), residues: 576 loop : -2.25 (0.10), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 219 TYR 0.023 0.001 TYR O 166 PHE 0.022 0.001 PHE G 65 TRP 0.007 0.001 TRP J 58 Details of bonding type rmsd covalent geometry : bond 0.00274 (29088) covalent geometry : angle 0.60844 (39776) hydrogen bonds : bond 0.02996 ( 654) hydrogen bonds : angle 5.28871 ( 2016) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 372 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8226 (m) REVERT: A 79 MET cc_start: 0.8802 (mmt) cc_final: 0.8540 (mmt) REVERT: B 34 GLN cc_start: 0.9091 (mp10) cc_final: 0.8776 (mp10) REVERT: C 25 SER cc_start: 0.9233 (m) cc_final: 0.8953 (p) REVERT: D 34 GLN cc_start: 0.8590 (mp10) cc_final: 0.8286 (mp10) REVERT: D 202 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7361 (p0) REVERT: E 12 MET cc_start: 0.8728 (ppp) cc_final: 0.8452 (ppp) REVERT: E 129 LEU cc_start: 0.8613 (mm) cc_final: 0.8392 (tp) REVERT: F 131 GLU cc_start: 0.8238 (mp0) cc_final: 0.7948 (mp0) REVERT: F 201 GLU cc_start: 0.8289 (pm20) cc_final: 0.7931 (pm20) REVERT: F 219 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7112 (ptt-90) REVERT: H 236 GLU cc_start: 0.7617 (pt0) cc_final: 0.7185 (pt0) REVERT: I 149 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7336 (mtp85) REVERT: I 219 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7599 (mtt180) REVERT: J 79 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8385 (mmt) REVERT: J 219 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7252 (mtp180) REVERT: K 25 SER cc_start: 0.9144 (m) cc_final: 0.8717 (p) REVERT: K 79 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7815 (mtt) REVERT: K 90 ILE cc_start: 0.8749 (tt) cc_final: 0.8434 (tp) REVERT: K 149 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8440 (mtp85) REVERT: K 219 ARG cc_start: 0.7681 (mtt180) cc_final: 0.6408 (mtm-85) REVERT: L 57 ASP cc_start: 0.7366 (p0) cc_final: 0.6411 (p0) REVERT: L 149 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7714 (mtp85) REVERT: L 219 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7727 (mtt180) REVERT: M 79 MET cc_start: 0.8084 (mmm) cc_final: 0.7729 (mtt) REVERT: M 96 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8727 (m) REVERT: N 131 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7987 (mm-30) REVERT: N 236 GLU cc_start: 0.7343 (pp20) cc_final: 0.7087 (tm-30) REVERT: O 22 MET cc_start: 0.9115 (ttt) cc_final: 0.8896 (ttt) REVERT: O 139 ASP cc_start: 0.8321 (p0) cc_final: 0.7830 (p0) REVERT: P 180 TYR cc_start: 0.7585 (t80) cc_final: 0.7328 (t80) outliers start: 97 outliers final: 75 residues processed: 448 average time/residue: 0.1798 time to fit residues: 129.6215 Evaluate side-chains 432 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 352 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 38 TYR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 215 ARG Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain I residue 38 TYR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 79 MET Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 79 MET Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 123 ASP Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 38 TYR Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 176 GLN Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 217 ASP Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 163 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 275 optimal weight: 4.9990 chunk 333 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.086429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.069058 restraints weight = 72452.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071383 restraints weight = 36280.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.072936 restraints weight = 23060.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.074005 restraints weight = 16938.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.074712 restraints weight = 13635.549| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 29088 Z= 0.367 Angle : 0.814 17.409 39776 Z= 0.412 Chirality : 0.050 0.283 4480 Planarity : 0.005 0.046 5360 Dihedral : 5.657 24.363 4080 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.30 % Allowed : 22.80 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.73 (0.12), residues: 3760 helix: -1.28 (0.32), residues: 288 sheet: -0.12 (0.18), residues: 768 loop : -2.61 (0.10), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG O 219 TYR 0.029 0.002 TYR O 166 PHE 0.024 0.002 PHE J 65 TRP 0.009 0.002 TRP D 76 Details of bonding type rmsd covalent geometry : bond 0.00852 (29088) covalent geometry : angle 0.81431 (39776) hydrogen bonds : bond 0.03866 ( 654) hydrogen bonds : angle 5.57139 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4111.08 seconds wall clock time: 72 minutes 2.26 seconds (4322.26 seconds total)