Starting phenix.real_space_refine on Tue Jun 24 06:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikk_60657/06_2025/9ikk_60657_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikk_60657/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ikk_60657/06_2025/9ikk_60657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikk_60657/06_2025/9ikk_60657.map" model { file = "/net/cci-nas-00/data/ceres_data/9ikk_60657/06_2025/9ikk_60657_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikk_60657/06_2025/9ikk_60657_neut.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.68, per 1000 atoms: 0.62 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: 7.64 Conformation dependent library (CDL) restraints added in 8.6 seconds 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: 6.53 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: 27.69 Time building geometry restraints manager: 9.45 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: 0.28 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' 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: 7.530 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: 1.190 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 95.810 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.830 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: 0.020 Load rotamer database and sin/cos tables:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.190 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (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 TRP 0.006 0.001 TRP F 76 PHE 0.007 0.001 PHE P 82 TYR 0.011 0.001 TYR I 180 ARG 0.004 0.000 ARG K 149 Details of bonding type rmsd hydrogen bonds : bond 0.17537 ( 654) hydrogen bonds : angle 9.31428 ( 2016) covalent geometry : bond 0.00328 (29088) covalent geometry : angle 0.70448 (39776) *********************** 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 : 3.170 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: 0.7126 (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: 0.8453 (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: 0.7901 (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: 0.8230 (tp) REVERT: G 219 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7434 (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: 0.6750 (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: 0.4131 time to fit residues: 383.9880 Evaluate side-chains 377 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 375 time to evaluate : 3.565 ------------------------------------------------------------------------------- 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 310 optimal weight: 0.9980 chunk 278 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 288 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 chunk 334 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 23 GLN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.088925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.071566 restraints weight = 71869.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.073971 restraints weight = 35365.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.075617 restraints weight = 22266.214| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 29088 Z= 0.317 Angle : 0.774 13.866 39776 Z= 0.398 Chirality : 0.050 0.181 4480 Planarity : 0.005 0.046 5360 Dihedral : 5.568 31.782 4082 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.27 % Allowed : 17.52 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.13), residues: 3760 helix: -2.23 (0.29), residues: 304 sheet: 0.98 (0.20), residues: 656 loop : -2.14 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 58 PHE 0.017 0.002 PHE L 179 TYR 0.023 0.002 TYR I 222 ARG 0.008 0.001 ARG F 219 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 654) hydrogen bonds : angle 6.30760 ( 2016) covalent geometry : bond 0.00743 (29088) covalent geometry : angle 0.77390 (39776) *********************** 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 489 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 388 time to evaluate : 3.471 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: B 34 GLN cc_start: 0.8856 (mp10) cc_final: 0.8479 (mp10) REVERT: B 235 VAL cc_start: 0.8458 (t) cc_final: 0.8208 (m) REVERT: C 25 SER cc_start: 0.9206 (m) cc_final: 0.8981 (p) REVERT: C 207 ASP cc_start: 0.8099 (p0) cc_final: 0.7883 (t0) REVERT: D 34 GLN cc_start: 0.8867 (mp10) cc_final: 0.8602 (mp10) REVERT: E 23 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6491 (tp-100) REVERT: E 149 ARG cc_start: 0.8341 (mtp85) cc_final: 0.8007 (mtt90) REVERT: G 34 GLN cc_start: 0.8635 (mp10) cc_final: 0.7916 (mp10) REVERT: G 90 ILE cc_start: 0.8467 (tt) cc_final: 0.8108 (tp) REVERT: G 176 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.7055 (tp40) REVERT: H 102 GLN cc_start: 0.8702 (tt0) cc_final: 0.8408 (tt0) REVERT: I 22 MET cc_start: 0.8694 (ttp) cc_final: 0.8455 (ttp) REVERT: I 34 GLN cc_start: 0.8542 (mp10) cc_final: 0.8143 (mp10) REVERT: I 219 ARG cc_start: 0.8403 (mtt180) cc_final: 0.7946 (mtt180) REVERT: J 3 ILE cc_start: 0.8516 (mm) cc_final: 0.8305 (mm) REVERT: J 34 GLN cc_start: 0.8698 (mp10) cc_final: 0.8451 (mp10) REVERT: J 90 ILE cc_start: 0.8973 (tt) cc_final: 0.8735 (tp) REVERT: J 208 GLU cc_start: 0.8318 (pp20) cc_final: 0.8003 (pp20) REVERT: K 90 ILE cc_start: 0.8786 (tt) cc_final: 0.8486 (tp) REVERT: K 95 ILE cc_start: 0.8829 (mm) cc_final: 0.8551 (mt) REVERT: K 208 GLU cc_start: 0.8026 (pp20) cc_final: 0.7802 (pp20) REVERT: K 219 ARG cc_start: 0.7546 (mtt180) cc_final: 0.7149 (mtt90) REVERT: L 79 MET cc_start: 0.8554 (tpt) cc_final: 0.8315 (mtt) REVERT: L 205 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.8029 (p0) REVERT: M 25 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.8060 (p) REVERT: N 25 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8210 (p) REVERT: N 79 MET cc_start: 0.8910 (tpp) cc_final: 0.8535 (tpp) REVERT: N 131 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7315 (mm-30) REVERT: O 126 ARG cc_start: 0.7416 (ptt90) cc_final: 0.7132 (ptt90) REVERT: P 5 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: P 25 SER cc_start: 0.8670 (OUTLIER) cc_final: 0.8403 (p) outliers start: 101 outliers final: 56 residues processed: 447 average time/residue: 0.4125 time to fit residues: 292.5700 Evaluate side-chains 399 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 336 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU 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 C residue 208 GLU 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 199 THR Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 55 THR 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 G residue 25 SER Chi-restraints excluded: chain G residue 42 LEU 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 I residue 25 SER Chi-restraints excluded: chain I residue 199 THR 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 199 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 199 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 205 ASN 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 131 GLU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 213 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 199 THR Chi-restraints excluded: chain N residue 234 MET Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain P residue 5 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 55 THR 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 Chi-restraints excluded: chain P residue 235 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 271 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 299 optimal weight: 7.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- 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 B 205 ASN ** 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** E 23 GLN E 110 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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** ** 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 L 205 ASN M 34 GLN M 110 ASN M 133 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.088966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.071542 restraints weight = 71785.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.073981 restraints weight = 34834.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075645 restraints weight = 21788.195| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 29088 Z= 0.243 Angle : 0.675 12.424 39776 Z= 0.344 Chirality : 0.047 0.171 4480 Planarity : 0.005 0.052 5360 Dihedral : 5.359 27.732 4082 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.21 % Allowed : 18.13 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.13), residues: 3760 helix: -2.16 (0.29), residues: 304 sheet: 0.72 (0.20), residues: 656 loop : -2.17 (0.10), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 58 PHE 0.017 0.001 PHE K 65 TYR 0.018 0.002 TYR F 180 ARG 0.006 0.001 ARG N 215 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 654) hydrogen bonds : angle 5.85417 ( 2016) covalent geometry : bond 0.00570 (29088) covalent geometry : angle 0.67470 (39776) *********************** 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 495 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 365 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7735 (mp10) cc_final: 0.7445 (mp10) REVERT: B 235 VAL cc_start: 0.8593 (t) cc_final: 0.8376 (m) REVERT: C 25 SER cc_start: 0.9234 (m) cc_final: 0.8986 (p) REVERT: D 34 GLN cc_start: 0.8817 (mp10) cc_final: 0.8551 (mp10) REVERT: E 149 ARG cc_start: 0.8388 (mtp85) cc_final: 0.8176 (mtt90) REVERT: F 131 GLU cc_start: 0.8110 (mp0) cc_final: 0.7581 (mp0) REVERT: G 90 ILE cc_start: 0.8486 (tt) cc_final: 0.8114 (tp) REVERT: G 95 ILE cc_start: 0.9148 (mm) cc_final: 0.8854 (mt) REVERT: G 219 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7381 (mtt90) REVERT: H 102 GLN cc_start: 0.8720 (tt0) cc_final: 0.8470 (tt0) REVERT: I 34 GLN cc_start: 0.8609 (mp10) cc_final: 0.8203 (mp10) REVERT: I 219 ARG cc_start: 0.8391 (mtt180) cc_final: 0.7942 (mtt180) REVERT: J 3 ILE cc_start: 0.8749 (mm) cc_final: 0.8504 (mm) REVERT: J 90 ILE cc_start: 0.8993 (tt) cc_final: 0.8755 (tp) REVERT: J 208 GLU cc_start: 0.8310 (pp20) cc_final: 0.8068 (pp20) REVERT: K 90 ILE cc_start: 0.8844 (tt) cc_final: 0.8617 (tp) REVERT: K 95 ILE cc_start: 0.8834 (mm) cc_final: 0.8545 (mt) REVERT: K 208 GLU cc_start: 0.8190 (pp20) cc_final: 0.7937 (pp20) REVERT: K 219 ARG cc_start: 0.7526 (mtt180) cc_final: 0.7301 (mtt180) REVERT: L 79 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8061 (mtt) REVERT: L 96 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8826 (m) REVERT: L 205 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8222 (p0) REVERT: M 25 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8236 (p) REVERT: M 79 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8184 (tpp) REVERT: M 96 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8699 (m) REVERT: N 131 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7447 (mm-30) REVERT: N 231 LYS cc_start: 0.8879 (tttt) cc_final: 0.8538 (mtpp) REVERT: N 236 GLU cc_start: 0.7112 (pt0) cc_final: 0.6840 (pt0) REVERT: O 126 ARG cc_start: 0.7446 (ptt90) cc_final: 0.7195 (ptt90) REVERT: P 5 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: P 25 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8412 (p) outliers start: 130 outliers final: 79 residues processed: 459 average time/residue: 0.4089 time to fit residues: 302.0803 Evaluate side-chains 428 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 341 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 188 VAL 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 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 E residue 25 SER 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 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 48 VAL Chi-restraints excluded: chain F residue 93 LEU 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 97 VAL Chi-restraints excluded: chain G residue 188 VAL 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 97 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 5 GLU 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 214 VAL 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 109 THR Chi-restraints excluded: chain K residue 112 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 205 ASN Chi-restraints excluded: chain L residue 214 VAL 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 96 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 124 THR 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 57 ASP Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 188 VAL 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 P residue 5 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 38 TYR Chi-restraints excluded: chain P residue 55 THR 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 172 optimal weight: 0.0770 chunk 109 optimal weight: 9.9990 chunk 344 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 296 optimal weight: 10.0000 overall best weight: 2.8144 ------------------------------------------------------------------------------- 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 205 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 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 GLN G 205 ASN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 ASN J 205 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 ASN M 34 GLN O 133 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.072232 restraints weight = 71915.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074693 restraints weight = 34382.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.076368 restraints weight = 21278.148| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29088 Z= 0.187 Angle : 0.632 11.195 39776 Z= 0.323 Chirality : 0.045 0.157 4480 Planarity : 0.004 0.041 5360 Dihedral : 5.171 27.478 4082 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.34 % Allowed : 19.17 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.13), residues: 3760 helix: -2.29 (0.29), residues: 304 sheet: 0.53 (0.20), residues: 656 loop : -2.16 (0.10), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 58 PHE 0.017 0.001 PHE K 65 TYR 0.016 0.001 TYR O 195 ARG 0.004 0.000 ARG N 215 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 654) hydrogen bonds : angle 5.63734 ( 2016) covalent geometry : bond 0.00439 (29088) covalent geometry : angle 0.63176 (39776) *********************** 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 506 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 372 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7298 (mt-10) REVERT: A 51 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8297 (m) REVERT: B 79 MET cc_start: 0.9172 (tpp) cc_final: 0.8770 (mmt) REVERT: B 235 VAL cc_start: 0.8589 (t) cc_final: 0.8360 (m) REVERT: C 25 SER cc_start: 0.9213 (m) cc_final: 0.8962 (p) REVERT: D 34 GLN cc_start: 0.8749 (mp10) cc_final: 0.8445 (mp10) REVERT: D 235 VAL cc_start: 0.8679 (t) cc_final: 0.8469 (m) REVERT: E 22 MET cc_start: 0.8415 (tmm) cc_final: 0.8074 (tmm) REVERT: E 79 MET cc_start: 0.8260 (tpp) cc_final: 0.8026 (tpp) REVERT: F 131 GLU cc_start: 0.8185 (mp0) cc_final: 0.7818 (mp0) REVERT: G 90 ILE cc_start: 0.8442 (tt) cc_final: 0.8076 (tp) REVERT: G 95 ILE cc_start: 0.9095 (mm) cc_final: 0.8825 (mt) REVERT: G 219 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7442 (mtt90) REVERT: H 96 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9090 (m) REVERT: H 102 GLN cc_start: 0.8737 (tt0) cc_final: 0.8526 (tt0) REVERT: H 110 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7309 (p0) REVERT: I 34 GLN cc_start: 0.8575 (mp10) cc_final: 0.8164 (mp10) REVERT: I 131 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7342 (mm-30) REVERT: I 219 ARG cc_start: 0.8369 (mtt180) cc_final: 0.7890 (mtt180) REVERT: J 34 GLN cc_start: 0.8737 (mp10) cc_final: 0.8486 (mp10) REVERT: J 90 ILE cc_start: 0.9030 (tt) cc_final: 0.8790 (tp) REVERT: J 205 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8230 (t0) REVERT: K 79 MET cc_start: 0.8426 (tpp) cc_final: 0.7895 (mtt) REVERT: K 90 ILE cc_start: 0.8813 (tt) cc_final: 0.8599 (tp) REVERT: K 219 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7315 (mtt180) REVERT: L 79 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8134 (mtt) REVERT: L 96 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8879 (m) REVERT: L 205 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8347 (t0) REVERT: M 96 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8759 (m) REVERT: N 25 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8359 (p) REVERT: N 51 SER cc_start: 0.9183 (OUTLIER) cc_final: 0.8928 (p) REVERT: N 131 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7534 (mm-30) REVERT: N 231 LYS cc_start: 0.8888 (tttt) cc_final: 0.8529 (mtpp) REVERT: O 126 ARG cc_start: 0.7375 (ptt90) cc_final: 0.7163 (ptt90) REVERT: O 150 TYR cc_start: 0.8833 (m-80) cc_final: 0.8622 (m-10) REVERT: O 231 LYS cc_start: 0.9021 (tttt) cc_final: 0.8779 (mtpt) REVERT: P 5 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: P 25 SER cc_start: 0.8686 (m) cc_final: 0.8388 (p) outliers start: 134 outliers final: 87 residues processed: 470 average time/residue: 0.3785 time to fit residues: 285.3398 Evaluate side-chains 440 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 342 time to evaluate : 3.263 ------------------------------------------------------------------------------- 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 188 VAL 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 93 LEU Chi-restraints excluded: chain B residue 97 VAL 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 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 214 VAL 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 48 VAL Chi-restraints excluded: chain F residue 93 LEU 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 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 52 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 151 ILE 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 J residue 5 GLU Chi-restraints excluded: chain J residue 25 SER 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 205 ASN Chi-restraints excluded: chain J residue 214 VAL 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 199 THR Chi-restraints excluded: chain K residue 214 VAL 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 151 ILE Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 205 ASN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 124 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 57 ASP Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 199 THR 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 P residue 5 GLU 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 188 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 345 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 23 GLN C 133 ASN ** F 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 23 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 ASN L 205 ASN M 34 GLN N 155 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.086760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.069598 restraints weight = 72517.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.071961 restraints weight = 35676.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.073565 restraints weight = 22543.096| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3857 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= 0.369 Angle : 0.792 18.229 39776 Z= 0.401 Chirality : 0.050 0.195 4480 Planarity : 0.005 0.045 5360 Dihedral : 5.800 31.442 4082 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.44 % Allowed : 19.66 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.12), residues: 3760 helix: -1.35 (0.30), residues: 304 sheet: 0.06 (0.18), residues: 784 loop : -2.49 (0.10), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 76 PHE 0.018 0.002 PHE B 179 TYR 0.022 0.002 TYR F 180 ARG 0.005 0.001 ARG N 219 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 654) hydrogen bonds : angle 5.78541 ( 2016) covalent geometry : bond 0.00858 (29088) covalent geometry : angle 0.79202 (39776) *********************** 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 522 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 354 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7462 (mt-10) REVERT: A 234 MET cc_start: 0.8831 (tmm) cc_final: 0.8438 (tmm) REVERT: B 79 MET cc_start: 0.9199 (tpp) cc_final: 0.8868 (mmt) REVERT: C 25 SER cc_start: 0.9266 (m) cc_final: 0.8996 (p) REVERT: C 112 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7526 (t) REVERT: D 34 GLN cc_start: 0.8858 (mp10) cc_final: 0.8590 (mp10) REVERT: D 202 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7944 (p0) REVERT: E 149 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8375 (mtt90) REVERT: G 95 ILE cc_start: 0.9195 (mm) cc_final: 0.8973 (mt) REVERT: H 96 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9190 (m) REVERT: H 102 GLN cc_start: 0.8872 (tt0) cc_final: 0.8649 (tt0) REVERT: H 110 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7359 (p0) REVERT: H 231 LYS cc_start: 0.8853 (tttt) cc_final: 0.8649 (tttt) REVERT: I 25 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8398 (p) REVERT: I 34 GLN cc_start: 0.8631 (mp10) cc_final: 0.8198 (mp10) REVERT: I 219 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7954 (mtt180) REVERT: I 236 GLU cc_start: 0.8048 (pt0) cc_final: 0.7806 (pt0) REVERT: J 34 GLN cc_start: 0.8685 (mp10) cc_final: 0.8480 (mp10) REVERT: J 90 ILE cc_start: 0.9264 (tt) cc_final: 0.8967 (tp) REVERT: J 149 ARG cc_start: 0.8547 (mtp85) cc_final: 0.7483 (mtp85) REVERT: K 25 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9016 (p) REVERT: K 90 ILE cc_start: 0.9052 (tt) cc_final: 0.8749 (tp) REVERT: K 95 ILE cc_start: 0.8868 (mm) cc_final: 0.8634 (mt) REVERT: K 219 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7246 (mtt90) REVERT: L 96 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8954 (m) REVERT: L 149 ARG cc_start: 0.8420 (mtp85) cc_final: 0.7863 (mtp85) REVERT: L 176 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6353 (tt0) REVERT: L 205 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8009 (p0) REVERT: M 25 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8405 (p) REVERT: M 79 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7700 (mtt) REVERT: M 96 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8944 (m) REVERT: N 79 MET cc_start: 0.8821 (tpp) cc_final: 0.8505 (tpp) REVERT: N 131 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7972 (mm-30) REVERT: N 231 LYS cc_start: 0.8927 (tttt) cc_final: 0.8505 (mtpp) REVERT: O 22 MET cc_start: 0.9238 (ttt) cc_final: 0.8833 (ttt) REVERT: O 79 MET cc_start: 0.8274 (mmm) cc_final: 0.7956 (mtt) REVERT: O 126 ARG cc_start: 0.7383 (ptt90) cc_final: 0.7171 (ptt90) REVERT: P 5 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: P 176 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.6059 (tp40) outliers start: 168 outliers final: 124 residues processed: 480 average time/residue: 0.3614 time to fit residues: 281.1577 Evaluate side-chains 470 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 332 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 109 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 93 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 55 THR 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 97 VAL Chi-restraints excluded: chain D residue 109 THR 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 D residue 202 ASP Chi-restraints excluded: chain E residue 23 GLN 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 23 GLN 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 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 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 110 ASN 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 I residue 22 MET 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 J residue 5 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 55 THR 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 23 GLN 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 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 K residue 234 MET 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 151 ILE Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 205 ASN 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 79 MET Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 124 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 48 VAL Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 199 THR 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 109 THR Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 183 ILE 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 5 GLU Chi-restraints excluded: chain P residue 12 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 228 LEU Chi-restraints excluded: chain P residue 234 MET Chi-restraints excluded: chain P residue 235 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 148 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 350 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 155 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN ** 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 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 ASN L 205 ASN M 34 GLN N 155 ASN P 78 ASN P 205 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074043 restraints weight = 70973.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.076525 restraints weight = 34626.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078215 restraints weight = 21663.369| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29088 Z= 0.133 Angle : 0.603 9.481 39776 Z= 0.311 Chirality : 0.044 0.257 4480 Planarity : 0.004 0.048 5360 Dihedral : 5.093 25.771 4082 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.21 % Allowed : 21.70 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.12), residues: 3760 helix: -1.26 (0.37), residues: 208 sheet: 0.09 (0.18), residues: 784 loop : -2.30 (0.10), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 58 PHE 0.025 0.001 PHE K 65 TYR 0.014 0.001 TYR N 180 ARG 0.005 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 654) hydrogen bonds : angle 5.46236 ( 2016) covalent geometry : bond 0.00310 (29088) covalent geometry : angle 0.60255 (39776) *********************** 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 508 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 378 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8288 (m) REVERT: B 79 MET cc_start: 0.9156 (tpp) cc_final: 0.8785 (mmt) REVERT: C 25 SER cc_start: 0.9224 (m) cc_final: 0.8894 (p) REVERT: C 112 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7490 (t) REVERT: D 34 GLN cc_start: 0.8594 (mp10) cc_final: 0.8311 (mp10) REVERT: D 202 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7855 (p0) REVERT: F 195 TYR cc_start: 0.8257 (m-80) cc_final: 0.7566 (m-80) REVERT: G 219 ARG cc_start: 0.7942 (mtt180) cc_final: 0.7727 (mtt180) REVERT: H 96 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9149 (m) REVERT: H 110 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7308 (p0) REVERT: H 180 TYR cc_start: 0.7071 (t80) cc_final: 0.6838 (t80) REVERT: H 236 GLU cc_start: 0.7701 (pt0) cc_final: 0.7249 (pt0) REVERT: I 34 GLN cc_start: 0.8593 (mp10) cc_final: 0.8185 (mp10) REVERT: I 149 ARG cc_start: 0.8376 (mtp85) cc_final: 0.7557 (mtp85) REVERT: I 219 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7857 (mtt90) REVERT: J 34 GLN cc_start: 0.8578 (mp10) cc_final: 0.8322 (mp10) REVERT: J 90 ILE cc_start: 0.9033 (tt) cc_final: 0.8775 (tp) REVERT: K 25 SER cc_start: 0.9244 (OUTLIER) cc_final: 0.8883 (p) REVERT: K 90 ILE cc_start: 0.8900 (tt) cc_final: 0.8686 (tp) REVERT: K 219 ARG cc_start: 0.7602 (mtt180) cc_final: 0.7355 (mtt180) REVERT: L 79 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8073 (mtt) REVERT: L 149 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7872 (mtp85) REVERT: L 205 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.8006 (p0) REVERT: L 219 ARG cc_start: 0.8154 (mtt180) cc_final: 0.7818 (mtt180) REVERT: N 131 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7876 (mm-30) REVERT: O 22 MET cc_start: 0.9137 (ttt) cc_final: 0.8910 (ttt) REVERT: O 79 MET cc_start: 0.8191 (mmm) cc_final: 0.7695 (mtt) REVERT: P 5 GLU cc_start: 0.8176 (pm20) cc_final: 0.7843 (pm20) REVERT: P 219 ARG cc_start: 0.7505 (mtt180) cc_final: 0.7300 (ptp-170) outliers start: 130 outliers final: 83 residues processed: 474 average time/residue: 0.4039 time to fit residues: 306.3755 Evaluate side-chains 428 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 337 time to evaluate : 3.276 ------------------------------------------------------------------------------- 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 109 THR 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 93 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 23 GLN 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 97 VAL Chi-restraints excluded: chain E residue 199 THR 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 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 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 H residue 25 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 110 ASN 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 J residue 5 GLU 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 209 THR 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 109 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain L residue 79 MET 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 205 ASN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 124 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain O residue 25 SER 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 188 VAL Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 234 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 51 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 315 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 23 GLN C 155 ASN ** 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** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 ASN L 205 ASN M 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.089662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.072421 restraints weight = 71174.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074874 restraints weight = 34877.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076533 restraints weight = 21853.455| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3845 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= 0.204 Angle : 0.654 12.913 39776 Z= 0.333 Chirality : 0.045 0.181 4480 Planarity : 0.004 0.052 5360 Dihedral : 5.156 23.045 4080 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.18 % Allowed : 21.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.12), residues: 3760 helix: -1.25 (0.37), residues: 208 sheet: 0.06 (0.18), residues: 784 loop : -2.32 (0.10), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 76 PHE 0.022 0.001 PHE K 65 TYR 0.017 0.001 TYR N 195 ARG 0.006 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 654) hydrogen bonds : angle 5.42269 ( 2016) covalent geometry : bond 0.00477 (29088) covalent geometry : angle 0.65377 (39776) *********************** 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 471 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 342 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8274 (m) REVERT: A 79 MET cc_start: 0.8796 (mmt) cc_final: 0.8349 (mmt) REVERT: B 79 MET cc_start: 0.9139 (tpp) cc_final: 0.8719 (mmt) REVERT: C 25 SER cc_start: 0.9231 (m) cc_final: 0.8899 (p) REVERT: D 34 GLN cc_start: 0.8698 (mp10) cc_final: 0.8402 (mp10) REVERT: E 22 MET cc_start: 0.8303 (tmm) cc_final: 0.8076 (tmm) REVERT: F 131 GLU cc_start: 0.8073 (mp0) cc_final: 0.7817 (mp0) REVERT: G 79 MET cc_start: 0.8501 (mtp) cc_final: 0.8280 (mtt) REVERT: H 96 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.9204 (m) REVERT: H 180 TYR cc_start: 0.7155 (t80) cc_final: 0.6933 (t80) REVERT: H 231 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8416 (tttt) REVERT: H 236 GLU cc_start: 0.7829 (pt0) cc_final: 0.7390 (pt0) REVERT: I 25 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8376 (p) REVERT: I 34 GLN cc_start: 0.8610 (mp10) cc_final: 0.8195 (mp10) REVERT: I 131 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7395 (mm-30) REVERT: I 219 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7824 (mtt180) REVERT: J 5 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: J 90 ILE cc_start: 0.9167 (tt) cc_final: 0.8943 (tp) REVERT: K 25 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.8928 (p) REVERT: K 79 MET cc_start: 0.8283 (tpp) cc_final: 0.7634 (mtt) REVERT: K 90 ILE cc_start: 0.9002 (tt) cc_final: 0.8760 (tp) REVERT: K 95 ILE cc_start: 0.8844 (mm) cc_final: 0.8616 (mt) REVERT: L 149 ARG cc_start: 0.8372 (mtp85) cc_final: 0.7884 (mtp85) REVERT: L 205 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8197 (p0) REVERT: L 219 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7800 (mtt180) REVERT: M 79 MET cc_start: 0.8286 (mmm) cc_final: 0.7714 (mtt) REVERT: N 131 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7995 (mm-30) REVERT: O 22 MET cc_start: 0.9184 (ttt) cc_final: 0.8943 (ttt) REVERT: O 79 MET cc_start: 0.8218 (mmm) cc_final: 0.7821 (mtt) REVERT: O 208 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7405 (tm-30) REVERT: P 5 GLU cc_start: 0.8226 (pm20) cc_final: 0.7895 (pm20) REVERT: P 219 ARG cc_start: 0.7584 (mtt180) cc_final: 0.7334 (ptp-170) outliers start: 129 outliers final: 103 residues processed: 439 average time/residue: 0.3931 time to fit residues: 277.8135 Evaluate side-chains 435 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 325 time to evaluate : 3.393 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 225 VAL 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 E residue 23 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 56 VAL 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 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 52 VAL Chi-restraints excluded: chain H residue 96 THR 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 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 J residue 5 GLU 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 214 VAL 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 109 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain L residue 55 THR 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 205 ASN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 124 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 161 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 48 VAL Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 209 THR 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 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 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 188 VAL Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 234 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 3 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 216 optimal weight: 0.5980 chunk 144 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 23 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 ASN ** 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 205 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 ASN L 205 ASN M 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072093 restraints weight = 71790.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.074488 restraints weight = 35319.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076096 restraints weight = 22272.367| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29088 Z= 0.164 Angle : 0.630 11.233 39776 Z= 0.322 Chirality : 0.045 0.204 4480 Planarity : 0.004 0.048 5360 Dihedral : 5.050 20.178 4080 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.08 % Allowed : 21.83 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.12), residues: 3760 helix: -1.29 (0.37), residues: 208 sheet: 0.04 (0.18), residues: 784 loop : -2.31 (0.10), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 76 PHE 0.021 0.001 PHE K 65 TYR 0.019 0.001 TYR K 195 ARG 0.005 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 654) hydrogen bonds : angle 5.39431 ( 2016) covalent geometry : bond 0.00387 (29088) covalent geometry : angle 0.63000 (39776) *********************** 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 478 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 352 time to evaluate : 3.044 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: 0.8755 (OUTLIER) cc_final: 0.8238 (m) REVERT: B 79 MET cc_start: 0.9143 (tpp) cc_final: 0.8698 (mmt) REVERT: C 25 SER cc_start: 0.9245 (m) cc_final: 0.8968 (p) REVERT: D 34 GLN cc_start: 0.8620 (mp10) cc_final: 0.8284 (mp10) REVERT: D 234 MET cc_start: 0.7909 (ptp) cc_final: 0.7645 (ptp) REVERT: E 22 MET cc_start: 0.8333 (tmm) cc_final: 0.8096 (tmm) REVERT: F 131 GLU cc_start: 0.8084 (mp0) cc_final: 0.7835 (mp0) REVERT: H 180 TYR cc_start: 0.7168 (t80) cc_final: 0.6947 (t80) REVERT: H 236 GLU cc_start: 0.7837 (pt0) cc_final: 0.7360 (pt0) REVERT: I 25 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8272 (p) REVERT: I 34 GLN cc_start: 0.8602 (mp10) cc_final: 0.8147 (mp10) REVERT: I 219 ARG cc_start: 0.8304 (mtt180) cc_final: 0.7831 (mtt180) REVERT: J 5 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8401 (pt0) REVERT: J 90 ILE cc_start: 0.9009 (tt) cc_final: 0.8800 (tp) REVERT: K 25 SER cc_start: 0.9276 (OUTLIER) cc_final: 0.8895 (p) REVERT: K 79 MET cc_start: 0.8408 (tpp) cc_final: 0.7872 (mtt) REVERT: K 90 ILE cc_start: 0.8973 (tt) cc_final: 0.8710 (tp) REVERT: K 95 ILE cc_start: 0.8849 (mm) cc_final: 0.8622 (mt) REVERT: L 149 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7928 (mtp85) REVERT: L 205 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.7938 (p0) REVERT: L 219 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7818 (mtt180) REVERT: M 79 MET cc_start: 0.8286 (mmm) cc_final: 0.7879 (mtt) REVERT: N 79 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7974 (mtt) REVERT: N 131 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7954 (mm-30) REVERT: O 22 MET cc_start: 0.9172 (ttt) cc_final: 0.8933 (ttt) REVERT: O 79 MET cc_start: 0.8253 (mmm) cc_final: 0.7943 (mtt) REVERT: P 5 GLU cc_start: 0.8247 (pm20) cc_final: 0.7935 (pm20) REVERT: P 219 ARG cc_start: 0.7589 (mtt180) cc_final: 0.7147 (ptp-170) outliers start: 126 outliers final: 103 residues processed: 447 average time/residue: 0.3751 time to fit residues: 269.5197 Evaluate side-chains 446 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 337 time to evaluate : 3.023 ------------------------------------------------------------------------------- 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 51 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 225 VAL 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 E residue 23 GLN 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 97 VAL Chi-restraints excluded: chain E residue 199 THR 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 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 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 151 ILE Chi-restraints excluded: chain H residue 215 ARG Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 5 GLU 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 124 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 214 VAL 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 109 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 234 MET 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 176 GLN Chi-restraints excluded: chain L residue 205 ASN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 124 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 161 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 57 ASP Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 209 THR 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 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 38 TYR 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 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 140 optimal weight: 0.0270 chunk 231 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 269 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 170 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 chunk 166 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- 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** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN M 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.073595 restraints weight = 71109.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.076064 restraints weight = 34322.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.077704 restraints weight = 21351.499| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29088 Z= 0.127 Angle : 0.601 10.167 39776 Z= 0.309 Chirality : 0.044 0.211 4480 Planarity : 0.004 0.048 5360 Dihedral : 4.853 21.845 4080 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.40 % Allowed : 22.51 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.12), residues: 3760 helix: -2.47 (0.30), residues: 288 sheet: 0.06 (0.20), residues: 656 loop : -2.17 (0.10), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 76 PHE 0.022 0.001 PHE F 65 TYR 0.016 0.001 TYR P 135 ARG 0.008 0.000 ARG O 215 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 654) hydrogen bonds : angle 5.34416 ( 2016) covalent geometry : bond 0.00299 (29088) covalent geometry : angle 0.60108 (39776) *********************** 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 469 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 364 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7918 (pm20) REVERT: A 51 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8242 (m) REVERT: B 79 MET cc_start: 0.9136 (tpp) cc_final: 0.8687 (mmt) REVERT: C 25 SER cc_start: 0.9200 (m) cc_final: 0.8864 (p) REVERT: C 82 PHE cc_start: 0.7194 (m-10) cc_final: 0.6885 (m-80) REVERT: D 34 GLN cc_start: 0.8578 (mp10) cc_final: 0.8271 (mp10) REVERT: E 22 MET cc_start: 0.8236 (tmm) cc_final: 0.8035 (tmm) REVERT: F 131 GLU cc_start: 0.8016 (mp0) cc_final: 0.7805 (mp0) REVERT: F 195 TYR cc_start: 0.8248 (m-80) cc_final: 0.7477 (m-80) REVERT: H 180 TYR cc_start: 0.7083 (t80) cc_final: 0.6882 (t80) REVERT: H 231 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8407 (tttt) REVERT: H 236 GLU cc_start: 0.7707 (pt0) cc_final: 0.7277 (pt0) REVERT: I 25 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8234 (p) REVERT: I 34 GLN cc_start: 0.8588 (mp10) cc_final: 0.8140 (mp10) REVERT: I 219 ARG cc_start: 0.8325 (mtt180) cc_final: 0.8006 (mtt90) REVERT: J 5 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: J 149 ARG cc_start: 0.8533 (mtp85) cc_final: 0.8316 (mtp85) REVERT: K 25 SER cc_start: 0.9227 (m) cc_final: 0.8842 (p) REVERT: K 79 MET cc_start: 0.8299 (tpp) cc_final: 0.7710 (mtt) REVERT: K 90 ILE cc_start: 0.8854 (tt) cc_final: 0.8641 (tp) REVERT: K 95 ILE cc_start: 0.8869 (mm) cc_final: 0.8622 (mt) REVERT: L 57 ASP cc_start: 0.7436 (p0) cc_final: 0.7226 (p0) REVERT: L 219 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7818 (mtt180) REVERT: M 79 MET cc_start: 0.8232 (mmm) cc_final: 0.7815 (mtt) REVERT: N 131 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7921 (mm-30) REVERT: O 79 MET cc_start: 0.8234 (mmm) cc_final: 0.7778 (mtt) REVERT: P 5 GLU cc_start: 0.8253 (pm20) cc_final: 0.7902 (pm20) REVERT: P 219 ARG cc_start: 0.7517 (mtt180) cc_final: 0.7115 (ptp-170) outliers start: 105 outliers final: 87 residues processed: 443 average time/residue: 0.3785 time to fit residues: 269.6683 Evaluate side-chains 437 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 346 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 38 TYR 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 51 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain E residue 23 GLN 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 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 124 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 202 ASP 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 231 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 5 GLU 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 214 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 VAL 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 199 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 234 MET 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 L residue 228 LEU Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 124 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 161 VAL 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 57 ASP Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 42 LEU 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 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 188 VAL Chi-restraints excluded: chain P residue 214 VAL 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 234 optimal weight: 10.0000 chunk 254 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 229 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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** ** 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 ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 ASN M 34 GLN N 155 ASN ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.087173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.069459 restraints weight = 71600.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.071888 restraints weight = 34950.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.073541 restraints weight = 21838.478| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 29088 Z= 0.243 Angle : 0.695 14.780 39776 Z= 0.352 Chirality : 0.046 0.237 4480 Planarity : 0.004 0.047 5360 Dihedral : 5.250 20.735 4080 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.40 % Allowed : 22.57 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.12), residues: 3760 helix: -1.02 (0.40), residues: 192 sheet: -0.05 (0.18), residues: 784 loop : -2.35 (0.10), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 76 PHE 0.020 0.001 PHE K 65 TYR 0.021 0.002 TYR M 166 ARG 0.008 0.001 ARG L 149 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 654) hydrogen bonds : angle 5.46746 ( 2016) covalent geometry : bond 0.00566 (29088) covalent geometry : angle 0.69511 (39776) ********************** 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 448 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 343 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7847 (mp0) REVERT: B 79 MET cc_start: 0.9136 (tpp) cc_final: 0.8707 (mmt) REVERT: C 25 SER cc_start: 0.9269 (m) cc_final: 0.8971 (p) REVERT: C 79 MET cc_start: 0.9475 (tpt) cc_final: 0.9019 (mmm) REVERT: D 34 GLN cc_start: 0.8701 (mp10) cc_final: 0.8410 (mp10) REVERT: E 22 MET cc_start: 0.8351 (tmm) cc_final: 0.8105 (tmm) REVERT: F 131 GLU cc_start: 0.8114 (mp0) cc_final: 0.7784 (mp0) REVERT: F 201 GLU cc_start: 0.8336 (pm20) cc_final: 0.7922 (pm20) REVERT: G 131 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: H 236 GLU cc_start: 0.7975 (pt0) cc_final: 0.7449 (pt0) REVERT: I 25 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8277 (p) REVERT: I 34 GLN cc_start: 0.8609 (mp10) cc_final: 0.8146 (mp10) REVERT: I 219 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7786 (mtt180) REVERT: J 5 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8419 (pt0) REVERT: J 207 ASP cc_start: 0.7788 (p0) cc_final: 0.7510 (t0) REVERT: K 25 SER cc_start: 0.9301 (m) cc_final: 0.8909 (p) REVERT: K 90 ILE cc_start: 0.9022 (tt) cc_final: 0.8796 (tp) REVERT: L 219 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7793 (mtt180) REVERT: M 79 MET cc_start: 0.8335 (mmm) cc_final: 0.7931 (mtt) REVERT: N 131 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7967 (mm-30) REVERT: O 22 MET cc_start: 0.9226 (ttt) cc_final: 0.8865 (ttt) REVERT: O 79 MET cc_start: 0.8299 (mmm) cc_final: 0.7927 (mtt) REVERT: P 5 GLU cc_start: 0.8324 (pm20) cc_final: 0.7992 (pm20) outliers start: 105 outliers final: 95 residues processed: 424 average time/residue: 0.3850 time to fit residues: 263.3932 Evaluate side-chains 432 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 334 time to evaluate : 3.439 ------------------------------------------------------------------------------- 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 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 51 SER Chi-restraints excluded: chain B residue 55 THR 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 C residue 214 VAL 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 E residue 23 GLN 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 97 VAL Chi-restraints excluded: chain E residue 129 LEU 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 48 VAL 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 131 GLU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 202 ASP 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 I residue 25 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 5 GLU 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 23 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 VAL 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 199 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 234 MET 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 176 GLN Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 124 THR Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 161 VAL 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 57 ASP Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 51 SER 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 12 MET Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 38 TYR 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 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 365 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 297 optimal weight: 0.3980 chunk 11 optimal weight: 0.0970 chunk 347 optimal weight: 2.9990 chunk 320 optimal weight: 0.3980 chunk 273 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 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 110 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.073430 restraints weight = 71336.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075862 restraints weight = 35053.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077519 restraints weight = 21970.798| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3992 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= 0.135 Angle : 0.617 10.045 39776 Z= 0.317 Chirality : 0.044 0.199 4480 Planarity : 0.004 0.047 5360 Dihedral : 4.908 18.977 4080 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.11 % Allowed : 23.02 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.12), residues: 3760 helix: -2.46 (0.30), residues: 288 sheet: -0.06 (0.19), residues: 656 loop : -2.19 (0.10), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 58 PHE 0.018 0.001 PHE K 65 TYR 0.023 0.001 TYR O 166 ARG 0.008 0.000 ARG O 215 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 654) hydrogen bonds : angle 5.36176 ( 2016) covalent geometry : bond 0.00318 (29088) covalent geometry : angle 0.61656 (39776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9123.70 seconds wall clock time: 159 minutes 49.60 seconds (9589.60 seconds total)