Starting phenix.real_space_refine on Sun Aug 24 09:55:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fk7_29249/08_2025/8fk7_29249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fk7_29249/08_2025/8fk7_29249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fk7_29249/08_2025/8fk7_29249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fk7_29249/08_2025/8fk7_29249.map" model { file = "/net/cci-nas-00/data/ceres_data/8fk7_29249/08_2025/8fk7_29249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fk7_29249/08_2025/8fk7_29249.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 sd= 0.028 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 60 5.16 5 C 12620 2.51 5 N 3280 2.21 5 O 3780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19740 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "D" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "I" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "J" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "K" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "L" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "M" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "N" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "O" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "P" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "R" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "S" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "T" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 987 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Time building chain proxies: 3.85, per 1000 atoms: 0.20 Number of scatterers: 19740 At special positions: 0 Unit cell: (99.36, 100.44, 199.8, 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 60 16.00 O 3780 8.00 N 3280 7.00 C 12620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 117 " distance=2.03 Simple disulfide: pdb=" SG CYS E 93 " - pdb=" SG CYS E 117 " distance=2.03 Simple disulfide: pdb=" SG CYS F 93 " - pdb=" SG CYS F 117 " distance=2.03 Simple disulfide: pdb=" SG CYS G 93 " - pdb=" SG CYS G 117 " distance=2.03 Simple disulfide: pdb=" SG CYS H 93 " - pdb=" SG CYS H 117 " distance=2.03 Simple disulfide: pdb=" SG CYS I 93 " - pdb=" SG CYS I 117 " distance=2.03 Simple disulfide: pdb=" SG CYS J 93 " - pdb=" SG CYS J 117 " distance=2.03 Simple disulfide: pdb=" SG CYS K 93 " - pdb=" SG CYS K 117 " distance=2.03 Simple disulfide: pdb=" SG CYS L 93 " - pdb=" SG CYS L 117 " distance=2.03 Simple disulfide: pdb=" SG CYS M 93 " - pdb=" SG CYS M 117 " distance=2.03 Simple disulfide: pdb=" SG CYS N 93 " - pdb=" SG CYS N 117 " distance=2.03 Simple disulfide: pdb=" SG CYS O 93 " - pdb=" SG CYS O 117 " distance=2.02 Simple disulfide: pdb=" SG CYS P 93 " - pdb=" SG CYS P 117 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 93 " - pdb=" SG CYS Q 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 93 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS S 93 " - pdb=" SG CYS S 117 " distance=2.03 Simple disulfide: pdb=" SG CYS T 93 " - pdb=" SG CYS T 117 " distance=2.03 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: 1.20 Conformation dependent library (CDL) restraints added in 779.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 40 sheets defined 28.0% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 9 through 47 removed outlier: 3.927A pdb=" N ALA A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 47 Processing helix chain 'C' and resid 10 through 47 Processing helix chain 'D' and resid 10 through 47 Processing helix chain 'E' and resid 10 through 47 Processing helix chain 'F' and resid 10 through 47 Processing helix chain 'G' and resid 10 through 47 Processing helix chain 'H' and resid 10 through 47 Processing helix chain 'I' and resid 10 through 47 Processing helix chain 'J' and resid 10 through 47 Processing helix chain 'K' and resid 10 through 47 Processing helix chain 'L' and resid 10 through 47 Processing helix chain 'M' and resid 10 through 47 Processing helix chain 'N' and resid 10 through 47 Processing helix chain 'O' and resid 10 through 47 Processing helix chain 'P' and resid 10 through 47 Processing helix chain 'Q' and resid 10 through 47 Processing helix chain 'R' and resid 10 through 47 Processing helix chain 'S' and resid 10 through 47 Processing helix chain 'T' and resid 10 through 48 removed outlier: 3.863A pdb=" N ALA T 48 " --> pdb=" O GLU T 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 60 removed outlier: 5.373A pdb=" N ILE A 54 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG A 69 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 56 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 103 removed outlier: 12.654A pdb=" N GLY A 95 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 11.598A pdb=" N LEU A 84 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N LEU A 97 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N TYR A 82 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N SER A 99 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER A 80 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 80 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR A 125 " --> pdb=" O PHE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 60 removed outlier: 5.820A pdb=" N ILE B 54 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 69 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA B 56 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 103 removed outlier: 12.299A pdb=" N GLY B 95 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N LEU B 84 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 11.420A pdb=" N LEU B 97 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 11.581A pdb=" N TYR B 82 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 10.759A pdb=" N SER B 99 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER B 80 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 101 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 80 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR B 125 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 141 " --> pdb=" O TYR B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 60 removed outlier: 5.535A pdb=" N ILE C 54 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG C 69 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA C 56 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 91 through 103 removed outlier: 12.622A pdb=" N GLY C 95 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 11.589A pdb=" N LEU C 84 " --> pdb=" O GLY C 95 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N LEU C 97 " --> pdb=" O TYR C 82 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N TYR C 82 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 10.799A pdb=" N SER C 99 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER C 80 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 76 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 80 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR C 125 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 141 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 60 removed outlier: 7.221A pdb=" N ASN D 67 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL D 57 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER D 65 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS D 59 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 91 through 103 removed outlier: 12.705A pdb=" N GLY D 95 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 11.667A pdb=" N LEU D 84 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 11.446A pdb=" N LEU D 97 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N TYR D 82 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N SER D 99 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER D 80 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 101 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 80 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 60 removed outlier: 5.797A pdb=" N ILE E 54 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG E 69 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA E 56 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 103 removed outlier: 12.604A pdb=" N GLY E 95 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N LEU E 84 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 11.499A pdb=" N LEU E 97 " --> pdb=" O TYR E 82 " (cutoff:3.500A) removed outlier: 11.671A pdb=" N TYR E 82 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N SER E 99 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER E 80 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER E 80 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE E 126 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR E 125 " --> pdb=" O PHE E 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 60 removed outlier: 5.170A pdb=" N ILE F 54 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG F 69 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA F 56 " --> pdb=" O ASN F 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 91 through 103 removed outlier: 12.505A pdb=" N GLY F 95 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 11.517A pdb=" N LEU F 84 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 11.503A pdb=" N LEU F 97 " --> pdb=" O TYR F 82 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N TYR F 82 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 10.776A pdb=" N SER F 99 " --> pdb=" O SER F 80 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER F 80 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER F 80 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR F 125 " --> pdb=" O PHE F 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 53 through 60 removed outlier: 5.374A pdb=" N ILE G 54 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG G 69 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA G 56 " --> pdb=" O ASN G 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 91 through 103 removed outlier: 12.579A pdb=" N GLY G 95 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 11.479A pdb=" N LEU G 84 " --> pdb=" O GLY G 95 " (cutoff:3.500A) removed outlier: 11.385A pdb=" N LEU G 97 " --> pdb=" O TYR G 82 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N TYR G 82 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N SER G 99 " --> pdb=" O SER G 80 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER G 80 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER G 80 " --> pdb=" O VAL G 130 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR G 125 " --> pdb=" O PHE G 141 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE G 141 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 52 through 60 removed outlier: 5.907A pdb=" N ILE H 54 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ARG H 69 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA H 56 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 91 through 103 removed outlier: 12.508A pdb=" N GLY H 95 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N LEU H 84 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 11.373A pdb=" N LEU H 97 " --> pdb=" O TYR H 82 " (cutoff:3.500A) removed outlier: 11.577A pdb=" N TYR H 82 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N SER H 99 " --> pdb=" O SER H 80 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER H 80 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER H 80 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR H 125 " --> pdb=" O PHE H 141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 53 through 60 removed outlier: 7.153A pdb=" N ASN I 67 " --> pdb=" O GLU I 55 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL I 57 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER I 65 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS I 59 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 91 through 103 removed outlier: 12.582A pdb=" N GLY I 95 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N LEU I 84 " --> pdb=" O GLY I 95 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N LEU I 97 " --> pdb=" O TYR I 82 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N TYR I 82 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N SER I 99 " --> pdb=" O SER I 80 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER I 80 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER I 80 " --> pdb=" O VAL I 130 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR I 125 " --> pdb=" O PHE I 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 53 through 60 removed outlier: 5.133A pdb=" N ILE J 54 " --> pdb=" O ARG J 69 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG J 69 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA J 56 " --> pdb=" O ASN J 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 91 through 103 removed outlier: 12.669A pdb=" N GLY J 95 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N LEU J 84 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N LEU J 97 " --> pdb=" O TYR J 82 " (cutoff:3.500A) removed outlier: 11.695A pdb=" N TYR J 82 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N SER J 99 " --> pdb=" O SER J 80 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER J 80 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER J 80 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR J 125 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE J 141 " --> pdb=" O TYR J 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 53 through 60 removed outlier: 5.415A pdb=" N ILE K 54 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG K 69 " --> pdb=" O ILE K 54 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA K 56 " --> pdb=" O ASN K 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 91 through 103 removed outlier: 12.691A pdb=" N GLY K 95 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N LEU K 84 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N LEU K 97 " --> pdb=" O TYR K 82 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N TYR K 82 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N SER K 99 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N SER K 80 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER K 80 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR K 125 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE K 141 " --> pdb=" O TYR K 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 52 through 60 removed outlier: 5.340A pdb=" N ILE L 54 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG L 69 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA L 56 " --> pdb=" O ASN L 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 91 through 103 removed outlier: 12.608A pdb=" N GLY L 95 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 11.615A pdb=" N LEU L 84 " --> pdb=" O GLY L 95 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N LEU L 97 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 11.746A pdb=" N TYR L 82 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N SER L 99 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N SER L 80 " --> pdb=" O SER L 99 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER L 80 " --> pdb=" O VAL L 130 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR L 125 " --> pdb=" O PHE L 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 53 through 60 removed outlier: 5.319A pdb=" N ILE M 54 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG M 69 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA M 56 " --> pdb=" O ASN M 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 91 through 103 removed outlier: 12.555A pdb=" N GLY M 95 " --> pdb=" O LEU M 84 " (cutoff:3.500A) removed outlier: 11.547A pdb=" N LEU M 84 " --> pdb=" O GLY M 95 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N LEU M 97 " --> pdb=" O TYR M 82 " (cutoff:3.500A) removed outlier: 11.668A pdb=" N TYR M 82 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N SER M 99 " --> pdb=" O SER M 80 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N SER M 80 " --> pdb=" O SER M 99 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER M 80 " --> pdb=" O VAL M 130 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR M 125 " --> pdb=" O PHE M 141 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE M 141 " --> pdb=" O TYR M 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 53 through 60 removed outlier: 5.413A pdb=" N ILE N 54 " --> pdb=" O ARG N 69 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG N 69 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA N 56 " --> pdb=" O ASN N 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 91 through 103 removed outlier: 12.691A pdb=" N GLY N 95 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 11.663A pdb=" N LEU N 84 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 11.514A pdb=" N LEU N 97 " --> pdb=" O TYR N 82 " (cutoff:3.500A) removed outlier: 11.727A pdb=" N TYR N 82 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N SER N 99 " --> pdb=" O SER N 80 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER N 80 " --> pdb=" O SER N 99 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER N 80 " --> pdb=" O VAL N 130 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR N 125 " --> pdb=" O PHE N 141 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE N 141 " --> pdb=" O TYR N 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 53 through 60 removed outlier: 7.187A pdb=" N ASN O 67 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL O 57 " --> pdb=" O SER O 65 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER O 65 " --> pdb=" O VAL O 57 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS O 59 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR O 63 " --> pdb=" O LYS O 59 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 91 through 103 removed outlier: 12.634A pdb=" N GLY O 95 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N LEU O 84 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 11.360A pdb=" N LEU O 97 " --> pdb=" O TYR O 82 " (cutoff:3.500A) removed outlier: 11.676A pdb=" N TYR O 82 " --> pdb=" O LEU O 97 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N SER O 99 " --> pdb=" O SER O 80 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N SER O 80 " --> pdb=" O SER O 99 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER O 80 " --> pdb=" O VAL O 130 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR O 125 " --> pdb=" O PHE O 141 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 53 through 60 removed outlier: 5.258A pdb=" N ILE P 54 " --> pdb=" O ARG P 69 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG P 69 " --> pdb=" O ILE P 54 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA P 56 " --> pdb=" O ASN P 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 91 through 103 removed outlier: 12.685A pdb=" N GLY P 95 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N LEU P 84 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N LEU P 97 " --> pdb=" O TYR P 82 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N TYR P 82 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 10.979A pdb=" N SER P 99 " --> pdb=" O SER P 80 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N SER P 80 " --> pdb=" O SER P 99 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER P 80 " --> pdb=" O VAL P 130 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR P 125 " --> pdb=" O PHE P 141 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 53 through 60 removed outlier: 5.189A pdb=" N ILE Q 54 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG Q 69 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA Q 56 " --> pdb=" O ASN Q 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 91 through 103 removed outlier: 12.758A pdb=" N GLY Q 95 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 11.781A pdb=" N LEU Q 84 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 11.530A pdb=" N LEU Q 97 " --> pdb=" O TYR Q 82 " (cutoff:3.500A) removed outlier: 11.760A pdb=" N TYR Q 82 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N SER Q 99 " --> pdb=" O SER Q 80 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER Q 80 " --> pdb=" O SER Q 99 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER Q 80 " --> pdb=" O VAL Q 130 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR Q 125 " --> pdb=" O PHE Q 141 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE Q 141 " --> pdb=" O TYR Q 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 53 through 60 removed outlier: 5.376A pdb=" N ILE R 54 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG R 69 " --> pdb=" O ILE R 54 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA R 56 " --> pdb=" O ASN R 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 91 through 103 removed outlier: 12.640A pdb=" N GLY R 95 " --> pdb=" O LEU R 84 " (cutoff:3.500A) removed outlier: 11.577A pdb=" N LEU R 84 " --> pdb=" O GLY R 95 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N LEU R 97 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N TYR R 82 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 10.899A pdb=" N SER R 99 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER R 80 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN R 101 " --> pdb=" O ILE R 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL R 76 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER R 80 " --> pdb=" O VAL R 130 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR R 125 " --> pdb=" O PHE R 141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 52 through 60 removed outlier: 5.367A pdb=" N ILE S 54 " --> pdb=" O ARG S 69 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG S 69 " --> pdb=" O ILE S 54 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA S 56 " --> pdb=" O ASN S 67 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 91 through 103 removed outlier: 12.696A pdb=" N GLY S 95 " --> pdb=" O LEU S 84 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N LEU S 84 " --> pdb=" O GLY S 95 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N LEU S 97 " --> pdb=" O TYR S 82 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N TYR S 82 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 10.890A pdb=" N SER S 99 " --> pdb=" O SER S 80 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER S 80 " --> pdb=" O SER S 99 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER S 80 " --> pdb=" O VAL S 130 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR S 125 " --> pdb=" O PHE S 141 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 53 through 60 removed outlier: 5.262A pdb=" N ILE T 54 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG T 69 " --> pdb=" O ILE T 54 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA T 56 " --> pdb=" O ASN T 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 91 through 103 removed outlier: 12.719A pdb=" N GLY T 95 " --> pdb=" O LEU T 84 " (cutoff:3.500A) removed outlier: 11.682A pdb=" N LEU T 84 " --> pdb=" O GLY T 95 " (cutoff:3.500A) removed outlier: 11.453A pdb=" N LEU T 97 " --> pdb=" O TYR T 82 " (cutoff:3.500A) removed outlier: 11.710A pdb=" N TYR T 82 " --> pdb=" O LEU T 97 " (cutoff:3.500A) removed outlier: 10.883A pdb=" N SER T 99 " --> pdb=" O SER T 80 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N SER T 80 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER T 80 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR T 125 " --> pdb=" O PHE T 141 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3240 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: 3.31 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6380 1.34 - 1.46: 3550 1.46 - 1.58: 9990 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 20000 Sorted by residual: bond pdb=" CB THR K 40 " pdb=" CG2 THR K 40 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB THR G 40 " pdb=" CG2 THR G 40 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB THR I 40 " pdb=" CG2 THR I 40 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" CB THR J 40 " pdb=" CG2 THR J 40 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.27e-01 bond pdb=" CG ARG R 133 " pdb=" CD ARG R 133 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.97e-01 ... (remaining 19995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 26631 1.35 - 2.71: 612 2.71 - 4.06: 147 4.06 - 5.41: 46 5.41 - 6.77: 4 Bond angle restraints: 27440 Sorted by residual: angle pdb=" CB ARG B 124 " pdb=" CG ARG B 124 " pdb=" CD ARG B 124 " ideal model delta sigma weight residual 111.30 116.80 -5.50 2.30e+00 1.89e-01 5.73e+00 angle pdb=" C ALA Q 86 " pdb=" N THR Q 87 " pdb=" CA THR Q 87 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.72e+00 angle pdb=" C ALA S 86 " pdb=" N THR S 87 " pdb=" CA THR S 87 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.42e+00 angle pdb=" C ALA T 86 " pdb=" N THR T 87 " pdb=" CA THR T 87 " ideal model delta sigma weight residual 121.54 125.98 -4.44 1.91e+00 2.74e-01 5.40e+00 angle pdb=" CB ARG R 133 " pdb=" CG ARG R 133 " pdb=" CD ARG R 133 " ideal model delta sigma weight residual 111.30 116.64 -5.34 2.30e+00 1.89e-01 5.39e+00 ... (remaining 27435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 11233 17.77 - 35.55: 687 35.55 - 53.32: 101 53.32 - 71.09: 21 71.09 - 88.87: 18 Dihedral angle restraints: 12060 sinusoidal: 4240 harmonic: 7820 Sorted by residual: dihedral pdb=" CB CYS O 93 " pdb=" SG CYS O 93 " pdb=" SG CYS O 117 " pdb=" CB CYS O 117 " ideal model delta sinusoidal sigma weight residual -86.00 2.87 -88.87 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS K 93 " pdb=" SG CYS K 93 " pdb=" SG CYS K 117 " pdb=" CB CYS K 117 " ideal model delta sinusoidal sigma weight residual 93.00 19.70 73.30 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CB CYS I 93 " pdb=" SG CYS I 93 " pdb=" SG CYS I 117 " pdb=" CB CYS I 117 " ideal model delta sinusoidal sigma weight residual 93.00 19.91 73.09 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 12057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2632 0.042 - 0.084: 649 0.084 - 0.125: 343 0.125 - 0.167: 35 0.167 - 0.209: 1 Chirality restraints: 3660 Sorted by residual: chirality pdb=" CB ILE B 126 " pdb=" CA ILE B 126 " pdb=" CG1 ILE B 126 " pdb=" CG2 ILE B 126 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE E 126 " pdb=" CA ILE E 126 " pdb=" CG1 ILE E 126 " pdb=" CG2 ILE E 126 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA GLN H 45 " pdb=" N GLN H 45 " pdb=" C GLN H 45 " pdb=" CB GLN H 45 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 3657 not shown) Planarity restraints: 3400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 133 " 0.134 9.50e-02 1.11e+02 6.04e-02 2.93e+00 pdb=" NE ARG R 133 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG R 133 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG R 133 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG R 133 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL Q 36 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C VAL Q 36 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL Q 36 " 0.011 2.00e-02 2.50e+03 pdb=" N THR Q 37 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 36 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C VAL K 36 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL K 36 " 0.010 2.00e-02 2.50e+03 pdb=" N THR K 37 " 0.009 2.00e-02 2.50e+03 ... (remaining 3397 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 547 2.70 - 3.25: 19841 3.25 - 3.80: 31220 3.80 - 4.35: 34971 4.35 - 4.90: 62564 Nonbonded interactions: 149143 Sorted by model distance: nonbonded pdb=" OG SER L 47 " pdb=" OH TYR O 35 " model vdw 2.156 3.040 nonbonded pdb=" OG SER G 47 " pdb=" OH TYR J 35 " model vdw 2.167 3.040 nonbonded pdb=" OE2 GLU L 44 " pdb=" NH2 ARG O 38 " model vdw 2.182 3.120 nonbonded pdb=" OG SER D 47 " pdb=" OH TYR G 35 " model vdw 2.193 3.040 nonbonded pdb=" OG SER C 47 " pdb=" OH TYR F 35 " model vdw 2.196 3.040 ... (remaining 149138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.380 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 0.039 20020 Z= 0.120 Angle : 0.558 6.767 27480 Z= 0.293 Chirality : 0.046 0.209 3660 Planarity : 0.004 0.060 3400 Dihedral : 11.636 80.980 6960 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.16), residues: 2680 helix: 3.78 (0.16), residues: 760 sheet: 1.99 (0.18), residues: 800 loop : -0.21 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 133 TYR 0.021 0.002 TYR A 29 PHE 0.021 0.001 PHE T 32 TRP 0.022 0.003 TRP P 31 Details of bonding type rmsd covalent geometry : bond 0.00255 (20000) covalent geometry : angle 0.55783 (27440) SS BOND : bond 0.00265 ( 20) SS BOND : angle 0.48901 ( 40) hydrogen bonds : bond 0.15738 ( 1119) hydrogen bonds : angle 5.87346 ( 3240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8461 (ptp90) cc_final: 0.8194 (ttp-110) REVERT: A 46 LEU cc_start: 0.9150 (mm) cc_final: 0.8763 (mm) REVERT: B 29 TYR cc_start: 0.8648 (t80) cc_final: 0.8349 (t80) REVERT: B 31 TRP cc_start: 0.8477 (t60) cc_final: 0.7742 (t60) REVERT: B 84 LEU cc_start: 0.8439 (mt) cc_final: 0.8195 (mt) REVERT: B 104 ASP cc_start: 0.8679 (m-30) cc_final: 0.8469 (m-30) REVERT: C 96 SER cc_start: 0.8525 (t) cc_final: 0.8314 (t) REVERT: C 124 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7875 (tpp80) REVERT: D 69 ARG cc_start: 0.9120 (tpp80) cc_final: 0.8805 (tpt-90) REVERT: E 70 ASN cc_start: 0.8680 (t0) cc_final: 0.8237 (t0) REVERT: F 30 LEU cc_start: 0.9061 (mm) cc_final: 0.8821 (tp) REVERT: F 51 GLN cc_start: 0.8574 (mp10) cc_final: 0.8350 (mp10) REVERT: G 29 TYR cc_start: 0.8890 (t80) cc_final: 0.8633 (t80) REVERT: H 119 LEU cc_start: 0.7687 (mp) cc_final: 0.7373 (mp) REVERT: J 91 MET cc_start: 0.8419 (ptt) cc_final: 0.7675 (ppp) REVERT: J 111 ILE cc_start: 0.9427 (mm) cc_final: 0.9191 (mt) REVERT: K 70 ASN cc_start: 0.8707 (t0) cc_final: 0.8312 (t0) REVERT: L 46 LEU cc_start: 0.9250 (mt) cc_final: 0.9043 (mt) REVERT: L 104 ASP cc_start: 0.8517 (t70) cc_final: 0.8227 (t0) REVERT: M 35 TYR cc_start: 0.8549 (t80) cc_final: 0.8177 (t80) REVERT: M 52 LEU cc_start: 0.9137 (mp) cc_final: 0.8824 (mt) REVERT: M 91 MET cc_start: 0.8716 (ptm) cc_final: 0.8414 (ptt) REVERT: M 104 ASP cc_start: 0.8360 (m-30) cc_final: 0.8032 (m-30) REVERT: N 38 ARG cc_start: 0.8656 (ptt-90) cc_final: 0.7778 (ttp-110) REVERT: N 50 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6624 (mt-10) REVERT: N 73 GLU cc_start: 0.8290 (pm20) cc_final: 0.7998 (pm20) REVERT: N 133 ARG cc_start: 0.8756 (ttm110) cc_final: 0.8523 (ttm110) REVERT: O 73 GLU cc_start: 0.8353 (mp0) cc_final: 0.8079 (mp0) REVERT: O 91 MET cc_start: 0.8499 (ptt) cc_final: 0.8219 (ptm) REVERT: P 29 TYR cc_start: 0.8615 (t80) cc_final: 0.8285 (t80) REVERT: P 104 ASP cc_start: 0.8368 (m-30) cc_final: 0.8027 (m-30) REVERT: P 109 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8043 (mm-40) REVERT: Q 40 THR cc_start: 0.8307 (m) cc_final: 0.8075 (m) REVERT: Q 45 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8351 (tp40) REVERT: Q 104 ASP cc_start: 0.8419 (m-30) cc_final: 0.8080 (m-30) REVERT: Q 136 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7332 (mt-10) REVERT: R 73 GLU cc_start: 0.8116 (mp0) cc_final: 0.7832 (mp0) REVERT: R 91 MET cc_start: 0.9019 (ptm) cc_final: 0.8808 (ptm) REVERT: R 104 ASP cc_start: 0.8243 (t0) cc_final: 0.7580 (m-30) REVERT: S 46 LEU cc_start: 0.8465 (mm) cc_final: 0.7542 (mm) REVERT: S 73 GLU cc_start: 0.8475 (mp0) cc_final: 0.8203 (mp0) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.1321 time to fit residues: 97.0356 Evaluate side-chains 343 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 ASN R 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.088759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.075125 restraints weight = 60655.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.076760 restraints weight = 43318.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.077945 restraints weight = 34119.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.078822 restraints weight = 28584.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.079395 restraints weight = 25035.258| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20020 Z= 0.150 Angle : 0.553 5.566 27480 Z= 0.298 Chirality : 0.046 0.155 3660 Planarity : 0.004 0.093 3400 Dihedral : 3.710 18.238 2860 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.09 % Allowed : 2.45 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.15), residues: 2680 helix: 3.91 (0.15), residues: 760 sheet: 1.90 (0.17), residues: 860 loop : -0.45 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 124 TYR 0.014 0.002 TYR N 35 PHE 0.011 0.001 PHE P 32 TRP 0.019 0.003 TRP A 31 Details of bonding type rmsd covalent geometry : bond 0.00334 (20000) covalent geometry : angle 0.55294 (27440) SS BOND : bond 0.00171 ( 20) SS BOND : angle 0.51519 ( 40) hydrogen bonds : bond 0.04959 ( 1119) hydrogen bonds : angle 4.51256 ( 3240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 438 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.8798 (tpp80) cc_final: 0.8124 (tpp80) REVERT: B 70 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8999 (m-40) REVERT: C 124 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7648 (tpp80) REVERT: E 70 ASN cc_start: 0.8723 (t0) cc_final: 0.8142 (t0) REVERT: F 11 ILE cc_start: 0.8568 (mp) cc_final: 0.8316 (mm) REVERT: G 29 TYR cc_start: 0.8779 (t80) cc_final: 0.8551 (t80) REVERT: H 29 TYR cc_start: 0.8135 (t80) cc_final: 0.7500 (t80) REVERT: I 124 ARG cc_start: 0.7367 (tpp80) cc_final: 0.7124 (mmt90) REVERT: J 44 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8110 (tm-30) REVERT: J 46 LEU cc_start: 0.8609 (mt) cc_final: 0.8280 (mt) REVERT: K 70 ASN cc_start: 0.8872 (t0) cc_final: 0.8502 (t0) REVERT: L 119 LEU cc_start: 0.8609 (mt) cc_final: 0.8230 (mt) REVERT: M 38 ARG cc_start: 0.8202 (mtm110) cc_final: 0.7834 (mtm110) REVERT: M 91 MET cc_start: 0.8582 (ptm) cc_final: 0.8340 (ptt) REVERT: M 126 ILE cc_start: 0.8597 (mp) cc_final: 0.8366 (mp) REVERT: N 73 GLU cc_start: 0.8374 (pm20) cc_final: 0.8098 (pm20) REVERT: O 104 ASP cc_start: 0.8509 (m-30) cc_final: 0.8169 (m-30) REVERT: Q 38 ARG cc_start: 0.8535 (ptt90) cc_final: 0.8139 (ptt-90) REVERT: Q 104 ASP cc_start: 0.8279 (m-30) cc_final: 0.8022 (m-30) REVERT: Q 119 LEU cc_start: 0.9070 (mt) cc_final: 0.8569 (mp) REVERT: R 73 GLU cc_start: 0.8203 (mp0) cc_final: 0.7961 (mp0) REVERT: R 104 ASP cc_start: 0.8146 (t0) cc_final: 0.7570 (m-30) REVERT: S 46 LEU cc_start: 0.8316 (mm) cc_final: 0.7569 (mm) REVERT: S 73 GLU cc_start: 0.8396 (mp0) cc_final: 0.8168 (mp0) REVERT: S 104 ASP cc_start: 0.8015 (m-30) cc_final: 0.7795 (m-30) outliers start: 2 outliers final: 0 residues processed: 439 average time/residue: 0.1295 time to fit residues: 86.9718 Evaluate side-chains 318 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 188 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN I 42 GLN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 ASN P 70 ASN Q 70 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073792 restraints weight = 61609.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075439 restraints weight = 43801.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076643 restraints weight = 34393.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077528 restraints weight = 28675.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.078109 restraints weight = 25011.479| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20020 Z= 0.155 Angle : 0.545 6.241 27480 Z= 0.293 Chirality : 0.045 0.183 3660 Planarity : 0.004 0.071 3400 Dihedral : 3.715 17.866 2860 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.14 % Allowed : 3.47 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.15), residues: 2680 helix: 3.93 (0.15), residues: 760 sheet: 1.89 (0.16), residues: 860 loop : -0.43 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 133 TYR 0.022 0.002 TYR A 35 PHE 0.010 0.001 PHE J 32 TRP 0.021 0.003 TRP K 31 Details of bonding type rmsd covalent geometry : bond 0.00349 (20000) covalent geometry : angle 0.54467 (27440) SS BOND : bond 0.00237 ( 20) SS BOND : angle 0.66084 ( 40) hydrogen bonds : bond 0.04966 ( 1119) hydrogen bonds : angle 4.21474 ( 3240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 419 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8593 (ptp-170) cc_final: 0.8343 (mtm-85) REVERT: D 124 ARG cc_start: 0.7408 (mmt180) cc_final: 0.7154 (mmt180) REVERT: E 70 ASN cc_start: 0.8861 (t0) cc_final: 0.8334 (t0) REVERT: H 29 TYR cc_start: 0.8238 (t80) cc_final: 0.7633 (t80) REVERT: H 119 LEU cc_start: 0.7481 (mp) cc_final: 0.7059 (mp) REVERT: H 124 ARG cc_start: 0.8006 (tpp80) cc_final: 0.7462 (tpp80) REVERT: I 46 LEU cc_start: 0.8941 (tp) cc_final: 0.8676 (tp) REVERT: I 124 ARG cc_start: 0.7700 (tpp80) cc_final: 0.7352 (tpp80) REVERT: J 44 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8116 (tm-30) REVERT: J 46 LEU cc_start: 0.8584 (mt) cc_final: 0.8360 (mt) REVERT: K 70 ASN cc_start: 0.8778 (t0) cc_final: 0.8357 (t0) REVERT: L 42 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8298 (tm-30) REVERT: L 46 LEU cc_start: 0.9086 (mt) cc_final: 0.8329 (mt) REVERT: L 118 ASN cc_start: 0.8836 (p0) cc_final: 0.8626 (p0) REVERT: L 119 LEU cc_start: 0.8632 (mt) cc_final: 0.8217 (mt) REVERT: M 35 TYR cc_start: 0.8480 (t80) cc_final: 0.8205 (t80) REVERT: M 38 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7903 (mtm110) REVERT: M 91 MET cc_start: 0.8581 (ptm) cc_final: 0.8328 (ptt) REVERT: N 50 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7493 (mt-10) REVERT: N 73 GLU cc_start: 0.8465 (pm20) cc_final: 0.8158 (pm20) REVERT: O 45 GLN cc_start: 0.8561 (tp40) cc_final: 0.7686 (tp40) REVERT: O 46 LEU cc_start: 0.8761 (mm) cc_final: 0.8533 (mm) REVERT: O 104 ASP cc_start: 0.8317 (m-30) cc_final: 0.8085 (m-30) REVERT: Q 38 ARG cc_start: 0.8458 (ptt90) cc_final: 0.8254 (tmm160) REVERT: Q 45 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8649 (tp40) REVERT: R 73 GLU cc_start: 0.8190 (mp0) cc_final: 0.7945 (mp0) REVERT: R 101 GLN cc_start: 0.7850 (mp10) cc_final: 0.7610 (mp10) REVERT: R 104 ASP cc_start: 0.7968 (t0) cc_final: 0.7480 (m-30) REVERT: S 73 GLU cc_start: 0.8430 (mp0) cc_final: 0.8186 (mp0) REVERT: S 104 ASP cc_start: 0.8173 (m-30) cc_final: 0.7962 (m-30) REVERT: T 50 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6917 (mt-10) REVERT: T 133 ARG cc_start: 0.8382 (ptp-110) cc_final: 0.7923 (ptp-110) outliers start: 3 outliers final: 0 residues processed: 421 average time/residue: 0.1310 time to fit residues: 83.6719 Evaluate side-chains 316 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 56 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 chunk 158 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 236 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN E 51 GLN F 42 GLN F 102 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN T 70 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.090383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.076867 restraints weight = 60478.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.078572 restraints weight = 42865.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079803 restraints weight = 33434.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.080653 restraints weight = 27799.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.081250 restraints weight = 24378.999| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20020 Z= 0.110 Angle : 0.511 5.638 27480 Z= 0.270 Chirality : 0.046 0.202 3660 Planarity : 0.004 0.068 3400 Dihedral : 3.571 18.812 2860 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.14 % Allowed : 1.76 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.16), residues: 2680 helix: 3.99 (0.15), residues: 760 sheet: 1.94 (0.17), residues: 860 loop : -0.48 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 38 TYR 0.015 0.001 TYR J 35 PHE 0.016 0.001 PHE P 32 TRP 0.018 0.003 TRP K 31 Details of bonding type rmsd covalent geometry : bond 0.00230 (20000) covalent geometry : angle 0.51059 (27440) SS BOND : bond 0.00365 ( 20) SS BOND : angle 0.54885 ( 40) hydrogen bonds : bond 0.04344 ( 1119) hydrogen bonds : angle 4.07537 ( 3240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 433 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8475 (ptp-170) cc_final: 0.8272 (mtm-85) REVERT: B 70 ASN cc_start: 0.9305 (OUTLIER) cc_final: 0.8913 (m-40) REVERT: C 69 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.7862 (ttm-80) REVERT: E 70 ASN cc_start: 0.8697 (t0) cc_final: 0.8324 (t0) REVERT: F 11 ILE cc_start: 0.8494 (mp) cc_final: 0.8248 (mm) REVERT: H 29 TYR cc_start: 0.8166 (t80) cc_final: 0.7592 (t80) REVERT: K 70 ASN cc_start: 0.8697 (t0) cc_final: 0.8444 (t0) REVERT: L 44 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8082 (tm-30) REVERT: L 46 LEU cc_start: 0.9112 (mt) cc_final: 0.8364 (mt) REVERT: M 91 MET cc_start: 0.8533 (ptm) cc_final: 0.8238 (ptt) REVERT: N 29 TYR cc_start: 0.8589 (t80) cc_final: 0.8261 (t80) REVERT: N 44 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7932 (tm-30) REVERT: N 82 TYR cc_start: 0.8335 (m-10) cc_final: 0.8102 (m-80) REVERT: N 133 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8361 (ttm110) REVERT: O 68 VAL cc_start: 0.9406 (t) cc_final: 0.8993 (m) REVERT: O 104 ASP cc_start: 0.8239 (m-30) cc_final: 0.8010 (m-30) REVERT: Q 37 THR cc_start: 0.8788 (m) cc_final: 0.8525 (p) REVERT: Q 38 ARG cc_start: 0.8347 (ptt90) cc_final: 0.7982 (ptt-90) REVERT: Q 73 GLU cc_start: 0.8211 (pm20) cc_final: 0.7939 (pm20) REVERT: Q 104 ASP cc_start: 0.8107 (m-30) cc_final: 0.7874 (m-30) REVERT: R 101 GLN cc_start: 0.7792 (mp10) cc_final: 0.7574 (mp10) REVERT: S 11 ILE cc_start: 0.8287 (mm) cc_final: 0.8075 (mm) REVERT: S 73 GLU cc_start: 0.8538 (mp0) cc_final: 0.8255 (mp0) REVERT: S 104 ASP cc_start: 0.8073 (m-30) cc_final: 0.7841 (m-30) REVERT: T 70 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8089 (m-40) REVERT: T 133 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.7808 (ptp-110) outliers start: 3 outliers final: 0 residues processed: 435 average time/residue: 0.1330 time to fit residues: 87.1923 Evaluate side-chains 315 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 313 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 96 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 177 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 72 optimal weight: 0.0970 chunk 159 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 191 optimal weight: 0.9980 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.076491 restraints weight = 59888.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.078151 restraints weight = 42664.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.079369 restraints weight = 33531.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.080162 restraints weight = 27961.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.080690 restraints weight = 24574.867| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20020 Z= 0.117 Angle : 0.513 6.793 27480 Z= 0.272 Chirality : 0.046 0.164 3660 Planarity : 0.004 0.066 3400 Dihedral : 3.536 15.719 2860 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.16), residues: 2680 helix: 4.02 (0.15), residues: 760 sheet: 1.95 (0.17), residues: 860 loop : -0.50 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 124 TYR 0.015 0.001 TYR J 35 PHE 0.010 0.001 PHE F 32 TRP 0.019 0.003 TRP K 31 Details of bonding type rmsd covalent geometry : bond 0.00254 (20000) covalent geometry : angle 0.51261 (27440) SS BOND : bond 0.00164 ( 20) SS BOND : angle 0.52573 ( 40) hydrogen bonds : bond 0.04372 ( 1119) hydrogen bonds : angle 4.00899 ( 3240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8473 (ptp-170) cc_final: 0.8093 (ttp-110) REVERT: C 51 GLN cc_start: 0.8929 (mp10) cc_final: 0.8680 (mp10) REVERT: C 124 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7744 (tpp80) REVERT: E 70 ASN cc_start: 0.8884 (t0) cc_final: 0.8473 (t0) REVERT: F 11 ILE cc_start: 0.8507 (mp) cc_final: 0.8278 (mm) REVERT: F 30 LEU cc_start: 0.9224 (pp) cc_final: 0.8641 (tp) REVERT: H 29 TYR cc_start: 0.8116 (t80) cc_final: 0.7581 (t80) REVERT: H 119 LEU cc_start: 0.7604 (mp) cc_final: 0.7053 (mp) REVERT: H 124 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7683 (tpp80) REVERT: I 45 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7147 (tt0) REVERT: J 118 ASN cc_start: 0.8395 (p0) cc_final: 0.8109 (p0) REVERT: K 70 ASN cc_start: 0.8703 (t0) cc_final: 0.8272 (t0) REVERT: L 46 LEU cc_start: 0.9142 (mt) cc_final: 0.8809 (mt) REVERT: L 68 VAL cc_start: 0.9129 (t) cc_final: 0.8768 (m) REVERT: L 104 ASP cc_start: 0.8614 (t0) cc_final: 0.8402 (m-30) REVERT: N 29 TYR cc_start: 0.8568 (t80) cc_final: 0.8135 (t80) REVERT: N 44 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7913 (tm-30) REVERT: Q 37 THR cc_start: 0.8818 (m) cc_final: 0.8534 (p) REVERT: Q 73 GLU cc_start: 0.8262 (pm20) cc_final: 0.7832 (pm20) REVERT: Q 104 ASP cc_start: 0.8066 (m-30) cc_final: 0.7762 (m-30) REVERT: S 11 ILE cc_start: 0.8327 (mm) cc_final: 0.8111 (mm) REVERT: S 73 GLU cc_start: 0.8553 (mp0) cc_final: 0.8266 (mp0) REVERT: S 104 ASP cc_start: 0.8036 (m-30) cc_final: 0.7789 (m-30) REVERT: T 133 ARG cc_start: 0.8481 (ptp-110) cc_final: 0.8034 (ptp90) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.1302 time to fit residues: 82.7721 Evaluate side-chains 314 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 37 optimal weight: 10.0000 chunk 246 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 258 optimal weight: 0.0670 chunk 6 optimal weight: 7.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN F 42 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.089909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076332 restraints weight = 60241.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.077968 restraints weight = 43071.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079180 restraints weight = 33888.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.079984 restraints weight = 28265.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080667 restraints weight = 24871.029| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20020 Z= 0.121 Angle : 0.518 6.238 27480 Z= 0.273 Chirality : 0.046 0.213 3660 Planarity : 0.004 0.060 3400 Dihedral : 3.520 16.871 2860 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.16), residues: 2680 helix: 3.99 (0.15), residues: 760 sheet: 1.77 (0.17), residues: 880 loop : -0.41 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 124 TYR 0.019 0.001 TYR F 35 PHE 0.015 0.001 PHE P 32 TRP 0.020 0.003 TRP K 31 Details of bonding type rmsd covalent geometry : bond 0.00264 (20000) covalent geometry : angle 0.51762 (27440) SS BOND : bond 0.00145 ( 20) SS BOND : angle 0.55440 ( 40) hydrogen bonds : bond 0.04379 ( 1119) hydrogen bonds : angle 3.98980 ( 3240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.660 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: A 38 ARG cc_start: 0.8454 (ptp-170) cc_final: 0.8117 (ttp-110) REVERT: C 124 ARG cc_start: 0.8042 (tpp80) cc_final: 0.7550 (tpp80) REVERT: E 70 ASN cc_start: 0.8937 (t0) cc_final: 0.8416 (t0) REVERT: F 11 ILE cc_start: 0.8473 (mp) cc_final: 0.8234 (mm) REVERT: F 30 LEU cc_start: 0.9315 (pp) cc_final: 0.8646 (tp) REVERT: H 29 TYR cc_start: 0.8254 (t80) cc_final: 0.7679 (t80) REVERT: H 119 LEU cc_start: 0.7524 (mp) cc_final: 0.6949 (mp) REVERT: I 45 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7099 (tt0) REVERT: K 70 ASN cc_start: 0.8763 (t0) cc_final: 0.8444 (t0) REVERT: K 124 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7278 (mmm160) REVERT: L 46 LEU cc_start: 0.9134 (mt) cc_final: 0.8765 (mt) REVERT: L 68 VAL cc_start: 0.9152 (t) cc_final: 0.8776 (m) REVERT: L 104 ASP cc_start: 0.8544 (t0) cc_final: 0.8311 (m-30) REVERT: M 91 MET cc_start: 0.8362 (ptm) cc_final: 0.7893 (ptt) REVERT: N 29 TYR cc_start: 0.8552 (t80) cc_final: 0.8133 (t80) REVERT: N 44 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7985 (tm-30) REVERT: N 133 ARG cc_start: 0.8524 (ttm110) cc_final: 0.8302 (ttm110) REVERT: O 45 GLN cc_start: 0.8479 (tp40) cc_final: 0.7672 (tp40) REVERT: P 133 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.7888 (mtp85) REVERT: P 143 SER cc_start: 0.8488 (t) cc_final: 0.8246 (t) REVERT: Q 38 ARG cc_start: 0.8065 (ptt-90) cc_final: 0.7736 (ttp-170) REVERT: Q 73 GLU cc_start: 0.8187 (pm20) cc_final: 0.7795 (pm20) REVERT: S 73 GLU cc_start: 0.8550 (mp0) cc_final: 0.8281 (mp0) REVERT: S 104 ASP cc_start: 0.7957 (m-30) cc_final: 0.7705 (m-30) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.1214 time to fit residues: 76.5221 Evaluate side-chains 313 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 244 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN P 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076138 restraints weight = 60144.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077810 restraints weight = 43210.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078969 restraints weight = 33965.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079761 restraints weight = 28570.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.080477 restraints weight = 25170.593| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20020 Z= 0.126 Angle : 0.527 10.176 27480 Z= 0.278 Chirality : 0.046 0.209 3660 Planarity : 0.004 0.047 3400 Dihedral : 3.517 16.282 2860 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.05 % Allowed : 1.34 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.16), residues: 2680 helix: 4.02 (0.15), residues: 760 sheet: 1.97 (0.17), residues: 860 loop : -0.59 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 38 TYR 0.014 0.001 TYR G 35 PHE 0.022 0.001 PHE A 141 TRP 0.020 0.003 TRP K 31 Details of bonding type rmsd covalent geometry : bond 0.00276 (20000) covalent geometry : angle 0.52697 (27440) SS BOND : bond 0.00144 ( 20) SS BOND : angle 0.59476 ( 40) hydrogen bonds : bond 0.04476 ( 1119) hydrogen bonds : angle 3.96517 ( 3240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 0.699 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: symmetry clash REVERT: A 38 ARG cc_start: 0.8475 (ptp-170) cc_final: 0.8099 (ttp-110) REVERT: C 37 THR cc_start: 0.7776 (m) cc_final: 0.7562 (t) REVERT: E 52 LEU cc_start: 0.8827 (mt) cc_final: 0.8264 (mt) REVERT: E 70 ASN cc_start: 0.8889 (t0) cc_final: 0.8501 (m-40) REVERT: E 73 GLU cc_start: 0.7806 (mp0) cc_final: 0.7358 (tt0) REVERT: F 11 ILE cc_start: 0.8462 (mp) cc_final: 0.8220 (mm) REVERT: F 30 LEU cc_start: 0.9343 (pp) cc_final: 0.8664 (tp) REVERT: H 29 TYR cc_start: 0.8228 (t80) cc_final: 0.7586 (t80) REVERT: H 119 LEU cc_start: 0.7534 (mp) cc_final: 0.6991 (mp) REVERT: H 124 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7487 (tpp80) REVERT: I 37 THR cc_start: 0.9167 (p) cc_final: 0.8886 (t) REVERT: I 45 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7104 (tt0) REVERT: K 70 ASN cc_start: 0.8818 (t0) cc_final: 0.8463 (t0) REVERT: L 42 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8339 (tm-30) REVERT: L 46 LEU cc_start: 0.9088 (mt) cc_final: 0.8303 (mt) REVERT: L 68 VAL cc_start: 0.9148 (t) cc_final: 0.8782 (m) REVERT: L 104 ASP cc_start: 0.8522 (t0) cc_final: 0.8309 (m-30) REVERT: M 91 MET cc_start: 0.8378 (ptm) cc_final: 0.7962 (ptt) REVERT: M 124 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7498 (mmm160) REVERT: M 136 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8505 (mm-30) REVERT: N 133 ARG cc_start: 0.8577 (ttm110) cc_final: 0.8312 (ttm110) REVERT: O 104 ASP cc_start: 0.8091 (m-30) cc_final: 0.7851 (m-30) REVERT: P 29 TYR cc_start: 0.8673 (t80) cc_final: 0.8310 (t80) REVERT: P 133 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.7891 (mtp85) REVERT: P 143 SER cc_start: 0.8464 (t) cc_final: 0.8201 (t) REVERT: Q 38 ARG cc_start: 0.8157 (ptt-90) cc_final: 0.7809 (tmm160) REVERT: Q 50 GLU cc_start: 0.8608 (tp30) cc_final: 0.7044 (tt0) REVERT: Q 51 GLN cc_start: 0.9098 (pm20) cc_final: 0.8706 (pm20) REVERT: Q 136 GLU cc_start: 0.8620 (tp30) cc_final: 0.7670 (pt0) REVERT: S 41 SER cc_start: 0.9223 (p) cc_final: 0.8992 (t) REVERT: S 73 GLU cc_start: 0.8465 (mp0) cc_final: 0.8208 (mp0) REVERT: S 104 ASP cc_start: 0.8000 (m-30) cc_final: 0.7764 (m-30) outliers start: 1 outliers final: 0 residues processed: 413 average time/residue: 0.1272 time to fit residues: 80.5167 Evaluate side-chains 321 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 72 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 246 optimal weight: 0.5980 chunk 256 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 70 ASN N 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.077167 restraints weight = 59776.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078796 restraints weight = 42508.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.080024 restraints weight = 33515.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.080922 restraints weight = 27899.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081478 restraints weight = 24323.415| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20020 Z= 0.115 Angle : 0.532 11.573 27480 Z= 0.279 Chirality : 0.046 0.172 3660 Planarity : 0.004 0.068 3400 Dihedral : 3.520 16.561 2860 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.16), residues: 2680 helix: 4.03 (0.15), residues: 760 sheet: 1.79 (0.17), residues: 880 loop : -0.52 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 133 TYR 0.018 0.001 TYR H 35 PHE 0.020 0.001 PHE A 141 TRP 0.018 0.003 TRP J 31 Details of bonding type rmsd covalent geometry : bond 0.00246 (20000) covalent geometry : angle 0.53213 (27440) SS BOND : bond 0.00133 ( 20) SS BOND : angle 0.51998 ( 40) hydrogen bonds : bond 0.04322 ( 1119) hydrogen bonds : angle 3.94263 ( 3240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.682 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: symmetry clash REVERT: A 35 TYR cc_start: 0.8123 (t80) cc_final: 0.7893 (t80) REVERT: A 38 ARG cc_start: 0.8459 (ptp-170) cc_final: 0.8101 (ttp-110) REVERT: A 41 SER cc_start: 0.8759 (t) cc_final: 0.8452 (t) REVERT: B 50 GLU cc_start: 0.6929 (tt0) cc_final: 0.6346 (tt0) REVERT: C 124 ARG cc_start: 0.7716 (tpp80) cc_final: 0.7436 (tpp80) REVERT: E 70 ASN cc_start: 0.9013 (t0) cc_final: 0.8509 (t0) REVERT: F 11 ILE cc_start: 0.8430 (mp) cc_final: 0.8188 (mm) REVERT: H 29 TYR cc_start: 0.8187 (t80) cc_final: 0.7625 (t80) REVERT: H 119 LEU cc_start: 0.7573 (mp) cc_final: 0.7031 (mp) REVERT: I 29 TYR cc_start: 0.8508 (t80) cc_final: 0.8085 (t80) REVERT: I 37 THR cc_start: 0.9269 (p) cc_final: 0.8928 (t) REVERT: I 45 GLN cc_start: 0.7773 (tm-30) cc_final: 0.6979 (tt0) REVERT: K 70 ASN cc_start: 0.8692 (t0) cc_final: 0.8256 (t0) REVERT: K 119 LEU cc_start: 0.8376 (mp) cc_final: 0.8149 (mt) REVERT: L 42 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8352 (tm-30) REVERT: L 46 LEU cc_start: 0.9035 (mt) cc_final: 0.8265 (mt) REVERT: L 104 ASP cc_start: 0.8502 (t0) cc_final: 0.8293 (m-30) REVERT: N 29 TYR cc_start: 0.8494 (t80) cc_final: 0.7833 (t80) REVERT: N 46 LEU cc_start: 0.8949 (mt) cc_final: 0.8705 (mt) REVERT: O 104 ASP cc_start: 0.8039 (m-30) cc_final: 0.7835 (m-30) REVERT: P 29 TYR cc_start: 0.8720 (t80) cc_final: 0.8337 (t80) REVERT: P 133 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.7817 (mtp85) REVERT: P 143 SER cc_start: 0.8437 (t) cc_final: 0.8166 (t) REVERT: Q 38 ARG cc_start: 0.8101 (ptt-90) cc_final: 0.7749 (tmm160) REVERT: Q 50 GLU cc_start: 0.8527 (tp30) cc_final: 0.7071 (tt0) REVERT: Q 51 GLN cc_start: 0.9082 (pm20) cc_final: 0.8657 (pm20) REVERT: Q 73 GLU cc_start: 0.8020 (pm20) cc_final: 0.7813 (pm20) REVERT: Q 136 GLU cc_start: 0.8505 (tp30) cc_final: 0.7631 (pt0) REVERT: S 73 GLU cc_start: 0.8576 (mp0) cc_final: 0.8317 (mp0) REVERT: S 104 ASP cc_start: 0.8005 (m-30) cc_final: 0.7766 (m-30) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.1263 time to fit residues: 79.9783 Evaluate side-chains 318 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 158 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 253 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.077092 restraints weight = 59138.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078736 restraints weight = 42525.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.079921 restraints weight = 33646.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080721 restraints weight = 28193.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081429 restraints weight = 24798.626| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20020 Z= 0.123 Angle : 0.543 6.803 27480 Z= 0.284 Chirality : 0.046 0.164 3660 Planarity : 0.004 0.063 3400 Dihedral : 3.576 16.028 2860 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.16), residues: 2680 helix: 4.06 (0.15), residues: 760 sheet: 1.96 (0.17), residues: 860 loop : -0.64 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 124 TYR 0.022 0.001 TYR C 125 PHE 0.021 0.001 PHE T 32 TRP 0.023 0.003 TRP K 31 Details of bonding type rmsd covalent geometry : bond 0.00268 (20000) covalent geometry : angle 0.54247 (27440) SS BOND : bond 0.00144 ( 20) SS BOND : angle 0.59900 ( 40) hydrogen bonds : bond 0.04364 ( 1119) hydrogen bonds : angle 3.90928 ( 3240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TYR cc_start: 0.8158 (t80) cc_final: 0.7898 (t80) REVERT: A 38 ARG cc_start: 0.8444 (ptp-170) cc_final: 0.8091 (ttp-110) REVERT: C 124 ARG cc_start: 0.7848 (tpp80) cc_final: 0.6653 (tpp80) REVERT: E 44 GLU cc_start: 0.8118 (tt0) cc_final: 0.7375 (tp30) REVERT: E 70 ASN cc_start: 0.9019 (t0) cc_final: 0.8570 (t0) REVERT: E 73 GLU cc_start: 0.7762 (mp0) cc_final: 0.7370 (tt0) REVERT: F 11 ILE cc_start: 0.8461 (mp) cc_final: 0.8225 (mm) REVERT: H 29 TYR cc_start: 0.8165 (t80) cc_final: 0.7553 (t80) REVERT: H 38 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7694 (ptp90) REVERT: I 37 THR cc_start: 0.9279 (p) cc_final: 0.8928 (t) REVERT: I 38 ARG cc_start: 0.8269 (ptp90) cc_final: 0.7718 (ptt-90) REVERT: I 45 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7013 (tt0) REVERT: J 46 LEU cc_start: 0.8168 (mm) cc_final: 0.7621 (mm) REVERT: K 70 ASN cc_start: 0.8737 (t0) cc_final: 0.8309 (t0) REVERT: L 46 LEU cc_start: 0.8980 (mt) cc_final: 0.8702 (mt) REVERT: M 124 ARG cc_start: 0.7931 (mmm160) cc_final: 0.7408 (mmm160) REVERT: N 104 ASP cc_start: 0.8260 (t70) cc_final: 0.8016 (t0) REVERT: P 29 TYR cc_start: 0.8762 (t80) cc_final: 0.8361 (t80) REVERT: P 133 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.7806 (mtp85) REVERT: P 143 SER cc_start: 0.8425 (t) cc_final: 0.8158 (t) REVERT: Q 50 GLU cc_start: 0.8570 (tp30) cc_final: 0.7236 (tt0) REVERT: Q 51 GLN cc_start: 0.9128 (pm20) cc_final: 0.8527 (pm20) REVERT: Q 136 GLU cc_start: 0.8511 (tp30) cc_final: 0.7664 (pt0) REVERT: S 73 GLU cc_start: 0.8572 (mp0) cc_final: 0.8295 (mp0) REVERT: S 104 ASP cc_start: 0.7966 (m-30) cc_final: 0.7732 (m-30) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1521 time to fit residues: 92.4968 Evaluate side-chains 303 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 37 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 76 optimal weight: 0.0020 chunk 5 optimal weight: 0.0170 chunk 83 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 238 optimal weight: 20.0000 chunk 197 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 overall best weight: 1.9230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN E 42 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 102 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN M 70 ASN P 70 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.088604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074805 restraints weight = 60143.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076441 restraints weight = 43310.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.077561 restraints weight = 34279.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.078467 restraints weight = 28892.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.079150 restraints weight = 25259.094| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20020 Z= 0.153 Angle : 0.569 6.499 27480 Z= 0.300 Chirality : 0.046 0.164 3660 Planarity : 0.004 0.076 3400 Dihedral : 3.710 15.682 2860 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.05 % Allowed : 0.56 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.16), residues: 2680 helix: 3.97 (0.15), residues: 760 sheet: 1.59 (0.17), residues: 900 loop : -0.51 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 124 TYR 0.026 0.002 TYR C 125 PHE 0.020 0.002 PHE T 32 TRP 0.024 0.003 TRP K 31 Details of bonding type rmsd covalent geometry : bond 0.00347 (20000) covalent geometry : angle 0.56884 (27440) SS BOND : bond 0.00150 ( 20) SS BOND : angle 0.72838 ( 40) hydrogen bonds : bond 0.04768 ( 1119) hydrogen bonds : angle 3.97374 ( 3240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5360 Ramachandran restraints generated. 2680 Oldfield, 0 Emsley, 2680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8473 (ptp-170) cc_final: 0.8058 (ttp-110) REVERT: A 44 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8125 (tm-30) REVERT: C 96 SER cc_start: 0.8675 (t) cc_final: 0.8460 (t) REVERT: E 70 ASN cc_start: 0.8890 (t0) cc_final: 0.8461 (t0) REVERT: E 73 GLU cc_start: 0.7794 (mp0) cc_final: 0.7210 (tt0) REVERT: F 46 LEU cc_start: 0.9085 (mt) cc_final: 0.8865 (mt) REVERT: H 119 LEU cc_start: 0.7730 (mp) cc_final: 0.7067 (mp) REVERT: I 37 THR cc_start: 0.9277 (p) cc_final: 0.8881 (t) REVERT: I 38 ARG cc_start: 0.8490 (ptp90) cc_final: 0.8279 (ptp90) REVERT: I 45 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7057 (tt0) REVERT: J 73 GLU cc_start: 0.8388 (pm20) cc_final: 0.8168 (pm20) REVERT: K 70 ASN cc_start: 0.8813 (t0) cc_final: 0.8423 (t0) REVERT: L 38 ARG cc_start: 0.8777 (ptt-90) cc_final: 0.7818 (ptt-90) REVERT: L 46 LEU cc_start: 0.8962 (mt) cc_final: 0.8691 (mt) REVERT: L 140 THR cc_start: 0.7835 (m) cc_final: 0.7333 (m) REVERT: M 70 ASN cc_start: 0.9568 (OUTLIER) cc_final: 0.9089 (m-40) REVERT: M 124 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7440 (mmm160) REVERT: M 136 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8414 (mm-30) REVERT: N 38 ARG cc_start: 0.8544 (ptt-90) cc_final: 0.8344 (ptt-90) REVERT: N 104 ASP cc_start: 0.8419 (t70) cc_final: 0.8208 (t0) REVERT: P 29 TYR cc_start: 0.8858 (t80) cc_final: 0.8591 (t80) REVERT: P 133 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7838 (mtp85) REVERT: P 143 SER cc_start: 0.8486 (t) cc_final: 0.8217 (t) REVERT: Q 50 GLU cc_start: 0.8564 (tp30) cc_final: 0.7421 (tt0) REVERT: Q 51 GLN cc_start: 0.9183 (pm20) cc_final: 0.8550 (pm20) REVERT: Q 136 GLU cc_start: 0.8570 (tp30) cc_final: 0.7712 (pt0) REVERT: S 41 SER cc_start: 0.9219 (p) cc_final: 0.8973 (p) REVERT: S 73 GLU cc_start: 0.8486 (mp0) cc_final: 0.8241 (mp0) REVERT: S 104 ASP cc_start: 0.7998 (m-30) cc_final: 0.7743 (m-30) outliers start: 1 outliers final: 0 residues processed: 374 average time/residue: 0.1463 time to fit residues: 85.4950 Evaluate side-chains 299 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 46 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 243 optimal weight: 0.4980 chunk 175 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.077691 restraints weight = 59928.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.079328 restraints weight = 42621.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.080601 restraints weight = 33314.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081524 restraints weight = 27807.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082101 restraints weight = 24134.561| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20020 Z= 0.116 Angle : 0.551 6.339 27480 Z= 0.288 Chirality : 0.046 0.166 3660 Planarity : 0.004 0.075 3400 Dihedral : 3.598 15.335 2860 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.16), residues: 2680 helix: 3.96 (0.15), residues: 760 sheet: 1.94 (0.17), residues: 860 loop : -0.66 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 124 TYR 0.017 0.001 TYR Q 35 PHE 0.021 0.001 PHE T 32 TRP 0.023 0.003 TRP K 31 Details of bonding type rmsd covalent geometry : bond 0.00252 (20000) covalent geometry : angle 0.55091 (27440) SS BOND : bond 0.00124 ( 20) SS BOND : angle 0.54142 ( 40) hydrogen bonds : bond 0.04361 ( 1119) hydrogen bonds : angle 3.91670 ( 3240) =============================================================================== Job complete usr+sys time: 2605.47 seconds wall clock time: 46 minutes 15.30 seconds (2775.30 seconds total)