Starting phenix.real_space_refine on Mon Jun 16 18:09:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fk7_29249/06_2025/8fk7_29249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fk7_29249/06_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_29249/06_2025/8fk7_29249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fk7_29249/06_2025/8fk7_29249.map" model { file = "/net/cci-nas-00/data/ceres_data/8fk7_29249/06_2025/8fk7_29249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fk7_29249/06_2025/8fk7_29249.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.99, per 1000 atoms: 0.61 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: 4.79 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.23 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: 5.58 Time building geometry restraints manager: 5.66 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: 0.01 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 43.930 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (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 TRP 0.022 0.003 TRP P 31 PHE 0.021 0.001 PHE T 32 TYR 0.021 0.002 TYR A 29 ARG 0.015 0.001 ARG R 133 Details of bonding type rmsd hydrogen bonds : bond 0.15738 ( 1119) hydrogen bonds : angle 5.87346 ( 3240) SS BOND : bond 0.00265 ( 20) SS BOND : angle 0.48901 ( 40) covalent geometry : bond 0.00255 (20000) covalent geometry : angle 0.55783 (27440) *********************** 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 : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8461 (ptp90) cc_final: 0.8203 (ttp-110) REVERT: A 46 LEU cc_start: 0.9150 (mm) cc_final: 0.8764 (mm) REVERT: B 29 TYR cc_start: 0.8648 (t80) cc_final: 0.8351 (t80) REVERT: B 31 TRP cc_start: 0.8477 (t60) cc_final: 0.7744 (t60) REVERT: B 84 LEU cc_start: 0.8439 (mt) cc_final: 0.8192 (mt) REVERT: B 104 ASP cc_start: 0.8679 (m-30) cc_final: 0.8472 (m-30) REVERT: C 96 SER cc_start: 0.8525 (t) cc_final: 0.8313 (t) REVERT: C 124 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7879 (tpp80) REVERT: D 69 ARG cc_start: 0.9120 (tpp80) cc_final: 0.8810 (tpt-90) REVERT: E 70 ASN cc_start: 0.8680 (t0) cc_final: 0.8239 (t0) REVERT: F 30 LEU cc_start: 0.9061 (mm) cc_final: 0.8822 (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: 0.8635 (t80) REVERT: H 119 LEU cc_start: 0.7687 (mp) cc_final: 0.7373 (mp) REVERT: H 124 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7565 (tpp80) 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: 0.8315 (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: 0.8169 (t80) REVERT: M 52 LEU cc_start: 0.9137 (mp) cc_final: 0.8822 (mt) REVERT: M 91 MET cc_start: 0.8716 (ptm) cc_final: 0.8417 (ptt) REVERT: M 104 ASP cc_start: 0.8360 (m-30) cc_final: 0.8033 (m-30) REVERT: N 38 ARG cc_start: 0.8656 (ptt-90) cc_final: 0.7790 (ttp-110) REVERT: N 46 LEU cc_start: 0.9052 (mt) cc_final: 0.8777 (mm) REVERT: N 50 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6628 (mt-10) REVERT: N 73 GLU cc_start: 0.8290 (pm20) cc_final: 0.7979 (pm20) REVERT: N 133 ARG cc_start: 0.8756 (ttm110) cc_final: 0.8524 (ttm110) REVERT: O 73 GLU cc_start: 0.8353 (mp0) cc_final: 0.8081 (mp0) REVERT: O 91 MET cc_start: 0.8499 (ptt) cc_final: 0.8217 (ptm) REVERT: P 29 TYR cc_start: 0.8615 (t80) cc_final: 0.8284 (t80) REVERT: P 104 ASP cc_start: 0.8368 (m-30) cc_final: 0.8028 (m-30) REVERT: P 109 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8044 (mm-40) REVERT: Q 40 THR cc_start: 0.8307 (m) cc_final: 0.8089 (m) REVERT: Q 45 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8348 (tp40) REVERT: Q 104 ASP cc_start: 0.8419 (m-30) cc_final: 0.8077 (m-30) REVERT: Q 136 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7334 (mt-10) REVERT: R 73 GLU cc_start: 0.8116 (mp0) cc_final: 0.7833 (mp0) REVERT: R 91 MET cc_start: 0.9019 (ptm) cc_final: 0.8807 (ptm) REVERT: R 104 ASP cc_start: 0.8243 (t0) cc_final: 0.7581 (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: 0.8202 (mp0) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.3202 time to fit residues: 232.3723 Evaluate side-chains 344 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.0010 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 203 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 236 optimal weight: 0.8980 overall best weight: 1.2990 ------------------------------------------------------------------------------- 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 ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN R 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.089791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076173 restraints weight = 60305.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077824 restraints weight = 42974.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078963 restraints weight = 33805.407| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20020 Z= 0.135 Angle : 0.540 5.201 27480 Z= 0.290 Chirality : 0.046 0.160 3660 Planarity : 0.004 0.088 3400 Dihedral : 3.669 18.349 2860 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.15), residues: 2680 helix: 3.89 (0.15), residues: 760 sheet: 1.93 (0.16), residues: 860 loop : -0.46 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 31 PHE 0.012 0.001 PHE P 32 TYR 0.015 0.002 TYR N 35 ARG 0.010 0.001 ARG G 124 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 1119) hydrogen bonds : angle 4.52871 ( 3240) SS BOND : bond 0.00160 ( 20) SS BOND : angle 0.46385 ( 40) covalent geometry : bond 0.00296 (20000) covalent geometry : angle 0.54035 (27440) *********************** 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 448 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 2.190 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: 0.8374 (ptp90) cc_final: 0.8145 (ttp-110) REVERT: A 124 ARG cc_start: 0.8847 (tpp80) cc_final: 0.8112 (tpp80) REVERT: E 70 ASN cc_start: 0.8792 (t0) cc_final: 0.8226 (t0) REVERT: F 11 ILE cc_start: 0.8484 (mp) cc_final: 0.8223 (mm) REVERT: G 29 TYR cc_start: 0.8779 (t80) cc_final: 0.8537 (t80) REVERT: H 29 TYR cc_start: 0.8063 (t80) cc_final: 0.7465 (t80) REVERT: H 70 ASN cc_start: 0.8663 (t0) cc_final: 0.8276 (m-40) REVERT: H 119 LEU cc_start: 0.7532 (mp) cc_final: 0.7138 (mp) REVERT: I 124 ARG cc_start: 0.7352 (tpp80) cc_final: 0.7091 (mmt90) REVERT: J 46 LEU cc_start: 0.8615 (mt) cc_final: 0.8323 (mt) REVERT: K 70 ASN cc_start: 0.8868 (t0) cc_final: 0.8515 (t0) REVERT: L 136 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7968 (mt-10) REVERT: M 52 LEU cc_start: 0.9098 (mp) cc_final: 0.8880 (mt) REVERT: M 91 MET cc_start: 0.8517 (ptm) cc_final: 0.8265 (ptt) REVERT: N 46 LEU cc_start: 0.9132 (mt) cc_final: 0.8524 (mt) REVERT: N 73 GLU cc_start: 0.8439 (pm20) cc_final: 0.8150 (pm20) REVERT: O 104 ASP cc_start: 0.8528 (m-30) cc_final: 0.8181 (m-30) REVERT: Q 38 ARG cc_start: 0.8493 (ptt90) cc_final: 0.8183 (ptt-90) REVERT: Q 40 THR cc_start: 0.8220 (m) cc_final: 0.7997 (m) REVERT: Q 104 ASP cc_start: 0.8277 (m-30) cc_final: 0.7989 (m-30) REVERT: Q 119 LEU cc_start: 0.9098 (mt) cc_final: 0.8624 (mp) REVERT: R 73 GLU cc_start: 0.8268 (mp0) cc_final: 0.8023 (mp0) REVERT: R 104 ASP cc_start: 0.8099 (t0) cc_final: 0.7600 (m-30) REVERT: S 46 LEU cc_start: 0.8321 (mm) cc_final: 0.7572 (mm) REVERT: S 73 GLU cc_start: 0.8427 (mp0) cc_final: 0.8190 (mp0) REVERT: S 104 ASP cc_start: 0.7984 (m-30) cc_final: 0.7766 (m-30) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.3219 time to fit residues: 217.8412 Evaluate side-chains 326 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 243 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** F 102 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** M 45 GLN N 42 GLN 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 = 0.3344 r_free = 0.3344 target = 0.089918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076489 restraints weight = 60467.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.078165 restraints weight = 42837.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.079295 restraints weight = 33502.154| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1987 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= 0.123 Angle : 0.521 6.285 27480 Z= 0.279 Chirality : 0.046 0.172 3660 Planarity : 0.004 0.070 3400 Dihedral : 3.594 17.368 2860 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.15), residues: 2680 helix: 3.93 (0.15), residues: 760 sheet: 1.73 (0.16), residues: 880 loop : -0.35 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP K 31 PHE 0.006 0.001 PHE A 32 TYR 0.018 0.002 TYR A 35 ARG 0.005 0.001 ARG N 133 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 1119) hydrogen bonds : angle 4.21802 ( 3240) SS BOND : bond 0.00267 ( 20) SS BOND : angle 0.47974 ( 40) covalent geometry : bond 0.00267 (20000) covalent geometry : angle 0.52075 (27440) *********************** 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 439 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 438 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.7892 (ttm-80) REVERT: E 70 ASN cc_start: 0.8902 (t0) cc_final: 0.8384 (t0) REVERT: F 11 ILE cc_start: 0.8515 (mp) cc_final: 0.8273 (mm) REVERT: H 29 TYR cc_start: 0.8131 (t80) cc_final: 0.7538 (t80) REVERT: K 70 ASN cc_start: 0.8744 (t0) cc_final: 0.8393 (t0) REVERT: L 42 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8225 (tm-30) REVERT: L 46 LEU cc_start: 0.9147 (mt) cc_final: 0.8387 (mt) REVERT: L 136 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8050 (mt-10) REVERT: M 91 MET cc_start: 0.8573 (ptm) cc_final: 0.8279 (ptt) REVERT: N 46 LEU cc_start: 0.9101 (mt) cc_final: 0.8642 (mt) REVERT: N 53 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8682 (ttpt) REVERT: N 73 GLU cc_start: 0.8349 (pm20) cc_final: 0.8036 (pm20) REVERT: O 104 ASP cc_start: 0.8318 (m-30) cc_final: 0.8084 (m-30) REVERT: P 37 THR cc_start: 0.9292 (m) cc_final: 0.9004 (p) REVERT: Q 38 ARG cc_start: 0.8521 (ptt90) cc_final: 0.8164 (ptt-90) REVERT: R 133 ARG cc_start: 0.8415 (ttm110) cc_final: 0.8187 (mtp-110) REVERT: S 73 GLU cc_start: 0.8490 (mp0) cc_final: 0.8224 (mp0) REVERT: S 104 ASP cc_start: 0.8045 (m-30) cc_final: 0.7817 (m-30) outliers start: 1 outliers final: 0 residues processed: 439 average time/residue: 0.3260 time to fit residues: 214.9317 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 : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 151 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 243 optimal weight: 0.0970 chunk 135 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 71 optimal weight: 0.0170 chunk 90 optimal weight: 6.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- 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** E 51 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** P 70 ASN T 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.076490 restraints weight = 60272.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.078145 restraints weight = 42765.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.079357 restraints weight = 33577.886| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20020 Z= 0.118 Angle : 0.516 5.698 27480 Z= 0.273 Chirality : 0.046 0.234 3660 Planarity : 0.004 0.070 3400 Dihedral : 3.542 16.519 2860 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.09 % Allowed : 1.99 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.16), residues: 2680 helix: 3.95 (0.15), residues: 760 sheet: 1.92 (0.16), residues: 860 loop : -0.50 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP K 31 PHE 0.015 0.001 PHE P 32 TYR 0.017 0.001 TYR F 35 ARG 0.010 0.001 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 1119) hydrogen bonds : angle 4.08294 ( 3240) SS BOND : bond 0.00154 ( 20) SS BOND : angle 0.47378 ( 40) covalent geometry : bond 0.00256 (20000) covalent geometry : angle 0.51595 (27440) *********************** 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 426 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 424 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 GLN cc_start: 0.9079 (mp10) cc_final: 0.8861 (mp10) REVERT: C 69 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.7839 (ttm-80) REVERT: D 104 ASP cc_start: 0.7948 (m-30) cc_final: 0.7743 (m-30) REVERT: E 70 ASN cc_start: 0.8819 (t0) cc_final: 0.8370 (t0) REVERT: F 11 ILE cc_start: 0.8533 (mp) cc_final: 0.8295 (mm) REVERT: H 29 TYR cc_start: 0.8165 (t80) cc_final: 0.7595 (t80) REVERT: K 70 ASN cc_start: 0.8737 (t0) cc_final: 0.8373 (t0) REVERT: K 119 LEU cc_start: 0.8397 (mp) cc_final: 0.8167 (mt) REVERT: L 42 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8212 (tm-30) REVERT: L 44 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8341 (tm-30) REVERT: L 46 LEU cc_start: 0.9109 (mt) cc_final: 0.8328 (mt) REVERT: L 136 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7998 (mt-10) REVERT: M 91 MET cc_start: 0.8562 (ptm) cc_final: 0.8277 (ptt) REVERT: N 42 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8413 (tm-30) REVERT: N 44 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7980 (tm-30) REVERT: N 46 LEU cc_start: 0.9159 (mt) cc_final: 0.8487 (mt) REVERT: O 104 ASP cc_start: 0.8282 (m-30) cc_final: 0.8062 (m-30) REVERT: P 37 THR cc_start: 0.9268 (m) cc_final: 0.8953 (p) REVERT: P 104 ASP cc_start: 0.8296 (m-30) cc_final: 0.8085 (m-30) REVERT: Q 37 THR cc_start: 0.8872 (m) cc_final: 0.8590 (p) REVERT: Q 38 ARG cc_start: 0.8387 (ptt90) cc_final: 0.8040 (ptt-90) REVERT: Q 104 ASP cc_start: 0.8173 (m-30) cc_final: 0.7944 (m-30) REVERT: R 133 ARG cc_start: 0.8428 (ttm110) cc_final: 0.8211 (mtp85) REVERT: S 73 GLU cc_start: 0.8585 (mp0) cc_final: 0.8290 (mp0) REVERT: S 104 ASP cc_start: 0.8036 (m-30) cc_final: 0.7803 (m-30) REVERT: T 70 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8201 (m-40) outliers start: 2 outliers final: 0 residues processed: 425 average time/residue: 0.3191 time to fit residues: 205.1889 Evaluate side-chains 319 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 117 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 0.0570 chunk 168 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 124 optimal weight: 0.0570 chunk 176 optimal weight: 0.0020 chunk 113 optimal weight: 5.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- 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 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** ** H 70 ASN ** 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 P 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076186 restraints weight = 60712.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.077855 restraints weight = 43299.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079077 restraints weight = 33979.684| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20020 Z= 0.122 Angle : 0.515 6.995 27480 Z= 0.274 Chirality : 0.045 0.164 3660 Planarity : 0.004 0.077 3400 Dihedral : 3.528 15.751 2860 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.05 % Allowed : 1.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.16), residues: 2680 helix: 3.96 (0.15), residues: 760 sheet: 1.61 (0.17), residues: 900 loop : -0.40 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP K 31 PHE 0.013 0.001 PHE F 32 TYR 0.017 0.001 TYR S 35 ARG 0.009 0.001 ARG N 133 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 1119) hydrogen bonds : angle 4.00778 ( 3240) SS BOND : bond 0.00142 ( 20) SS BOND : angle 0.51982 ( 40) covalent geometry : bond 0.00269 (20000) covalent geometry : angle 0.51526 (27440) *********************** 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 417 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 416 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 51 GLN cc_start: 0.9100 (mp10) cc_final: 0.8855 (mp10) REVERT: C 69 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.7840 (ttm-80) REVERT: C 124 ARG cc_start: 0.7957 (tpp80) cc_final: 0.7680 (tpp80) REVERT: E 70 ASN cc_start: 0.8903 (t0) cc_final: 0.8374 (t0) REVERT: F 11 ILE cc_start: 0.8521 (mp) cc_final: 0.8285 (mm) REVERT: H 29 TYR cc_start: 0.8138 (t80) cc_final: 0.7595 (t80) REVERT: H 119 LEU cc_start: 0.7626 (mp) cc_final: 0.7078 (mp) REVERT: K 44 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7951 (tm-30) REVERT: K 70 ASN cc_start: 0.8767 (t0) cc_final: 0.8282 (t0) REVERT: K 119 LEU cc_start: 0.8346 (mp) cc_final: 0.8137 (mt) REVERT: L 42 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8250 (tm-30) REVERT: L 44 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8341 (tm-30) REVERT: L 46 LEU cc_start: 0.9022 (mt) cc_final: 0.8296 (mt) REVERT: M 91 MET cc_start: 0.8549 (ptm) cc_final: 0.8247 (ptt) REVERT: N 44 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8198 (tm-30) REVERT: N 46 LEU cc_start: 0.9146 (mt) cc_final: 0.8448 (mt) REVERT: O 104 ASP cc_start: 0.8264 (m-30) cc_final: 0.8022 (m-30) REVERT: Q 37 THR cc_start: 0.8875 (m) cc_final: 0.8624 (p) REVERT: Q 38 ARG cc_start: 0.8469 (ptt90) cc_final: 0.7949 (tmm160) REVERT: Q 73 GLU cc_start: 0.8194 (pm20) cc_final: 0.7955 (pm20) REVERT: Q 104 ASP cc_start: 0.8094 (m-30) cc_final: 0.7872 (m-30) REVERT: R 133 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8189 (mtp85) REVERT: S 73 GLU cc_start: 0.8615 (mp0) cc_final: 0.8306 (mp0) REVERT: S 104 ASP cc_start: 0.8015 (m-30) cc_final: 0.7779 (m-30) REVERT: T 133 ARG cc_start: 0.8413 (ptp-110) cc_final: 0.7906 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.3029 time to fit residues: 191.8129 Evaluate side-chains 309 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 205 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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** F 102 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** 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 45 GLN P 70 ASN ** 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 = 0.3299 r_free = 0.3299 target = 0.087451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073709 restraints weight = 61142.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.075333 restraints weight = 44032.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076478 restraints weight = 34819.121| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20020 Z= 0.179 Angle : 0.562 5.901 27480 Z= 0.300 Chirality : 0.046 0.229 3660 Planarity : 0.004 0.054 3400 Dihedral : 3.754 15.448 2860 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.16), residues: 2680 helix: 3.94 (0.15), residues: 760 sheet: 1.87 (0.16), residues: 860 loop : -0.47 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP K 31 PHE 0.014 0.002 PHE P 32 TYR 0.020 0.002 TYR H 35 ARG 0.021 0.001 ARG D 124 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 1119) hydrogen bonds : angle 4.13585 ( 3240) SS BOND : bond 0.00182 ( 20) SS BOND : angle 0.82601 ( 40) covalent geometry : bond 0.00408 (20000) covalent geometry : angle 0.56197 (27440) *********************** 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 399 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 SER cc_start: 0.8856 (t) cc_final: 0.8596 (t) REVERT: A 124 ARG cc_start: 0.8769 (tpp80) cc_final: 0.8427 (tpp80) REVERT: C 37 THR cc_start: 0.8008 (m) cc_final: 0.7805 (t) REVERT: E 70 ASN cc_start: 0.8846 (t0) cc_final: 0.8302 (t0) REVERT: F 30 LEU cc_start: 0.8942 (mm) cc_final: 0.8720 (tp) REVERT: F 104 ASP cc_start: 0.8628 (m-30) cc_final: 0.8425 (m-30) REVERT: H 119 LEU cc_start: 0.7668 (mp) cc_final: 0.7083 (mp) REVERT: K 44 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8206 (tt0) REVERT: K 70 ASN cc_start: 0.8844 (t0) cc_final: 0.8597 (t0) REVERT: K 124 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7424 (mmm160) REVERT: L 42 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8418 (tm-30) REVERT: L 44 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8549 (tm-30) REVERT: L 46 LEU cc_start: 0.9033 (mt) cc_final: 0.8363 (mt) REVERT: L 68 VAL cc_start: 0.9157 (t) cc_final: 0.8792 (m) REVERT: L 119 LEU cc_start: 0.8757 (mt) cc_final: 0.8432 (mt) REVERT: M 91 MET cc_start: 0.8578 (ptm) cc_final: 0.8321 (ptt) REVERT: M 104 ASP cc_start: 0.8200 (m-30) cc_final: 0.7957 (m-30) REVERT: N 42 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8490 (tm-30) REVERT: N 44 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8181 (tm-30) REVERT: N 46 LEU cc_start: 0.9067 (mt) cc_final: 0.8507 (mt) REVERT: O 104 ASP cc_start: 0.8259 (m-30) cc_final: 0.8041 (m-30) REVERT: O 126 ILE cc_start: 0.9425 (mt) cc_final: 0.9177 (tt) REVERT: P 29 TYR cc_start: 0.8736 (t80) cc_final: 0.8465 (t80) REVERT: Q 38 ARG cc_start: 0.8492 (ptt90) cc_final: 0.7852 (tmm160) REVERT: Q 50 GLU cc_start: 0.8579 (tp30) cc_final: 0.6794 (tt0) REVERT: Q 73 GLU cc_start: 0.8174 (pm20) cc_final: 0.7829 (pm20) REVERT: Q 104 ASP cc_start: 0.8253 (m-30) cc_final: 0.8023 (m-30) REVERT: Q 118 ASN cc_start: 0.8519 (p0) cc_final: 0.8317 (p0) REVERT: R 101 GLN cc_start: 0.7885 (mp10) cc_final: 0.7662 (mp10) REVERT: R 133 ARG cc_start: 0.8486 (ttm110) cc_final: 0.8123 (mtp85) REVERT: S 11 ILE cc_start: 0.8654 (mm) cc_final: 0.8448 (mm) REVERT: S 73 GLU cc_start: 0.8515 (mp0) cc_final: 0.8268 (mp0) REVERT: S 104 ASP cc_start: 0.8042 (m-30) cc_final: 0.7783 (m-30) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.3093 time to fit residues: 189.5011 Evaluate side-chains 306 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 213 optimal weight: 0.0980 chunk 145 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 207 optimal weight: 0.0060 chunk 211 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 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** P 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.076337 restraints weight = 59688.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.078023 restraints weight = 42578.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.079239 restraints weight = 33374.519| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20020 Z= 0.113 Angle : 0.524 5.992 27480 Z= 0.275 Chirality : 0.046 0.226 3660 Planarity : 0.004 0.078 3400 Dihedral : 3.593 13.723 2860 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.16), residues: 2680 helix: 3.98 (0.15), residues: 760 sheet: 1.92 (0.17), residues: 860 loop : -0.58 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP K 31 PHE 0.018 0.001 PHE N 32 TYR 0.017 0.001 TYR L 29 ARG 0.011 0.001 ARG N 133 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 1119) hydrogen bonds : angle 3.98680 ( 3240) SS BOND : bond 0.00391 ( 20) SS BOND : angle 0.68883 ( 40) covalent geometry : bond 0.00241 (20000) covalent geometry : angle 0.52358 (27440) *********************** 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 433 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TYR cc_start: 0.8133 (t80) cc_final: 0.7540 (t80) REVERT: A 37 THR cc_start: 0.9559 (m) cc_final: 0.9295 (p) REVERT: A 38 ARG cc_start: 0.8438 (ptt-90) cc_final: 0.8224 (ptp90) REVERT: A 41 SER cc_start: 0.8846 (t) cc_final: 0.8579 (t) REVERT: C 124 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7810 (tpp80) REVERT: E 70 ASN cc_start: 0.8976 (t0) cc_final: 0.8427 (t0) REVERT: F 11 ILE cc_start: 0.8521 (mp) cc_final: 0.8263 (mm) REVERT: F 46 LEU cc_start: 0.9142 (mt) cc_final: 0.8893 (mt) REVERT: H 29 TYR cc_start: 0.7908 (t80) cc_final: 0.7446 (t80) REVERT: K 70 ASN cc_start: 0.8675 (t0) cc_final: 0.8285 (t0) REVERT: L 42 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8350 (tm-30) REVERT: L 44 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8292 (tm-30) REVERT: L 46 LEU cc_start: 0.8977 (mt) cc_final: 0.8257 (mt) REVERT: L 68 VAL cc_start: 0.9127 (t) cc_final: 0.8763 (m) REVERT: L 119 LEU cc_start: 0.8675 (mt) cc_final: 0.8306 (mt) REVERT: M 91 MET cc_start: 0.8494 (ptm) cc_final: 0.8236 (ptt) REVERT: M 124 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7369 (mmm160) REVERT: N 29 TYR cc_start: 0.8442 (t80) cc_final: 0.8175 (t80) REVERT: N 44 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8249 (tm-30) REVERT: N 46 LEU cc_start: 0.9072 (mt) cc_final: 0.8447 (mt) REVERT: O 45 GLN cc_start: 0.8508 (tp40) cc_final: 0.7767 (tp40) REVERT: O 104 ASP cc_start: 0.8198 (m-30) cc_final: 0.7944 (m-30) REVERT: P 133 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.7921 (mtp85) REVERT: P 143 SER cc_start: 0.8517 (t) cc_final: 0.8282 (t) REVERT: Q 37 THR cc_start: 0.8874 (m) cc_final: 0.8634 (p) REVERT: Q 38 ARG cc_start: 0.8437 (ptt90) cc_final: 0.7929 (tmm160) REVERT: Q 50 GLU cc_start: 0.8414 (tp30) cc_final: 0.6712 (tt0) REVERT: Q 104 ASP cc_start: 0.8162 (m-30) cc_final: 0.7873 (m-30) REVERT: Q 118 ASN cc_start: 0.8434 (p0) cc_final: 0.8234 (p0) REVERT: R 101 GLN cc_start: 0.7872 (mp10) cc_final: 0.7660 (mp10) REVERT: R 133 ARG cc_start: 0.8312 (ttm110) cc_final: 0.8106 (mtp85) REVERT: S 73 GLU cc_start: 0.8576 (mp0) cc_final: 0.8279 (mp0) REVERT: S 104 ASP cc_start: 0.7988 (m-30) cc_final: 0.7720 (m-30) REVERT: T 50 GLU cc_start: 0.7569 (pt0) cc_final: 0.7325 (pt0) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.3218 time to fit residues: 209.4306 Evaluate side-chains 324 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 241 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 244 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 chunk 168 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 70 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.077870 restraints weight = 60084.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079561 restraints weight = 42919.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.080771 restraints weight = 33629.226| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20020 Z= 0.112 Angle : 0.541 12.130 27480 Z= 0.282 Chirality : 0.046 0.214 3660 Planarity : 0.004 0.073 3400 Dihedral : 3.560 15.485 2860 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.16), residues: 2680 helix: 3.96 (0.15), residues: 760 sheet: 1.96 (0.17), residues: 860 loop : -0.63 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP K 31 PHE 0.019 0.001 PHE T 32 TYR 0.020 0.001 TYR N 82 ARG 0.012 0.001 ARG N 133 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 1119) hydrogen bonds : angle 3.96041 ( 3240) SS BOND : bond 0.00136 ( 20) SS BOND : angle 0.53520 ( 40) covalent geometry : bond 0.00240 (20000) covalent geometry : angle 0.54129 (27440) *********************** 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 418 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.9544 (m) cc_final: 0.9282 (p) REVERT: A 41 SER cc_start: 0.8827 (t) cc_final: 0.8497 (t) REVERT: C 51 GLN cc_start: 0.8961 (mp10) cc_final: 0.8637 (mp10) REVERT: C 69 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7934 (ttm-80) REVERT: E 70 ASN cc_start: 0.8985 (t0) cc_final: 0.8576 (t0) REVERT: F 11 ILE cc_start: 0.8455 (mp) cc_final: 0.8230 (mm) REVERT: H 29 TYR cc_start: 0.7872 (t80) cc_final: 0.7314 (t80) REVERT: H 119 LEU cc_start: 0.7695 (mp) cc_final: 0.7043 (mp) REVERT: I 37 THR cc_start: 0.9126 (p) cc_final: 0.8750 (t) REVERT: I 44 GLU cc_start: 0.8390 (tp30) cc_final: 0.8054 (tp30) REVERT: K 70 ASN cc_start: 0.8739 (t0) cc_final: 0.8367 (t0) REVERT: K 119 LEU cc_start: 0.8331 (mp) cc_final: 0.8085 (mt) REVERT: L 42 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8317 (tm-30) REVERT: L 46 LEU cc_start: 0.8869 (mt) cc_final: 0.8210 (mt) REVERT: L 68 VAL cc_start: 0.9138 (t) cc_final: 0.8760 (m) REVERT: L 119 LEU cc_start: 0.8665 (mt) cc_final: 0.8422 (mt) REVERT: M 91 MET cc_start: 0.8426 (ptm) cc_final: 0.8156 (ptt) REVERT: M 133 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8067 (mtp-110) REVERT: N 29 TYR cc_start: 0.8381 (t80) cc_final: 0.7979 (t80) REVERT: N 42 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8393 (tm-30) REVERT: N 44 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8154 (tm-30) REVERT: N 46 LEU cc_start: 0.9056 (mt) cc_final: 0.8449 (mt) REVERT: O 104 ASP cc_start: 0.8081 (m-30) cc_final: 0.7844 (m-30) REVERT: P 133 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.7910 (mtp85) REVERT: P 143 SER cc_start: 0.8464 (t) cc_final: 0.8192 (t) REVERT: Q 38 ARG cc_start: 0.8334 (ptt90) cc_final: 0.7913 (tmm160) REVERT: Q 73 GLU cc_start: 0.8149 (pm20) cc_final: 0.7933 (pm20) REVERT: Q 104 ASP cc_start: 0.8092 (m-30) cc_final: 0.7869 (m-30) REVERT: Q 136 GLU cc_start: 0.8599 (tp30) cc_final: 0.7637 (pt0) REVERT: R 101 GLN cc_start: 0.7870 (mp10) cc_final: 0.7654 (mp10) REVERT: S 73 GLU cc_start: 0.8612 (mp0) cc_final: 0.8312 (mp0) REVERT: S 104 ASP cc_start: 0.7954 (m-30) cc_final: 0.7700 (m-30) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.3168 time to fit residues: 204.0249 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 : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 218 optimal weight: 0.2980 chunk 200 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 241 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 114 optimal weight: 0.0010 chunk 228 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 70 ASN F 42 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.077386 restraints weight = 59326.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079069 restraints weight = 42200.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.080307 restraints weight = 32975.107| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20020 Z= 0.123 Angle : 0.551 11.216 27480 Z= 0.287 Chirality : 0.046 0.278 3660 Planarity : 0.004 0.064 3400 Dihedral : 3.602 18.301 2860 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.16), residues: 2680 helix: 3.99 (0.15), residues: 760 sheet: 1.96 (0.17), residues: 860 loop : -0.65 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 31 PHE 0.014 0.001 PHE F 32 TYR 0.018 0.001 TYR C 125 ARG 0.014 0.001 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 1119) hydrogen bonds : angle 3.92834 ( 3240) SS BOND : bond 0.00133 ( 20) SS BOND : angle 0.56346 ( 40) covalent geometry : bond 0.00272 (20000) covalent geometry : angle 0.55113 (27440) *********************** 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 401 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.9523 (m) cc_final: 0.9266 (p) REVERT: A 41 SER cc_start: 0.8833 (t) cc_final: 0.8481 (t) REVERT: C 37 THR cc_start: 0.7829 (m) cc_final: 0.7606 (t) REVERT: E 70 ASN cc_start: 0.8946 (t0) cc_final: 0.8478 (t0) REVERT: F 11 ILE cc_start: 0.8435 (mp) cc_final: 0.8207 (mm) REVERT: H 29 TYR cc_start: 0.7902 (t80) cc_final: 0.7320 (t80) REVERT: H 119 LEU cc_start: 0.7663 (mp) cc_final: 0.7042 (mp) REVERT: I 37 THR cc_start: 0.9140 (p) cc_final: 0.8776 (t) REVERT: I 44 GLU cc_start: 0.8043 (tp30) cc_final: 0.7473 (tp30) REVERT: K 70 ASN cc_start: 0.8782 (t0) cc_final: 0.8373 (t0) REVERT: L 42 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8312 (tm-30) REVERT: L 46 LEU cc_start: 0.8894 (mt) cc_final: 0.8265 (mt) REVERT: L 68 VAL cc_start: 0.9134 (t) cc_final: 0.8736 (m) REVERT: L 140 THR cc_start: 0.7936 (m) cc_final: 0.7622 (m) REVERT: M 91 MET cc_start: 0.8417 (ptm) cc_final: 0.8174 (ptt) REVERT: M 104 ASP cc_start: 0.8104 (m-30) cc_final: 0.7844 (m-30) REVERT: M 124 ARG cc_start: 0.7934 (mmm160) cc_final: 0.7412 (mmm160) REVERT: M 133 ARG cc_start: 0.8326 (ttm110) cc_final: 0.7968 (mtp85) REVERT: N 29 TYR cc_start: 0.8373 (t80) cc_final: 0.8138 (t80) REVERT: N 37 THR cc_start: 0.9369 (m) cc_final: 0.9135 (p) REVERT: N 44 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8006 (tm-30) REVERT: O 104 ASP cc_start: 0.8046 (m-30) cc_final: 0.7826 (m-30) REVERT: O 126 ILE cc_start: 0.9389 (mt) cc_final: 0.9033 (tt) REVERT: P 133 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.7878 (mtp85) REVERT: P 143 SER cc_start: 0.8491 (t) cc_final: 0.8214 (t) REVERT: Q 38 ARG cc_start: 0.8339 (ptt90) cc_final: 0.8031 (ttp-170) REVERT: Q 50 GLU cc_start: 0.8446 (tp30) cc_final: 0.7175 (tt0) REVERT: Q 51 GLN cc_start: 0.8975 (pm20) cc_final: 0.8491 (pm20) REVERT: Q 118 ASN cc_start: 0.8473 (p0) cc_final: 0.8269 (p0) REVERT: Q 136 GLU cc_start: 0.8518 (tp30) cc_final: 0.7642 (pt0) REVERT: R 101 GLN cc_start: 0.7920 (mp10) cc_final: 0.7699 (mp10) REVERT: S 73 GLU cc_start: 0.8629 (mp0) cc_final: 0.8350 (mp0) REVERT: S 104 ASP cc_start: 0.7994 (m-30) cc_final: 0.7732 (m-30) REVERT: T 50 GLU cc_start: 0.7055 (pt0) cc_final: 0.6664 (pt0) REVERT: T 133 ARG cc_start: 0.8274 (ptp-170) cc_final: 0.7939 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.3129 time to fit residues: 191.3467 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 : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 165 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** F 42 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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** M 45 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 = 0.3371 r_free = 0.3371 target = 0.091366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077725 restraints weight = 59368.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079424 restraints weight = 42375.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.080612 restraints weight = 33132.046| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3194 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= 0.120 Angle : 0.557 11.019 27480 Z= 0.290 Chirality : 0.046 0.265 3660 Planarity : 0.004 0.061 3400 Dihedral : 3.602 16.770 2860 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.16), residues: 2680 helix: 3.97 (0.15), residues: 760 sheet: 1.96 (0.17), residues: 860 loop : -0.67 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP K 31 PHE 0.019 0.001 PHE C 32 TYR 0.029 0.002 TYR N 82 ARG 0.015 0.001 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 1119) hydrogen bonds : angle 3.90617 ( 3240) SS BOND : bond 0.00140 ( 20) SS BOND : angle 0.55334 ( 40) covalent geometry : bond 0.00264 (20000) covalent geometry : angle 0.55743 (27440) ********************** 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 403 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.9491 (m) cc_final: 0.9259 (p) REVERT: A 41 SER cc_start: 0.8812 (t) cc_final: 0.8484 (t) REVERT: C 37 THR cc_start: 0.7835 (m) cc_final: 0.7596 (t) REVERT: C 96 SER cc_start: 0.8687 (t) cc_final: 0.8478 (t) REVERT: C 124 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7574 (tpp80) REVERT: D 136 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8164 (mm-30) REVERT: E 70 ASN cc_start: 0.8945 (t0) cc_final: 0.8524 (t0) REVERT: F 11 ILE cc_start: 0.8447 (mp) cc_final: 0.8234 (mm) REVERT: H 29 TYR cc_start: 0.7936 (t80) cc_final: 0.7335 (t80) REVERT: H 119 LEU cc_start: 0.7694 (mp) cc_final: 0.7070 (mp) REVERT: I 37 THR cc_start: 0.9146 (p) cc_final: 0.8792 (t) REVERT: K 70 ASN cc_start: 0.8713 (t0) cc_final: 0.8266 (t0) REVERT: L 46 LEU cc_start: 0.8870 (mt) cc_final: 0.8260 (mt) REVERT: L 140 THR cc_start: 0.7930 (m) cc_final: 0.7604 (m) REVERT: M 91 MET cc_start: 0.8405 (ptm) cc_final: 0.8201 (ptt) REVERT: M 124 ARG cc_start: 0.7930 (mmm160) cc_final: 0.7470 (mmm160) REVERT: M 133 ARG cc_start: 0.8324 (ttm110) cc_final: 0.8046 (mtp85) REVERT: N 29 TYR cc_start: 0.8340 (t80) cc_final: 0.8048 (t80) REVERT: N 37 THR cc_start: 0.9291 (m) cc_final: 0.9075 (p) REVERT: O 46 LEU cc_start: 0.8486 (mm) cc_final: 0.8272 (mm) REVERT: O 104 ASP cc_start: 0.8072 (m-30) cc_final: 0.7869 (m-30) REVERT: P 104 ASP cc_start: 0.8266 (m-30) cc_final: 0.8063 (m-30) REVERT: P 133 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.7828 (mtp85) REVERT: P 143 SER cc_start: 0.8479 (t) cc_final: 0.8201 (t) REVERT: Q 38 ARG cc_start: 0.8311 (ptt90) cc_final: 0.7940 (ttp-170) REVERT: Q 50 GLU cc_start: 0.8563 (tp30) cc_final: 0.7437 (tt0) REVERT: Q 51 GLN cc_start: 0.9041 (pm20) cc_final: 0.8527 (pm20) REVERT: Q 118 ASN cc_start: 0.8492 (p0) cc_final: 0.8288 (p0) REVERT: Q 133 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7915 (ttm110) REVERT: Q 136 GLU cc_start: 0.8530 (tp30) cc_final: 0.7675 (pt0) REVERT: R 101 GLN cc_start: 0.7852 (mp10) cc_final: 0.7606 (mp10) REVERT: S 73 GLU cc_start: 0.8642 (mp0) cc_final: 0.8347 (mp0) REVERT: S 104 ASP cc_start: 0.7949 (m-30) cc_final: 0.7705 (m-30) REVERT: T 133 ARG cc_start: 0.8298 (ptp-170) cc_final: 0.7993 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.3208 time to fit residues: 198.8359 Evaluate side-chains 315 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.9980 chunk 252 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN F 42 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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** L 42 GLN P 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.090781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.077118 restraints weight = 60052.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078771 restraints weight = 43043.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.079996 restraints weight = 33919.229| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20020 Z= 0.130 Angle : 0.565 10.584 27480 Z= 0.294 Chirality : 0.046 0.262 3660 Planarity : 0.004 0.063 3400 Dihedral : 3.639 17.713 2860 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.16), residues: 2680 helix: 3.98 (0.15), residues: 760 sheet: 1.74 (0.17), residues: 880 loop : -0.57 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 31 PHE 0.021 0.001 PHE T 32 TYR 0.015 0.001 TYR L 29 ARG 0.015 0.001 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 1119) hydrogen bonds : angle 3.91452 ( 3240) SS BOND : bond 0.00127 ( 20) SS BOND : angle 0.58245 ( 40) covalent geometry : bond 0.00290 (20000) covalent geometry : angle 0.56475 (27440) =============================================================================== Job complete usr+sys time: 5940.72 seconds wall clock time: 105 minutes 35.10 seconds (6335.10 seconds total)