Starting phenix.real_space_refine on Tue Nov 19 08:27:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk7_29249/11_2024/8fk7_29249.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk7_29249/11_2024/8fk7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk7_29249/11_2024/8fk7_29249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk7_29249/11_2024/8fk7_29249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk7_29249/11_2024/8fk7_29249.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk7_29249/11_2024/8fk7_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 12.03, 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: 5.09 Conformation dependent library (CDL) restraints added in 3.0 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: 2.24 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: 6.34 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6380 1.34 - 1.46: 3550 1.46 - 1.58: 9990 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 20000 Sorted by residual: bond pdb=" CB THR K 40 " pdb=" CG2 THR K 40 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB THR G 40 " pdb=" CG2 THR G 40 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB THR I 40 " pdb=" CG2 THR I 40 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" CB THR J 40 " pdb=" CG2 THR J 40 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.27e-01 bond pdb=" CG ARG R 133 " pdb=" CD ARG R 133 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.97e-01 ... (remaining 19995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 26631 1.35 - 2.71: 612 2.71 - 4.06: 147 4.06 - 5.41: 46 5.41 - 6.77: 4 Bond angle restraints: 27440 Sorted by residual: angle pdb=" CB ARG B 124 " pdb=" CG ARG B 124 " pdb=" CD ARG B 124 " ideal model delta sigma weight residual 111.30 116.80 -5.50 2.30e+00 1.89e-01 5.73e+00 angle pdb=" C ALA Q 86 " pdb=" N THR Q 87 " pdb=" CA THR Q 87 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.72e+00 angle pdb=" C ALA S 86 " pdb=" N THR S 87 " pdb=" CA THR S 87 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.42e+00 angle pdb=" C ALA T 86 " pdb=" N THR T 87 " pdb=" CA THR T 87 " ideal model delta sigma weight residual 121.54 125.98 -4.44 1.91e+00 2.74e-01 5.40e+00 angle pdb=" CB ARG R 133 " pdb=" CG ARG R 133 " pdb=" CD ARG R 133 " ideal model delta sigma weight residual 111.30 116.64 -5.34 2.30e+00 1.89e-01 5.39e+00 ... (remaining 27435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 11233 17.77 - 35.55: 687 35.55 - 53.32: 101 53.32 - 71.09: 21 71.09 - 88.87: 18 Dihedral angle restraints: 12060 sinusoidal: 4240 harmonic: 7820 Sorted by residual: dihedral pdb=" CB CYS O 93 " pdb=" SG CYS O 93 " pdb=" SG CYS O 117 " pdb=" CB CYS O 117 " ideal model delta sinusoidal sigma weight residual -86.00 2.87 -88.87 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS K 93 " pdb=" SG CYS K 93 " pdb=" SG CYS K 117 " pdb=" CB CYS K 117 " ideal model delta sinusoidal sigma weight residual 93.00 19.70 73.30 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CB CYS I 93 " pdb=" SG CYS I 93 " pdb=" SG CYS I 117 " pdb=" CB CYS I 117 " ideal model delta sinusoidal sigma weight residual 93.00 19.91 73.09 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 12057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2632 0.042 - 0.084: 649 0.084 - 0.125: 343 0.125 - 0.167: 35 0.167 - 0.209: 1 Chirality restraints: 3660 Sorted by residual: chirality pdb=" CB ILE B 126 " pdb=" CA ILE B 126 " pdb=" CG1 ILE B 126 " pdb=" CG2 ILE B 126 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE E 126 " pdb=" CA ILE E 126 " pdb=" CG1 ILE E 126 " pdb=" CG2 ILE E 126 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA GLN H 45 " pdb=" N GLN H 45 " pdb=" C GLN H 45 " pdb=" CB GLN H 45 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 3657 not shown) Planarity restraints: 3400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 133 " 0.134 9.50e-02 1.11e+02 6.04e-02 2.93e+00 pdb=" NE ARG R 133 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG R 133 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG R 133 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG R 133 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL Q 36 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C VAL Q 36 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL Q 36 " 0.011 2.00e-02 2.50e+03 pdb=" N THR Q 37 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 36 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C VAL K 36 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL K 36 " 0.010 2.00e-02 2.50e+03 pdb=" N THR K 37 " 0.009 2.00e-02 2.50e+03 ... (remaining 3397 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 547 2.70 - 3.25: 19841 3.25 - 3.80: 31220 3.80 - 4.35: 34971 4.35 - 4.90: 62564 Nonbonded interactions: 149143 Sorted by model distance: nonbonded pdb=" OG SER L 47 " pdb=" OH TYR O 35 " model vdw 2.156 3.040 nonbonded pdb=" OG SER G 47 " pdb=" OH TYR J 35 " model vdw 2.167 3.040 nonbonded pdb=" OE2 GLU L 44 " pdb=" NH2 ARG O 38 " model vdw 2.182 3.120 nonbonded pdb=" OG SER D 47 " pdb=" OH TYR G 35 " model vdw 2.193 3.040 nonbonded pdb=" OG SER C 47 " pdb=" OH TYR F 35 " model vdw 2.196 3.040 ... (remaining 149138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 44.800 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.130 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.470 ------------------------------------------------------------------------------- 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 20000 Z= 0.170 Angle : 0.558 6.767 27440 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 *********************** 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 : 2.301 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: 0.3277 time to fit residues: 238.0488 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 : 2.184 ------------------------------------------------------------------------------- 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: 10.0000 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: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** 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** R 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20000 Z= 0.221 Angle : 0.550 5.433 27440 Z= 0.296 Chirality : 0.046 0.154 3660 Planarity : 0.004 0.082 3400 Dihedral : 3.743 18.252 2860 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % 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: 2.42 (0.15), residues: 2680 helix: 3.89 (0.15), residues: 760 sheet: 1.70 (0.17), residues: 880 loop : -0.31 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP O 31 PHE 0.012 0.001 PHE A 32 TYR 0.016 0.002 TYR N 35 ARG 0.009 0.001 ARG G 124 *********************** 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 441 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8155 (tpp80) REVERT: C 124 ARG cc_start: 0.8280 (tpp80) cc_final: 0.8050 (tpp80) REVERT: C 125 TYR cc_start: 0.6431 (m-10) cc_final: 0.6070 (m-10) REVERT: E 70 ASN cc_start: 0.8785 (t0) cc_final: 0.8063 (t0) REVERT: F 11 ILE cc_start: 0.8656 (mp) cc_final: 0.8401 (mm) REVERT: F 29 TYR cc_start: 0.8558 (t80) cc_final: 0.8275 (t80) REVERT: F 44 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8252 (tt0) REVERT: G 29 TYR cc_start: 0.8891 (t80) cc_final: 0.8677 (t80) REVERT: G 44 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8078 (tm-30) REVERT: H 29 TYR cc_start: 0.8172 (t80) cc_final: 0.7527 (t80) REVERT: H 46 LEU cc_start: 0.8311 (mm) cc_final: 0.8029 (mm) REVERT: H 119 LEU cc_start: 0.7700 (mp) cc_final: 0.7261 (mp) REVERT: J 44 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8179 (tm-30) REVERT: J 46 LEU cc_start: 0.8709 (mt) cc_final: 0.8383 (mt) REVERT: K 70 ASN cc_start: 0.8883 (t0) cc_final: 0.8432 (t0) REVERT: K 119 LEU cc_start: 0.8599 (mp) cc_final: 0.8379 (mt) REVERT: L 46 LEU cc_start: 0.9137 (mt) cc_final: 0.8934 (mt) REVERT: M 38 ARG cc_start: 0.8325 (mtm110) cc_final: 0.7975 (mtm110) REVERT: M 126 ILE cc_start: 0.8613 (mp) cc_final: 0.8396 (mp) REVERT: N 42 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8534 (tm-30) REVERT: N 46 LEU cc_start: 0.9156 (mt) cc_final: 0.8541 (mt) REVERT: N 73 GLU cc_start: 0.8475 (pm20) cc_final: 0.8139 (pm20) REVERT: O 45 GLN cc_start: 0.8747 (tp40) cc_final: 0.8518 (tp40) REVERT: O 104 ASP cc_start: 0.8821 (m-30) cc_final: 0.8475 (m-30) REVERT: P 29 TYR cc_start: 0.8722 (t80) cc_final: 0.8335 (t80) REVERT: Q 38 ARG cc_start: 0.8557 (ptt90) cc_final: 0.8336 (tmm160) REVERT: Q 101 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8414 (tm-30) REVERT: Q 104 ASP cc_start: 0.8618 (m-30) cc_final: 0.8338 (m-30) REVERT: Q 119 LEU cc_start: 0.9123 (mt) cc_final: 0.8752 (mt) REVERT: R 73 GLU cc_start: 0.8268 (mp0) cc_final: 0.8013 (mp0) REVERT: R 104 ASP cc_start: 0.8369 (t0) cc_final: 0.7632 (m-30) REVERT: S 46 LEU cc_start: 0.8351 (mm) cc_final: 0.7627 (mm) REVERT: S 73 GLU cc_start: 0.8585 (mp0) cc_final: 0.8318 (mp0) REVERT: S 104 ASP cc_start: 0.8489 (m-30) cc_final: 0.8275 (m-30) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.3276 time to fit residues: 217.5075 Evaluate side-chains 320 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 255 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 234 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20000 Z= 0.171 Angle : 0.522 6.276 27440 Z= 0.278 Chirality : 0.046 0.168 3660 Planarity : 0.004 0.071 3400 Dihedral : 3.604 16.032 2860 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.22 % 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 (0.15), residues: 2680 helix: 3.95 (0.15), residues: 760 sheet: 1.73 (0.16), residues: 880 loop : -0.34 (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 0.017 0.002 TYR A 35 ARG 0.005 0.001 ARG S 133 *********************** 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 430 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8685 (ptp-170) cc_final: 0.8413 (mtm-85) REVERT: C 125 TYR cc_start: 0.6607 (m-10) cc_final: 0.6260 (m-10) REVERT: C 136 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8119 (tt0) REVERT: D 124 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7252 (mmm160) REVERT: D 128 LYS cc_start: 0.7680 (tttt) cc_final: 0.7306 (ttpp) REVERT: E 70 ASN cc_start: 0.8931 (t0) cc_final: 0.8287 (t0) REVERT: F 11 ILE cc_start: 0.8560 (mp) cc_final: 0.8309 (mm) REVERT: F 104 ASP cc_start: 0.8746 (m-30) cc_final: 0.8523 (m-30) REVERT: G 44 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8075 (tm-30) REVERT: H 29 TYR cc_start: 0.8122 (t80) cc_final: 0.7571 (t80) REVERT: I 46 LEU cc_start: 0.9086 (tp) cc_final: 0.8883 (tp) REVERT: I 73 GLU cc_start: 0.8323 (mp0) cc_final: 0.8113 (mp0) REVERT: I 124 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7787 (tpp80) REVERT: J 46 LEU cc_start: 0.8650 (mt) cc_final: 0.8440 (mt) REVERT: K 70 ASN cc_start: 0.8699 (t0) cc_final: 0.8255 (t0) REVERT: K 119 LEU cc_start: 0.8628 (mp) cc_final: 0.8355 (mt) REVERT: L 42 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8234 (tm-30) REVERT: L 46 LEU cc_start: 0.9118 (mt) cc_final: 0.8377 (mt) REVERT: N 42 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8391 (tm-30) REVERT: N 46 LEU cc_start: 0.9170 (mt) cc_final: 0.8493 (mt) REVERT: N 53 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8723 (ttpt) REVERT: N 73 GLU cc_start: 0.8462 (pm20) cc_final: 0.8147 (pm20) REVERT: N 104 ASP cc_start: 0.8472 (t70) cc_final: 0.8243 (t0) REVERT: N 133 ARG cc_start: 0.8917 (ttm110) cc_final: 0.8668 (ttm110) REVERT: O 45 GLN cc_start: 0.8895 (tp40) cc_final: 0.8124 (tp40) REVERT: O 104 ASP cc_start: 0.8672 (m-30) cc_final: 0.8393 (m-30) REVERT: P 37 THR cc_start: 0.9352 (m) cc_final: 0.9028 (p) REVERT: Q 38 ARG cc_start: 0.8495 (ptt90) cc_final: 0.8114 (tmm160) REVERT: Q 101 GLN cc_start: 0.8596 (tp-100) cc_final: 0.8376 (tm-30) REVERT: Q 104 ASP cc_start: 0.8620 (m-30) cc_final: 0.8277 (m-30) REVERT: R 133 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8175 (mtp-110) REVERT: S 73 GLU cc_start: 0.8623 (mp0) cc_final: 0.8314 (mp0) REVERT: S 104 ASP cc_start: 0.8488 (m-30) cc_final: 0.8265 (m-30) outliers start: 1 outliers final: 1 residues processed: 430 average time/residue: 0.3393 time to fit residues: 218.3957 Evaluate side-chains 323 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 0.7980 chunk 177 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 112 optimal weight: 0.0970 chunk 158 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 124 optimal weight: 0.1980 chunk 224 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** 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 ** K 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN P 70 ASN Q 70 ASN T 70 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20000 Z= 0.145 Angle : 0.505 5.687 27440 Z= 0.267 Chirality : 0.046 0.202 3660 Planarity : 0.004 0.066 3400 Dihedral : 3.498 15.992 2860 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.19 % Allowed : 2.18 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.16), residues: 2680 helix: 3.92 (0.15), residues: 760 sheet: 1.71 (0.17), residues: 880 loop : -0.39 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP K 31 PHE 0.016 0.001 PHE P 32 TYR 0.018 0.001 TYR F 29 ARG 0.005 0.001 ARG G 124 *********************** 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 447 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 443 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8627 (ptp-170) cc_final: 0.8114 (ttp-110) REVERT: B 70 ASN cc_start: 0.9342 (OUTLIER) cc_final: 0.9010 (m-40) REVERT: C 69 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.7776 (ttm-80) REVERT: C 125 TYR cc_start: 0.6625 (m-10) cc_final: 0.6346 (m-10) REVERT: C 136 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8007 (tt0) REVERT: D 124 ARG cc_start: 0.7587 (tpp80) cc_final: 0.7153 (mmm160) REVERT: E 70 ASN cc_start: 0.8900 (t0) cc_final: 0.8314 (t0) REVERT: F 44 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8231 (tt0) REVERT: F 104 ASP cc_start: 0.8777 (m-30) cc_final: 0.8550 (m-30) REVERT: H 29 TYR cc_start: 0.8126 (t80) cc_final: 0.7576 (t80) REVERT: H 51 GLN cc_start: 0.8933 (mp10) cc_final: 0.8700 (mp10) REVERT: H 119 LEU cc_start: 0.7711 (mp) cc_final: 0.7183 (mp) REVERT: I 73 GLU cc_start: 0.8329 (mp0) cc_final: 0.8128 (mp0) REVERT: K 70 ASN cc_start: 0.8694 (t0) cc_final: 0.8203 (t0) REVERT: L 42 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8298 (tm-30) REVERT: L 44 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8429 (tm-30) REVERT: L 46 LEU cc_start: 0.9155 (mt) cc_final: 0.8417 (mt) REVERT: M 91 MET cc_start: 0.8775 (ptm) cc_final: 0.8446 (ptt) REVERT: N 37 THR cc_start: 0.9457 (m) cc_final: 0.9111 (p) REVERT: N 42 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8384 (tm-30) REVERT: N 44 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8382 (tm-30) REVERT: N 46 LEU cc_start: 0.9237 (mt) cc_final: 0.8524 (mt) REVERT: N 104 ASP cc_start: 0.8547 (t70) cc_final: 0.8289 (t0) REVERT: O 104 ASP cc_start: 0.8623 (m-30) cc_final: 0.8335 (m-30) REVERT: P 37 THR cc_start: 0.9333 (m) cc_final: 0.8993 (p) REVERT: P 104 ASP cc_start: 0.8389 (m-30) cc_final: 0.8170 (m-30) REVERT: Q 37 THR cc_start: 0.8921 (m) cc_final: 0.8603 (p) REVERT: Q 52 LEU cc_start: 0.9367 (mt) cc_final: 0.9163 (mt) REVERT: Q 73 GLU cc_start: 0.8295 (pm20) cc_final: 0.7946 (pm20) REVERT: Q 104 ASP cc_start: 0.8521 (m-30) cc_final: 0.8170 (m-30) REVERT: R 133 ARG cc_start: 0.8521 (ttm110) cc_final: 0.8225 (mtp85) REVERT: S 73 GLU cc_start: 0.8738 (mp0) cc_final: 0.8385 (mp0) REVERT: S 104 ASP cc_start: 0.8470 (m-30) cc_final: 0.8227 (m-30) REVERT: T 70 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8023 (m-40) REVERT: T 76 VAL cc_start: 0.8329 (t) cc_final: 0.8082 (t) outliers start: 4 outliers final: 0 residues processed: 447 average time/residue: 0.3566 time to fit residues: 240.5175 Evaluate side-chains 331 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 329 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 173 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN ** 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 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** ** K 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20000 Z= 0.320 Angle : 0.595 8.521 27440 Z= 0.319 Chirality : 0.046 0.163 3660 Planarity : 0.005 0.092 3400 Dihedral : 3.938 19.905 2860 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.16), residues: 2680 helix: 3.80 (0.15), residues: 760 sheet: 1.74 (0.16), residues: 860 loop : -0.45 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP K 31 PHE 0.018 0.002 PHE G 32 TYR 0.020 0.002 TYR J 35 ARG 0.007 0.001 ARG I 38 *********************** 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 398 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 THR cc_start: 0.8185 (m) cc_final: 0.7887 (t) REVERT: C 51 GLN cc_start: 0.9003 (mp10) cc_final: 0.8741 (mp10) REVERT: C 128 LYS cc_start: 0.7706 (tttt) cc_final: 0.7484 (ptmt) REVERT: C 136 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8059 (mt-10) REVERT: D 70 ASN cc_start: 0.8627 (t0) cc_final: 0.8298 (t0) REVERT: E 70 ASN cc_start: 0.8982 (t0) cc_final: 0.8347 (t0) REVERT: F 30 LEU cc_start: 0.9309 (pp) cc_final: 0.8722 (tp) REVERT: F 44 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8262 (tt0) REVERT: F 70 ASN cc_start: 0.8788 (t0) cc_final: 0.8471 (t0) REVERT: F 104 ASP cc_start: 0.8828 (m-30) cc_final: 0.8591 (m-30) REVERT: G 44 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8119 (tp30) REVERT: H 119 LEU cc_start: 0.7774 (mp) cc_final: 0.7229 (mp) REVERT: I 124 ARG cc_start: 0.8315 (tpp80) cc_final: 0.7849 (mmt90) REVERT: K 70 ASN cc_start: 0.8809 (t0) cc_final: 0.8357 (t0) REVERT: L 42 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8460 (tm-30) REVERT: L 44 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8628 (tm-30) REVERT: L 46 LEU cc_start: 0.9116 (mt) cc_final: 0.8471 (mt) REVERT: L 68 VAL cc_start: 0.9026 (t) cc_final: 0.8687 (m) REVERT: L 104 ASP cc_start: 0.8782 (t0) cc_final: 0.8557 (t0) REVERT: M 46 LEU cc_start: 0.8433 (mm) cc_final: 0.7998 (mm) REVERT: N 42 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8542 (tm-30) REVERT: N 44 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8286 (tm-30) REVERT: N 46 LEU cc_start: 0.9225 (mt) cc_final: 0.8576 (mt) REVERT: O 104 ASP cc_start: 0.8651 (m-30) cc_final: 0.8405 (m-30) REVERT: O 126 ILE cc_start: 0.9369 (mt) cc_final: 0.9038 (tt) REVERT: P 104 ASP cc_start: 0.8542 (m-30) cc_final: 0.8331 (m-30) REVERT: P 143 SER cc_start: 0.8508 (t) cc_final: 0.8233 (p) REVERT: Q 37 THR cc_start: 0.9018 (m) cc_final: 0.8739 (p) REVERT: Q 38 ARG cc_start: 0.8435 (ptt90) cc_final: 0.7917 (tmm160) REVERT: Q 50 GLU cc_start: 0.8640 (tp30) cc_final: 0.7202 (tt0) REVERT: Q 104 ASP cc_start: 0.8536 (m-30) cc_final: 0.8311 (m-30) REVERT: R 101 GLN cc_start: 0.7890 (mp10) cc_final: 0.7485 (mp10) REVERT: R 104 ASP cc_start: 0.8195 (t0) cc_final: 0.7748 (m-30) REVERT: R 133 ARG cc_start: 0.8592 (ttm110) cc_final: 0.8161 (mtp85) REVERT: S 73 GLU cc_start: 0.8666 (mp0) cc_final: 0.8366 (mp0) REVERT: T 126 ILE cc_start: 0.9332 (mp) cc_final: 0.8955 (tt) REVERT: T 133 ARG cc_start: 0.8483 (ptp-110) cc_final: 0.7942 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.3359 time to fit residues: 200.0593 Evaluate side-chains 300 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 208 optimal weight: 0.2980 chunk 116 optimal weight: 0.0770 chunk 20 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 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 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20000 Z= 0.235 Angle : 0.550 5.855 27440 Z= 0.293 Chirality : 0.046 0.216 3660 Planarity : 0.004 0.067 3400 Dihedral : 3.823 17.763 2860 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 2.29 (0.16), residues: 2680 helix: 3.90 (0.15), residues: 760 sheet: 1.66 (0.16), residues: 860 loop : -0.49 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 31 PHE 0.016 0.002 PHE P 32 TYR 0.019 0.002 TYR J 35 ARG 0.006 0.001 ARG M 124 *********************** 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 388 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 2.206 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8803 (ptp-170) cc_final: 0.8519 (mtm-85) REVERT: C 37 THR cc_start: 0.8055 (m) cc_final: 0.7808 (t) REVERT: C 50 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7098 (mm-30) REVERT: C 51 GLN cc_start: 0.9000 (mp10) cc_final: 0.8790 (mp10) REVERT: C 82 TYR cc_start: 0.7625 (m-10) cc_final: 0.7422 (m-10) REVERT: C 124 ARG cc_start: 0.8448 (tpp80) cc_final: 0.7949 (tpp80) REVERT: C 128 LYS cc_start: 0.7630 (tttt) cc_final: 0.7375 (ptmt) REVERT: C 136 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7910 (mt-10) REVERT: D 136 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8561 (mm-30) REVERT: E 70 ASN cc_start: 0.8983 (t0) cc_final: 0.8332 (t0) REVERT: F 30 LEU cc_start: 0.9316 (pp) cc_final: 0.8702 (tp) REVERT: F 70 ASN cc_start: 0.8742 (t0) cc_final: 0.8454 (t0) REVERT: G 44 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8086 (tp30) REVERT: H 29 TYR cc_start: 0.8129 (t80) cc_final: 0.7469 (t80) REVERT: I 124 ARG cc_start: 0.8326 (tpp80) cc_final: 0.7862 (tpp80) REVERT: K 70 ASN cc_start: 0.8774 (t0) cc_final: 0.8406 (t0) REVERT: K 119 LEU cc_start: 0.8654 (mp) cc_final: 0.8316 (mt) REVERT: K 124 ARG cc_start: 0.8007 (tpp80) cc_final: 0.7460 (mmm160) REVERT: L 42 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8434 (tm-30) REVERT: L 44 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8428 (tm-30) REVERT: L 46 LEU cc_start: 0.9079 (mt) cc_final: 0.8440 (mt) REVERT: L 68 VAL cc_start: 0.9049 (t) cc_final: 0.8677 (m) REVERT: L 119 LEU cc_start: 0.8823 (mt) cc_final: 0.8460 (mt) REVERT: M 91 MET cc_start: 0.8854 (ptm) cc_final: 0.8576 (ptt) REVERT: N 32 PHE cc_start: 0.9208 (t80) cc_final: 0.8965 (t80) REVERT: N 42 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8488 (tm-30) REVERT: N 44 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8276 (tm-30) REVERT: N 46 LEU cc_start: 0.9177 (mt) cc_final: 0.8545 (mt) REVERT: O 45 GLN cc_start: 0.8893 (tp40) cc_final: 0.8070 (tp40) REVERT: O 104 ASP cc_start: 0.8620 (m-30) cc_final: 0.8367 (m-30) REVERT: O 126 ILE cc_start: 0.9375 (mt) cc_final: 0.9082 (tt) REVERT: P 29 TYR cc_start: 0.8780 (t80) cc_final: 0.8403 (t80) REVERT: P 104 ASP cc_start: 0.8508 (m-30) cc_final: 0.8308 (m-30) REVERT: P 143 SER cc_start: 0.8547 (t) cc_final: 0.8299 (t) REVERT: Q 37 THR cc_start: 0.9006 (m) cc_final: 0.8749 (p) REVERT: Q 38 ARG cc_start: 0.8402 (ptt90) cc_final: 0.8127 (ptt-90) REVERT: Q 50 GLU cc_start: 0.8667 (tp30) cc_final: 0.7140 (tt0) REVERT: Q 73 GLU cc_start: 0.8430 (pm20) cc_final: 0.7987 (pm20) REVERT: Q 104 ASP cc_start: 0.8505 (m-30) cc_final: 0.8208 (m-30) REVERT: R 101 GLN cc_start: 0.7817 (mp10) cc_final: 0.7418 (mp10) REVERT: R 133 ARG cc_start: 0.8547 (ttm110) cc_final: 0.8141 (mtp85) REVERT: S 73 GLU cc_start: 0.8663 (mp0) cc_final: 0.8374 (mp0) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.3250 time to fit residues: 190.7686 Evaluate side-chains 298 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 0.0670 chunk 115 optimal weight: 10.0000 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 ASN M 70 ASN P 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20000 Z= 0.189 Angle : 0.533 7.290 27440 Z= 0.282 Chirality : 0.046 0.192 3660 Planarity : 0.004 0.067 3400 Dihedral : 3.714 16.636 2860 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.05 % Allowed : 1.57 % Favored : 98.38 % 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: 2.21 (0.16), residues: 2680 helix: 3.96 (0.15), residues: 760 sheet: 1.36 (0.17), residues: 900 loop : -0.44 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP K 31 PHE 0.019 0.002 PHE T 32 TYR 0.019 0.002 TYR B 35 ARG 0.007 0.001 ARG M 124 *********************** 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 403 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 402 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8743 (ptp-170) cc_final: 0.8226 (ttp-110) REVERT: B 29 TYR cc_start: 0.8827 (t80) cc_final: 0.8559 (t80) REVERT: B 125 TYR cc_start: 0.7729 (m-80) cc_final: 0.7470 (m-10) REVERT: C 50 GLU cc_start: 0.7261 (mm-30) cc_final: 0.7010 (mm-30) REVERT: C 51 GLN cc_start: 0.9107 (mp10) cc_final: 0.8859 (mp10) REVERT: C 82 TYR cc_start: 0.7668 (m-10) cc_final: 0.7455 (m-10) REVERT: C 124 ARG cc_start: 0.8381 (tpp80) cc_final: 0.8042 (tpp80) REVERT: E 70 ASN cc_start: 0.8982 (t0) cc_final: 0.8278 (t0) REVERT: F 30 LEU cc_start: 0.9310 (pp) cc_final: 0.8668 (tp) REVERT: F 70 ASN cc_start: 0.8689 (t0) cc_final: 0.8434 (t0) REVERT: F 104 ASP cc_start: 0.8841 (m-30) cc_final: 0.8633 (m-30) REVERT: H 29 TYR cc_start: 0.8088 (t80) cc_final: 0.7467 (t80) REVERT: H 119 LEU cc_start: 0.7782 (mp) cc_final: 0.7100 (mp) REVERT: I 124 ARG cc_start: 0.8227 (tpp80) cc_final: 0.7769 (tpp80) REVERT: K 70 ASN cc_start: 0.8685 (t0) cc_final: 0.8178 (t0) REVERT: K 119 LEU cc_start: 0.8646 (mp) cc_final: 0.8361 (mt) REVERT: K 124 ARG cc_start: 0.7938 (tpp80) cc_final: 0.7684 (mmm160) REVERT: L 42 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8415 (tm-30) REVERT: L 44 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8394 (tm-30) REVERT: L 46 LEU cc_start: 0.9063 (mt) cc_final: 0.8391 (mt) REVERT: L 68 VAL cc_start: 0.9030 (t) cc_final: 0.8664 (m) REVERT: L 119 LEU cc_start: 0.8808 (mt) cc_final: 0.8432 (mt) REVERT: M 91 MET cc_start: 0.8758 (ptm) cc_final: 0.8489 (ptt) REVERT: N 37 THR cc_start: 0.9474 (m) cc_final: 0.9264 (p) REVERT: N 42 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8481 (tm-30) REVERT: N 44 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8309 (tm-30) REVERT: N 46 LEU cc_start: 0.9136 (mt) cc_final: 0.8493 (mt) REVERT: N 104 ASP cc_start: 0.8564 (t70) cc_final: 0.8354 (t0) REVERT: O 45 GLN cc_start: 0.8927 (tp40) cc_final: 0.8136 (tp40) REVERT: O 104 ASP cc_start: 0.8573 (m-30) cc_final: 0.8313 (m-30) REVERT: O 126 ILE cc_start: 0.9380 (mt) cc_final: 0.9113 (tt) REVERT: P 29 TYR cc_start: 0.8817 (t80) cc_final: 0.8410 (t80) REVERT: P 104 ASP cc_start: 0.8485 (m-30) cc_final: 0.8280 (m-30) REVERT: P 133 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.7942 (mtp85) REVERT: P 143 SER cc_start: 0.8521 (t) cc_final: 0.8255 (t) REVERT: Q 37 THR cc_start: 0.8980 (m) cc_final: 0.8694 (p) REVERT: Q 38 ARG cc_start: 0.8439 (ptt90) cc_final: 0.8164 (tmm160) REVERT: Q 50 GLU cc_start: 0.8447 (tp30) cc_final: 0.7020 (tt0) REVERT: Q 73 GLU cc_start: 0.8364 (pm20) cc_final: 0.7972 (pm20) REVERT: Q 104 ASP cc_start: 0.8426 (m-30) cc_final: 0.8138 (m-30) REVERT: Q 118 ASN cc_start: 0.8703 (p0) cc_final: 0.8502 (p0) REVERT: R 101 GLN cc_start: 0.7830 (mp10) cc_final: 0.7440 (mp10) REVERT: R 133 ARG cc_start: 0.8443 (ttm110) cc_final: 0.8070 (mtp85) REVERT: S 73 GLU cc_start: 0.8656 (mp0) cc_final: 0.8349 (mp0) REVERT: S 133 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7992 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 403 average time/residue: 0.3337 time to fit residues: 201.6434 Evaluate side-chains 303 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 75 optimal weight: 0.0370 chunk 49 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- 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 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 70 ASN P 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20000 Z= 0.245 Angle : 0.562 6.501 27440 Z= 0.296 Chirality : 0.046 0.227 3660 Planarity : 0.004 0.078 3400 Dihedral : 3.805 16.318 2860 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 2.17 (0.16), residues: 2680 helix: 3.92 (0.15), residues: 760 sheet: 1.31 (0.17), residues: 900 loop : -0.46 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 31 PHE 0.014 0.002 PHE P 32 TYR 0.023 0.002 TYR N 82 ARG 0.011 0.001 ARG N 133 *********************** 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 396 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8738 (ptp-170) cc_final: 0.8194 (ttp-110) REVERT: A 41 SER cc_start: 0.8985 (t) cc_final: 0.8676 (t) REVERT: C 37 THR cc_start: 0.8020 (m) cc_final: 0.7741 (t) REVERT: C 50 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7084 (mm-30) REVERT: C 51 GLN cc_start: 0.9093 (mp10) cc_final: 0.8766 (mp10) REVERT: C 96 SER cc_start: 0.8620 (t) cc_final: 0.8419 (t) REVERT: E 70 ASN cc_start: 0.8974 (t0) cc_final: 0.8228 (t0) REVERT: F 46 LEU cc_start: 0.9245 (mt) cc_final: 0.9003 (mt) REVERT: F 70 ASN cc_start: 0.8767 (t0) cc_final: 0.8436 (t0) REVERT: F 104 ASP cc_start: 0.8861 (m-30) cc_final: 0.8660 (m-30) REVERT: H 29 TYR cc_start: 0.8212 (t80) cc_final: 0.7559 (t80) REVERT: H 119 LEU cc_start: 0.7842 (mp) cc_final: 0.7163 (mp) REVERT: I 124 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7668 (tpp80) REVERT: K 70 ASN cc_start: 0.8809 (t0) cc_final: 0.8359 (t0) REVERT: K 119 LEU cc_start: 0.8634 (mp) cc_final: 0.8349 (mt) REVERT: L 38 ARG cc_start: 0.8921 (ptt-90) cc_final: 0.7948 (ptt-90) REVERT: L 42 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8451 (tm-30) REVERT: L 46 LEU cc_start: 0.9026 (mt) cc_final: 0.8408 (mt) REVERT: L 68 VAL cc_start: 0.9049 (t) cc_final: 0.8657 (m) REVERT: L 119 LEU cc_start: 0.8797 (mt) cc_final: 0.8570 (mt) REVERT: M 38 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7818 (mtm110) REVERT: M 52 LEU cc_start: 0.9098 (mt) cc_final: 0.8879 (mt) REVERT: M 91 MET cc_start: 0.8801 (ptm) cc_final: 0.8555 (ptt) REVERT: M 104 ASP cc_start: 0.8433 (m-30) cc_final: 0.8087 (m-30) REVERT: N 37 THR cc_start: 0.9548 (m) cc_final: 0.9277 (p) REVERT: N 38 ARG cc_start: 0.8590 (ptt-90) cc_final: 0.8128 (ttp-110) REVERT: N 44 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8191 (tm-30) REVERT: N 46 LEU cc_start: 0.9104 (mt) cc_final: 0.8627 (mt) REVERT: N 104 ASP cc_start: 0.8583 (t70) cc_final: 0.8379 (t0) REVERT: O 29 TYR cc_start: 0.8765 (t80) cc_final: 0.8497 (t80) REVERT: O 45 GLN cc_start: 0.8969 (tp40) cc_final: 0.8166 (tp40) REVERT: O 104 ASP cc_start: 0.8586 (m-30) cc_final: 0.8347 (m-30) REVERT: O 126 ILE cc_start: 0.9383 (mt) cc_final: 0.9098 (tt) REVERT: P 29 TYR cc_start: 0.8861 (t80) cc_final: 0.8387 (t80) REVERT: P 143 SER cc_start: 0.8526 (t) cc_final: 0.8272 (t) REVERT: Q 37 THR cc_start: 0.9027 (m) cc_final: 0.8727 (p) REVERT: Q 38 ARG cc_start: 0.8510 (ptt90) cc_final: 0.7861 (tmm160) REVERT: Q 50 GLU cc_start: 0.8429 (tp30) cc_final: 0.7134 (tt0) REVERT: Q 73 GLU cc_start: 0.8404 (pm20) cc_final: 0.8020 (pm20) REVERT: Q 104 ASP cc_start: 0.8467 (m-30) cc_final: 0.8163 (m-30) REVERT: Q 118 ASN cc_start: 0.8732 (p0) cc_final: 0.8501 (p0) REVERT: Q 136 GLU cc_start: 0.8598 (tp30) cc_final: 0.7510 (pt0) REVERT: R 101 GLN cc_start: 0.7904 (mp10) cc_final: 0.7464 (mp10) REVERT: R 133 ARG cc_start: 0.8465 (ttm110) cc_final: 0.8090 (mtp85) REVERT: S 41 SER cc_start: 0.9222 (p) cc_final: 0.8937 (t) REVERT: S 73 GLU cc_start: 0.8650 (mp0) cc_final: 0.8326 (mp0) REVERT: S 104 ASP cc_start: 0.8612 (m-30) cc_final: 0.8256 (m-30) REVERT: S 133 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7902 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.3368 time to fit residues: 200.8400 Evaluate side-chains 301 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN D 102 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 70 ASN P 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20000 Z= 0.233 Angle : 0.563 6.622 27440 Z= 0.297 Chirality : 0.046 0.200 3660 Planarity : 0.004 0.073 3400 Dihedral : 3.809 16.688 2860 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.05 % Allowed : 0.46 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.16), residues: 2680 helix: 3.94 (0.15), residues: 760 sheet: 1.25 (0.17), residues: 900 loop : -0.48 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 31 PHE 0.017 0.002 PHE C 32 TYR 0.017 0.002 TYR C 125 ARG 0.014 0.001 ARG H 124 *********************** 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 382 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8728 (ptp-170) cc_final: 0.8188 (ttp-110) REVERT: A 41 SER cc_start: 0.9011 (t) cc_final: 0.8712 (t) REVERT: C 37 THR cc_start: 0.7959 (m) cc_final: 0.7677 (t) REVERT: C 51 GLN cc_start: 0.9095 (mp10) cc_final: 0.8770 (mp10) REVERT: C 91 MET cc_start: 0.8885 (ptm) cc_final: 0.8614 (ptm) REVERT: C 124 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7918 (tpp80) REVERT: E 70 ASN cc_start: 0.8947 (t0) cc_final: 0.8229 (t0) REVERT: F 29 TYR cc_start: 0.8519 (t80) cc_final: 0.8253 (t80) REVERT: F 70 ASN cc_start: 0.8696 (t0) cc_final: 0.8469 (t0) REVERT: H 29 TYR cc_start: 0.8213 (t80) cc_final: 0.7585 (t80) REVERT: H 119 LEU cc_start: 0.7831 (mp) cc_final: 0.7160 (mp) REVERT: I 37 THR cc_start: 0.9250 (p) cc_final: 0.8841 (t) REVERT: I 124 ARG cc_start: 0.8173 (tpp80) cc_final: 0.7656 (tpp80) REVERT: K 44 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7566 (tt0) REVERT: K 70 ASN cc_start: 0.8722 (t0) cc_final: 0.8216 (t0) REVERT: L 38 ARG cc_start: 0.8909 (ptt-90) cc_final: 0.7957 (ptt-90) REVERT: L 42 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8409 (tm-30) REVERT: L 46 LEU cc_start: 0.8975 (mt) cc_final: 0.8393 (mt) REVERT: L 119 LEU cc_start: 0.8853 (mt) cc_final: 0.8470 (mt) REVERT: M 38 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7694 (mtm110) REVERT: M 52 LEU cc_start: 0.9093 (mt) cc_final: 0.8740 (mt) REVERT: M 70 ASN cc_start: 0.9499 (OUTLIER) cc_final: 0.9153 (m-40) REVERT: M 91 MET cc_start: 0.8795 (ptm) cc_final: 0.8540 (ptt) REVERT: N 37 THR cc_start: 0.9505 (m) cc_final: 0.9258 (p) REVERT: N 38 ARG cc_start: 0.8622 (ptt-90) cc_final: 0.8159 (ttp-110) REVERT: N 44 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8171 (tm-30) REVERT: N 46 LEU cc_start: 0.8955 (mt) cc_final: 0.8624 (mt) REVERT: O 45 GLN cc_start: 0.8992 (tp40) cc_final: 0.8196 (tp40) REVERT: O 104 ASP cc_start: 0.8516 (m-30) cc_final: 0.8299 (m-30) REVERT: O 126 ILE cc_start: 0.9382 (mt) cc_final: 0.9105 (tt) REVERT: P 29 TYR cc_start: 0.8848 (t80) cc_final: 0.8378 (t80) REVERT: P 104 ASP cc_start: 0.8544 (m-30) cc_final: 0.8307 (m-30) REVERT: P 143 SER cc_start: 0.8524 (t) cc_final: 0.8256 (t) REVERT: Q 37 THR cc_start: 0.9017 (m) cc_final: 0.8706 (p) REVERT: Q 38 ARG cc_start: 0.8523 (ptt90) cc_final: 0.7915 (tmm160) REVERT: Q 50 GLU cc_start: 0.8404 (tp30) cc_final: 0.7257 (tt0) REVERT: Q 104 ASP cc_start: 0.8466 (m-30) cc_final: 0.8169 (m-30) REVERT: Q 118 ASN cc_start: 0.8733 (p0) cc_final: 0.8526 (p0) REVERT: Q 136 GLU cc_start: 0.8669 (tp30) cc_final: 0.7635 (pt0) REVERT: R 101 GLN cc_start: 0.7900 (mp10) cc_final: 0.7435 (mp10) REVERT: R 133 ARG cc_start: 0.8470 (ttm110) cc_final: 0.8173 (mtp85) REVERT: S 73 GLU cc_start: 0.8637 (mp0) cc_final: 0.8330 (mp0) REVERT: S 104 ASP cc_start: 0.8619 (m-30) cc_final: 0.8261 (m-30) REVERT: S 133 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8102 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 382 average time/residue: 0.3220 time to fit residues: 187.7186 Evaluate side-chains 302 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 2.310 ------------------------------------------------------------------------------- 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: 0.5980 chunk 246 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 206 optimal weight: 0.0570 chunk 21 optimal weight: 0.0070 chunk 159 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- 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 102 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20000 Z= 0.152 Angle : 0.541 6.185 27440 Z= 0.281 Chirality : 0.046 0.203 3660 Planarity : 0.004 0.061 3400 Dihedral : 3.606 14.589 2860 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.05 % Allowed : 0.28 % 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: 2.28 (0.16), residues: 2680 helix: 4.04 (0.15), residues: 760 sheet: 1.65 (0.17), residues: 860 loop : -0.62 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 31 PHE 0.022 0.001 PHE T 32 TYR 0.021 0.001 TYR J 125 ARG 0.016 0.001 ARG H 124 ********************** 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 416 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8718 (ptp-170) cc_final: 0.8203 (ttp-110) REVERT: A 41 SER cc_start: 0.9029 (t) cc_final: 0.8736 (t) REVERT: A 91 MET cc_start: 0.7809 (ptm) cc_final: 0.7365 (ptt) REVERT: C 51 GLN cc_start: 0.9097 (mp10) cc_final: 0.8799 (mp10) REVERT: C 91 MET cc_start: 0.8763 (ptm) cc_final: 0.8514 (ptm) REVERT: C 124 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7779 (tpp80) REVERT: D 124 ARG cc_start: 0.7632 (tpp80) cc_final: 0.7055 (mmm160) REVERT: E 70 ASN cc_start: 0.9013 (t0) cc_final: 0.8341 (t0) REVERT: F 11 ILE cc_start: 0.8502 (mp) cc_final: 0.8282 (mm) REVERT: F 70 ASN cc_start: 0.8650 (t0) cc_final: 0.8386 (t0) REVERT: H 11 ILE cc_start: 0.8397 (mm) cc_final: 0.8168 (mm) REVERT: H 29 TYR cc_start: 0.7906 (t80) cc_final: 0.7297 (t80) REVERT: H 52 LEU cc_start: 0.8726 (mp) cc_final: 0.8459 (mt) REVERT: H 119 LEU cc_start: 0.7776 (mp) cc_final: 0.7123 (mp) REVERT: I 37 THR cc_start: 0.9154 (p) cc_final: 0.8786 (t) REVERT: I 124 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7618 (tpp80) REVERT: K 70 ASN cc_start: 0.8623 (t0) cc_final: 0.8199 (t0) REVERT: L 42 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8419 (tm-30) REVERT: L 46 LEU cc_start: 0.8917 (mt) cc_final: 0.8320 (mt) REVERT: L 140 THR cc_start: 0.7708 (m) cc_final: 0.7053 (m) REVERT: M 91 MET cc_start: 0.8686 (ptm) cc_final: 0.8409 (ptt) REVERT: N 29 TYR cc_start: 0.8434 (t80) cc_final: 0.7867 (t80) REVERT: N 37 THR cc_start: 0.9435 (m) cc_final: 0.9200 (p) REVERT: N 44 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8324 (tm-30) REVERT: N 46 LEU cc_start: 0.8994 (mt) cc_final: 0.8595 (mt) REVERT: N 104 ASP cc_start: 0.8464 (t70) cc_final: 0.8251 (t0) REVERT: O 45 GLN cc_start: 0.8957 (tp40) cc_final: 0.8205 (tp40) REVERT: O 126 ILE cc_start: 0.9372 (mt) cc_final: 0.9156 (tt) REVERT: P 143 SER cc_start: 0.8475 (t) cc_final: 0.8183 (t) REVERT: Q 35 TYR cc_start: 0.8269 (t80) cc_final: 0.7911 (t80) REVERT: Q 38 ARG cc_start: 0.8453 (ptt90) cc_final: 0.8142 (tmm160) REVERT: Q 44 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8312 (tt0) REVERT: Q 50 GLU cc_start: 0.8311 (tp30) cc_final: 0.7382 (tt0) REVERT: Q 51 GLN cc_start: 0.8851 (pm20) cc_final: 0.8416 (pm20) REVERT: Q 104 ASP cc_start: 0.8337 (m-30) cc_final: 0.8112 (m-30) REVERT: Q 136 GLU cc_start: 0.8572 (tp30) cc_final: 0.7613 (pt0) REVERT: R 101 GLN cc_start: 0.7743 (mp10) cc_final: 0.7373 (mp10) REVERT: R 133 ARG cc_start: 0.8386 (ttm110) cc_final: 0.8155 (mtp85) REVERT: S 73 GLU cc_start: 0.8746 (mp0) cc_final: 0.8420 (mp0) REVERT: S 104 ASP cc_start: 0.8453 (m-30) cc_final: 0.8085 (m-30) REVERT: T 76 VAL cc_start: 0.8261 (t) cc_final: 0.7917 (m) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.3253 time to fit residues: 205.6860 Evaluate side-chains 311 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 212 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 102 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 70 ASN P 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.074750 restraints weight = 60467.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076408 restraints weight = 43399.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.077609 restraints weight = 34154.218| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20000 Z= 0.247 Angle : 0.588 7.030 27440 Z= 0.309 Chirality : 0.046 0.196 3660 Planarity : 0.004 0.067 3400 Dihedral : 3.747 16.227 2860 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.05 % Allowed : 0.23 % Favored : 99.72 % 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: 2.18 (0.16), residues: 2680 helix: 4.04 (0.15), residues: 760 sheet: 1.30 (0.17), residues: 900 loop : -0.51 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 31 PHE 0.021 0.002 PHE T 32 TYR 0.028 0.002 TYR H 35 ARG 0.015 0.001 ARG H 124 =============================================================================== Job complete usr+sys time: 4192.66 seconds wall clock time: 77 minutes 51.98 seconds (4671.98 seconds total)