Starting phenix.real_space_refine on Thu Mar 21 00:19:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/03_2024/6w4o_21535.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/03_2024/6w4o_21535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/03_2024/6w4o_21535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/03_2024/6w4o_21535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/03_2024/6w4o_21535.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/03_2024/6w4o_21535.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14475 atoms to isotropic. 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 71 5.16 5 C 9185 2.51 5 N 2568 2.21 5 O 2651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 53": "OE1" <-> "OE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4": "NH1" <-> "NH2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "F ASP 31": "OD1" <-> "OD2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I GLU 24": "OE1" <-> "OE2" Residue "I GLU 38": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "I PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 36": "OD1" <-> "OD2" Residue "J ARG 58": "NH1" <-> "NH2" Residue "K PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 4": "NH1" <-> "NH2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 91": "OD1" <-> "OD2" Residue "M ASP 31": "OD1" <-> "OD2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "O ARG 2": "NH1" <-> "NH2" Residue "O PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ASP 92": "OD1" <-> "OD2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "O GLU 158": "OE1" <-> "OE2" Residue "O PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 175": "OE1" <-> "OE2" Residue "O TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 228": "OE1" <-> "OE2" Residue "O ARG 251": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14475 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1040 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1023 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1022 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain breaks: 1 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 994 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "E" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 994 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain breaks: 1 Chain: "F" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 988 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain breaks: 1 Chain: "G" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1041 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "I" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1023 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain breaks: 1 Chain: "J" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1022 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 994 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 994 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain breaks: 1 Chain: "M" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 988 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain breaks: 1 Chain: "O" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2352 Classifications: {'peptide': 293} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain breaks: 1 Time building chain proxies: 7.32, per 1000 atoms: 0.51 Number of scatterers: 14475 At special positions: 0 Unit cell: (121.03, 101.01, 137.41, 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 71 16.00 O 2651 8.00 N 2568 7.00 C 9185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.32 Conformation dependent library (CDL) restraints added in 2.6 seconds 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 35.8% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 17 through 35 Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.566A pdb=" N PHE A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.904A pdb=" N ARG A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 78' Processing helix chain 'B' and resid 3 through 21 removed outlier: 3.975A pdb=" N ILE B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 29 Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 49 through 58 removed outlier: 4.230A pdb=" N PHE B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 25 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 44 through 47 Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.972A pdb=" N PHE C 59 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 23 Processing helix chain 'D' and resid 25 through 32 Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 52 through 62 removed outlier: 4.271A pdb=" N PHE D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 59 " --> pdb=" O HIS D 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 21 removed outlier: 3.640A pdb=" N VAL E 11 " --> pdb=" O GLU E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 30 Processing helix chain 'E' and resid 39 through 43 Processing helix chain 'E' and resid 50 through 58 removed outlier: 4.359A pdb=" N PHE E 55 " --> pdb=" O ASP E 51 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR E 56 " --> pdb=" O PHE E 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.809A pdb=" N ILE F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 29 Processing helix chain 'F' and resid 38 through 42 Processing helix chain 'F' and resid 49 through 54 removed outlier: 4.323A pdb=" N PHE F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 35 Processing helix chain 'G' and resid 37 through 44 Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 64 through 73 removed outlier: 3.565A pdb=" N PHE G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR G 70 " --> pdb=" O PHE G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.907A pdb=" N ARG G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN G 78 " --> pdb=" O LEU G 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 73 through 78' Processing helix chain 'I' and resid 3 through 21 removed outlier: 3.976A pdb=" N ILE I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 29 Processing helix chain 'I' and resid 38 through 42 Processing helix chain 'I' and resid 49 through 58 removed outlier: 4.230A pdb=" N PHE I 54 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR I 55 " --> pdb=" O PHE I 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 25 Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 44 through 47 Processing helix chain 'J' and resid 54 through 63 removed outlier: 3.971A pdb=" N PHE J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR J 60 " --> pdb=" O PHE J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 23 Processing helix chain 'K' and resid 25 through 32 Processing helix chain 'K' and resid 41 through 45 Processing helix chain 'K' and resid 52 through 62 removed outlier: 4.269A pdb=" N PHE K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR K 58 " --> pdb=" O PHE K 54 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE K 59 " --> pdb=" O HIS K 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 removed outlier: 3.639A pdb=" N VAL L 11 " --> pdb=" O GLU L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 30 Processing helix chain 'L' and resid 39 through 43 Processing helix chain 'L' and resid 50 through 58 removed outlier: 4.360A pdb=" N PHE L 55 " --> pdb=" O ASP L 51 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR L 56 " --> pdb=" O PHE L 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 20 removed outlier: 3.809A pdb=" N ILE M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 29 Processing helix chain 'M' and resid 38 through 42 Processing helix chain 'M' and resid 49 through 54 removed outlier: 4.323A pdb=" N PHE M 54 " --> pdb=" O ASP M 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 6 Processing helix chain 'O' and resid 41 through 59 removed outlier: 3.543A pdb=" N HIS O 46 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS O 48 " --> pdb=" O ARG O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 96 removed outlier: 4.094A pdb=" N VAL O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA O 95 " --> pdb=" O GLU O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 121 removed outlier: 3.756A pdb=" N GLN O 110 " --> pdb=" O HIS O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 172 removed outlier: 3.598A pdb=" N LEU O 172 " --> pdb=" O PRO O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 178 Processing helix chain 'O' and resid 184 through 201 removed outlier: 3.688A pdb=" N LEU O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA O 190 " --> pdb=" O VAL O 186 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE O 197 " --> pdb=" O VAL O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 220 Processing helix chain 'O' and resid 233 through 244 Processing helix chain 'O' and resid 253 through 260 removed outlier: 3.603A pdb=" N LYS O 259 " --> pdb=" O ALA O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 263 through 270 Processing helix chain 'O' and resid 275 through 293 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.303A pdb=" N HIS A 138 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N GLY A 48 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 11.984A pdb=" N HIS A 140 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N THR A 50 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 11.990A pdb=" N SER A 142 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N PHE A 52 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL A 126 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE A 139 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 124 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 141 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU A 122 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N SER A 98 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU A 93 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS A 100 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 91 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA A 102 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 removed outlier: 7.255A pdb=" N HIS B 120 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 10.893A pdb=" N GLY B 33 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N HIS B 122 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N THR B 35 " --> pdb=" O HIS B 122 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N SER B 124 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N PHE B 37 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL B 108 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE B 121 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 106 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 123 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU B 104 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY B 125 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN B 102 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER B 80 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU B 75 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 82 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 73 " --> pdb=" O CYS B 82 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 84 " --> pdb=" O PRO B 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 52 removed outlier: 7.430A pdb=" N HIS C 126 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N GLY C 38 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 11.823A pdb=" N HIS C 128 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 11.184A pdb=" N THR C 40 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N SER C 130 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N PHE C 42 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE C 124 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS C 116 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS C 126 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE C 92 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASN C 76 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE C 94 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE C 74 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN C 96 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR C 72 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 49 through 50 removed outlier: 7.212A pdb=" N HIS D 120 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N GLY D 36 " --> pdb=" O HIS D 120 " (cutoff:3.500A) removed outlier: 11.593A pdb=" N HIS D 122 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N THR D 38 " --> pdb=" O HIS D 122 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N SER D 124 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 10.887A pdb=" N PHE D 40 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL D 108 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE D 121 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR D 106 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG D 123 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU D 104 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY D 125 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLN D 102 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER D 80 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU D 75 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS D 82 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE D 73 " --> pdb=" O CYS D 82 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA D 84 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 47 through 48 removed outlier: 9.061A pdb=" N GLN E 115 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N GLY E 34 " --> pdb=" O GLN E 115 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL E 117 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 36 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE E 116 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS E 108 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS E 118 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER E 78 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU E 73 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS E 80 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE E 71 " --> pdb=" O CYS E 80 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA E 82 " --> pdb=" O PRO E 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 46 through 47 removed outlier: 9.023A pdb=" N GLN F 114 " --> pdb=" O ASP F 31 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N GLY F 33 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL F 116 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL F 105 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE F 118 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR F 103 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG F 120 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU F 101 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLY F 122 " --> pdb=" O GLN F 99 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLN F 99 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N SER F 77 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU F 72 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS F 79 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE F 70 " --> pdb=" O CYS F 79 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA F 81 " --> pdb=" O PRO F 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 62 removed outlier: 7.303A pdb=" N HIS G 138 " --> pdb=" O ASP G 46 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N GLY G 48 " --> pdb=" O HIS G 138 " (cutoff:3.500A) removed outlier: 11.983A pdb=" N HIS G 140 " --> pdb=" O GLY G 48 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N THR G 50 " --> pdb=" O HIS G 140 " (cutoff:3.500A) removed outlier: 11.990A pdb=" N SER G 142 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N PHE G 52 " --> pdb=" O SER G 142 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL G 126 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE G 139 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR G 124 " --> pdb=" O PHE G 139 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG G 141 " --> pdb=" O GLU G 122 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU G 122 " --> pdb=" O ARG G 141 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N SER G 98 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU G 93 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS G 100 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE G 91 " --> pdb=" O CYS G 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA G 102 " --> pdb=" O PRO G 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 46 through 47 removed outlier: 7.256A pdb=" N HIS I 120 " --> pdb=" O ASP I 31 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N GLY I 33 " --> pdb=" O HIS I 120 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N HIS I 122 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N THR I 35 " --> pdb=" O HIS I 122 " (cutoff:3.500A) removed outlier: 11.782A pdb=" N SER I 124 " --> pdb=" O THR I 35 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N PHE I 37 " --> pdb=" O SER I 124 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL I 108 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE I 121 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR I 106 " --> pdb=" O PHE I 121 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG I 123 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU I 104 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY I 125 " --> pdb=" O GLN I 102 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLN I 102 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER I 80 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU I 75 " --> pdb=" O SER I 80 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS I 82 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE I 73 " --> pdb=" O CYS I 82 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA I 84 " --> pdb=" O PRO I 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 50 through 52 removed outlier: 7.432A pdb=" N HIS J 126 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N GLY J 38 " --> pdb=" O HIS J 126 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N HIS J 128 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N THR J 40 " --> pdb=" O HIS J 128 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N SER J 130 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 11.017A pdb=" N PHE J 42 " --> pdb=" O SER J 130 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE J 124 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N HIS J 116 " --> pdb=" O ILE J 124 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS J 126 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE J 92 " --> pdb=" O ASN J 76 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASN J 76 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE J 94 " --> pdb=" O ILE J 74 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE J 74 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN J 96 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N THR J 72 " --> pdb=" O GLN J 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 49 through 50 removed outlier: 7.212A pdb=" N HIS K 120 " --> pdb=" O ASP K 34 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N GLY K 36 " --> pdb=" O HIS K 120 " (cutoff:3.500A) removed outlier: 11.593A pdb=" N HIS K 122 " --> pdb=" O GLY K 36 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N THR K 38 " --> pdb=" O HIS K 122 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N SER K 124 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N PHE K 40 " --> pdb=" O SER K 124 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL K 108 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE K 121 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR K 106 " --> pdb=" O PHE K 121 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG K 123 " --> pdb=" O GLU K 104 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU K 104 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY K 125 " --> pdb=" O GLN K 102 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLN K 102 " --> pdb=" O GLY K 125 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER K 80 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU K 75 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS K 82 " --> pdb=" O ILE K 73 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE K 73 " --> pdb=" O CYS K 82 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA K 84 " --> pdb=" O PRO K 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 47 through 48 removed outlier: 9.060A pdb=" N GLN L 115 " --> pdb=" O ASP L 32 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N GLY L 34 " --> pdb=" O GLN L 115 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL L 117 " --> pdb=" O GLY L 34 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR L 36 " --> pdb=" O VAL L 117 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE L 116 " --> pdb=" O HIS L 108 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS L 108 " --> pdb=" O ILE L 116 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS L 118 " --> pdb=" O VAL L 106 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER L 78 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU L 73 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS L 80 " --> pdb=" O ILE L 71 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE L 71 " --> pdb=" O CYS L 80 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA L 82 " --> pdb=" O PRO L 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 46 through 47 removed outlier: 9.022A pdb=" N GLN M 114 " --> pdb=" O ASP M 31 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N GLY M 33 " --> pdb=" O GLN M 114 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL M 116 " --> pdb=" O GLY M 33 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL M 105 " --> pdb=" O VAL M 116 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE M 118 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR M 103 " --> pdb=" O PHE M 118 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG M 120 " --> pdb=" O GLU M 101 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU M 101 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLY M 122 " --> pdb=" O GLN M 99 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN M 99 " --> pdb=" O GLY M 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE M 94 " --> pdb=" O ASP M 90 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER M 77 " --> pdb=" O LEU M 72 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU M 72 " --> pdb=" O SER M 77 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS M 79 " --> pdb=" O ILE M 70 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE M 70 " --> pdb=" O CYS M 79 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA M 81 " --> pdb=" O PRO M 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 7 through 12 removed outlier: 5.693A pdb=" N LEU O 9 " --> pdb=" O VAL O 23 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL O 23 " --> pdb=" O LEU O 9 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU O 11 " --> pdb=" O ARG O 21 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA O 32 " --> pdb=" O PHE O 81 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP O 69 " --> pdb=" O ILE O 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 133 through 135 692 hydrogen bonds defined for protein. 1929 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4812 1.34 - 1.46: 3266 1.46 - 1.58: 6647 1.58 - 1.70: 2 1.70 - 1.82: 111 Bond restraints: 14838 Sorted by residual: bond pdb=" CA VAL O 269 " pdb=" C VAL O 269 " ideal model delta sigma weight residual 1.517 1.581 -0.064 1.49e-02 4.50e+03 1.84e+01 bond pdb=" N ALA O 270 " pdb=" CA ALA O 270 " ideal model delta sigma weight residual 1.452 1.505 -0.053 1.25e-02 6.40e+03 1.77e+01 bond pdb=" CD GLN O 215 " pdb=" OE1 GLN O 215 " ideal model delta sigma weight residual 1.231 1.287 -0.056 1.90e-02 2.77e+03 8.83e+00 bond pdb=" CG GLN O 215 " pdb=" CD GLN O 215 " ideal model delta sigma weight residual 1.516 1.581 -0.065 2.50e-02 1.60e+03 6.74e+00 bond pdb=" CD GLN O 215 " pdb=" NE2 GLN O 215 " ideal model delta sigma weight residual 1.328 1.376 -0.048 2.10e-02 2.27e+03 5.12e+00 ... (remaining 14833 not shown) Histogram of bond angle deviations from ideal: 97.17 - 104.87: 271 104.87 - 112.56: 7663 112.56 - 120.26: 5787 120.26 - 127.95: 6133 127.95 - 135.65: 210 Bond angle restraints: 20064 Sorted by residual: angle pdb=" N VAL O 269 " pdb=" CA VAL O 269 " pdb=" C VAL O 269 " ideal model delta sigma weight residual 112.90 126.42 -13.52 9.60e-01 1.09e+00 1.98e+02 angle pdb=" N TRP O 262 " pdb=" CA TRP O 262 " pdb=" C TRP O 262 " ideal model delta sigma weight residual 113.01 101.60 11.41 1.20e+00 6.94e-01 9.05e+01 angle pdb=" N ALA O 43 " pdb=" CA ALA O 43 " pdb=" C ALA O 43 " ideal model delta sigma weight residual 111.14 120.74 -9.60 1.08e+00 8.57e-01 7.91e+01 angle pdb=" N ALA O 270 " pdb=" CA ALA O 270 " pdb=" C ALA O 270 " ideal model delta sigma weight residual 110.36 122.23 -11.87 1.55e+00 4.16e-01 5.87e+01 angle pdb=" N SER O 267 " pdb=" CA SER O 267 " pdb=" C SER O 267 " ideal model delta sigma weight residual 111.28 103.26 8.02 1.09e+00 8.42e-01 5.41e+01 ... (remaining 20059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 8199 16.80 - 33.61: 472 33.61 - 50.41: 67 50.41 - 67.21: 23 67.21 - 84.01: 4 Dihedral angle restraints: 8765 sinusoidal: 3617 harmonic: 5148 Sorted by residual: dihedral pdb=" CA GLY O 150 " pdb=" C GLY O 150 " pdb=" N LEU O 151 " pdb=" CA LEU O 151 " ideal model delta harmonic sigma weight residual 180.00 135.15 44.85 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA PHE O 149 " pdb=" C PHE O 149 " pdb=" N GLY O 150 " pdb=" CA GLY O 150 " ideal model delta harmonic sigma weight residual 0.00 40.86 -40.86 0 5.00e+00 4.00e-02 6.68e+01 dihedral pdb=" C VAL O 269 " pdb=" N VAL O 269 " pdb=" CA VAL O 269 " pdb=" CB VAL O 269 " ideal model delta harmonic sigma weight residual -122.00 -140.50 18.50 0 2.50e+00 1.60e-01 5.48e+01 ... (remaining 8762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 2099 0.142 - 0.284: 32 0.284 - 0.425: 3 0.425 - 0.567: 0 0.567 - 0.709: 1 Chirality restraints: 2135 Sorted by residual: chirality pdb=" CA VAL O 269 " pdb=" N VAL O 269 " pdb=" C VAL O 269 " pdb=" CB VAL O 269 " both_signs ideal model delta sigma weight residual False 2.44 1.73 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA ALA O 43 " pdb=" N ALA O 43 " pdb=" C ALA O 43 " pdb=" CB ALA O 43 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ALA O 270 " pdb=" N ALA O 270 " pdb=" C ALA O 270 " pdb=" CB ALA O 270 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 2132 not shown) Planarity restraints: 2599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE O 149 " -0.025 2.00e-02 2.50e+03 1.66e-02 4.85e+00 pdb=" CG PHE O 149 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE O 149 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE O 149 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE O 149 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE O 149 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE O 149 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN O 127 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C ASN O 127 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN O 127 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU O 128 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 165 " -0.019 2.00e-02 2.50e+03 1.37e-02 3.30e+00 pdb=" CG PHE O 165 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE O 165 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE O 165 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE O 165 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE O 165 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE O 165 " -0.003 2.00e-02 2.50e+03 ... (remaining 2596 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.65: 8 1.65 - 2.46: 111 2.46 - 3.27: 14819 3.27 - 4.09: 37164 4.09 - 4.90: 67761 Warning: very small nonbonded interaction distances. Nonbonded interactions: 119863 Sorted by model distance: nonbonded pdb=" CE LYS K 31 " pdb=" CH2 TRP O 162 " model vdw 0.834 3.740 nonbonded pdb=" OE2 GLU K 27 " pdb=" N GLY O 164 " model vdw 1.118 2.520 nonbonded pdb=" CE LYS K 31 " pdb=" CZ2 TRP O 162 " model vdw 1.318 3.740 nonbonded pdb=" NZ LYS K 31 " pdb=" CH2 TRP O 162 " model vdw 1.336 3.420 nonbonded pdb=" O SER J 67 " pdb=" CD LYS O 39 " model vdw 1.352 3.440 ... (remaining 119858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 73 or resid 81 through 144)) selection = (chain 'B' and ((resid 2 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 3 through 58 or resid 63 through 126)) selection = (chain 'C' and ((resid 7 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 8 through 63 or resid 69 through 132)) selection = (chain 'D' and ((resid 5 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 6 through 61 or resid 63 through 126)) selection = (chain 'E' and ((resid 3 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 4 through 59 or resid 61 through 124)) selection = (chain 'F' and ((resid 2 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 3 through 58 or resid 60 through 123)) selection = (chain 'G' and ((resid 17 and (name CA or name C or name O or name CB or name CG \ 1 or name CG2)) or resid 18 through 73 or resid 81 through 144)) selection = (chain 'I' and ((resid 2 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 3 through 58 or resid 63 through 126)) selection = (chain 'J' and ((resid 7 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 8 through 63 or resid 69 through 132)) selection = (chain 'K' and ((resid 5 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 6 through 61 or resid 63 through 126)) selection = (chain 'L' and ((resid 3 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 4 through 59 or resid 61 through 124)) selection = (chain 'M' and ((resid 2 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 3 through 58 or resid 60 through 123)) } 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: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 14.070 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 38.020 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 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 : 0.004 0.065 14838 Z= 0.255 Angle : 0.776 13.525 20064 Z= 0.502 Chirality : 0.053 0.709 2135 Planarity : 0.003 0.028 2599 Dihedral : 10.845 84.015 5441 Min Nonbonded Distance : 0.834 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.04 % Favored : 96.73 % Rotamer: Outliers : 0.91 % Allowed : 5.45 % Favored : 93.64 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.18), residues: 1741 helix: -2.63 (0.16), residues: 530 sheet: 0.50 (0.20), residues: 582 loop : -0.78 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 262 HIS 0.005 0.001 HIS O 117 PHE 0.030 0.002 PHE O 149 TYR 0.018 0.002 TYR O 171 ARG 0.006 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 650 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8800 (tp) cc_final: 0.8584 (tp) REVERT: A 122 GLU cc_start: 0.6662 (mp0) cc_final: 0.6269 (mp0) REVERT: A 136 ILE cc_start: 0.7948 (mm) cc_final: 0.7264 (mm) REVERT: B 34 MET cc_start: 0.8172 (ttp) cc_final: 0.7956 (ppp) REVERT: B 49 LEU cc_start: 0.7597 (mp) cc_final: 0.6398 (mt) REVERT: B 92 LEU cc_start: 0.9079 (mt) cc_final: 0.8553 (mt) REVERT: C 19 LEU cc_start: 0.9071 (tp) cc_final: 0.8815 (tp) REVERT: C 76 ASN cc_start: 0.8148 (m-40) cc_final: 0.7914 (m110) REVERT: C 92 ILE cc_start: 0.8910 (mt) cc_final: 0.8081 (mp) REVERT: D 11 ILE cc_start: 0.9291 (mt) cc_final: 0.9024 (pt) REVERT: D 70 ASN cc_start: 0.8032 (m-40) cc_final: 0.7828 (m110) REVERT: D 92 LEU cc_start: 0.9161 (mt) cc_final: 0.8882 (pt) REVERT: E 74 MET cc_start: 0.6413 (mtm) cc_final: 0.5788 (mpp) REVERT: E 80 CYS cc_start: 0.7424 (t) cc_final: 0.7007 (m) REVERT: E 102 GLU cc_start: 0.6528 (mp0) cc_final: 0.5910 (mp0) REVERT: F 37 PHE cc_start: 0.8259 (m-80) cc_final: 0.7633 (m-10) REVERT: F 49 LEU cc_start: 0.7109 (mp) cc_final: 0.4844 (mt) REVERT: F 121 SER cc_start: 0.9066 (m) cc_final: 0.8745 (p) REVERT: G 22 ILE cc_start: 0.8876 (mm) cc_final: 0.8646 (mm) REVERT: G 29 LEU cc_start: 0.9021 (tp) cc_final: 0.8793 (tp) REVERT: G 44 MET cc_start: 0.8029 (mtm) cc_final: 0.7605 (ttm) REVERT: G 67 HIS cc_start: 0.7844 (m90) cc_final: 0.6796 (m170) REVERT: G 87 LEU cc_start: 0.8623 (mt) cc_final: 0.8190 (tp) REVERT: G 118 THR cc_start: 0.8307 (m) cc_final: 0.7971 (p) REVERT: G 122 GLU cc_start: 0.7613 (mp0) cc_final: 0.7268 (mp0) REVERT: I 14 LEU cc_start: 0.9116 (tp) cc_final: 0.8682 (tp) REVERT: I 97 ILE cc_start: 0.8419 (mt) cc_final: 0.8219 (mp) REVERT: I 121 PHE cc_start: 0.6619 (p90) cc_final: 0.6151 (p90) REVERT: J 19 LEU cc_start: 0.9560 (tp) cc_final: 0.9193 (tt) REVERT: J 20 ILE cc_start: 0.9641 (mm) cc_final: 0.9391 (tt) REVERT: J 75 LEU cc_start: 0.8666 (mt) cc_final: 0.8342 (tp) REVERT: J 76 ASN cc_start: 0.8185 (m-40) cc_final: 0.7531 (m-40) REVERT: K 17 LEU cc_start: 0.9264 (tp) cc_final: 0.9016 (tp) REVERT: K 32 MET cc_start: 0.9055 (mtm) cc_final: 0.8854 (mtp) REVERT: K 40 PHE cc_start: 0.8659 (m-80) cc_final: 0.8034 (m-10) REVERT: K 69 LEU cc_start: 0.8502 (mp) cc_final: 0.8133 (mm) REVERT: K 86 ILE cc_start: 0.8874 (mm) cc_final: 0.8620 (mm) REVERT: K 91 TYR cc_start: 0.8347 (p90) cc_final: 0.7630 (p90) REVERT: K 92 LEU cc_start: 0.8308 (mt) cc_final: 0.7945 (mt) REVERT: K 118 ILE cc_start: 0.8641 (mt) cc_final: 0.8259 (tp) REVERT: K 122 HIS cc_start: 0.8215 (t-90) cc_final: 0.5603 (t-90) REVERT: L 11 VAL cc_start: 0.9206 (p) cc_final: 0.8980 (m) REVERT: L 21 ASN cc_start: 0.9068 (m-40) cc_final: 0.8473 (p0) REVERT: M 14 LEU cc_start: 0.9421 (tp) cc_final: 0.9145 (tt) REVERT: M 37 PHE cc_start: 0.8596 (m-80) cc_final: 0.8151 (m-10) outliers start: 14 outliers final: 6 residues processed: 660 average time/residue: 0.3469 time to fit residues: 305.9632 Evaluate side-chains 299 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 293 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 157 optimal weight: 0.0980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN D 65 HIS ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 HIS ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 HIS G 73 ASN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 GLN ** M 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 GLN O 63 ASN O 119 HIS ** O 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14838 Z= 0.285 Angle : 0.735 13.667 20064 Z= 0.393 Chirality : 0.048 0.227 2135 Planarity : 0.005 0.067 2599 Dihedral : 4.979 31.847 1939 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.72 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.11 (0.19), residues: 1741 helix: -0.96 (0.20), residues: 529 sheet: 1.03 (0.20), residues: 593 loop : -0.16 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP O 162 HIS 0.020 0.002 HIS J 128 PHE 0.020 0.002 PHE E 57 TYR 0.027 0.002 TYR O 214 ARG 0.007 0.001 ARG J 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8185 (m-80) cc_final: 0.7557 (m-10) REVERT: A 122 GLU cc_start: 0.6331 (mp0) cc_final: 0.5813 (pm20) REVERT: B 45 LEU cc_start: 0.9504 (tp) cc_final: 0.9138 (tp) REVERT: C 57 HIS cc_start: 0.7301 (m90) cc_final: 0.7032 (m90) REVERT: D 37 MET cc_start: 0.7088 (tpt) cc_final: 0.6126 (tpt) REVERT: D 54 PHE cc_start: 0.7028 (t80) cc_final: 0.6821 (t80) REVERT: D 92 LEU cc_start: 0.9144 (mt) cc_final: 0.8735 (pt) REVERT: F 34 MET cc_start: 0.6429 (tpt) cc_final: 0.6019 (tpt) REVERT: F 40 GLU cc_start: 0.8942 (mp0) cc_final: 0.8553 (mp0) REVERT: F 49 LEU cc_start: 0.7292 (mp) cc_final: 0.5279 (mt) REVERT: G 44 MET cc_start: 0.8326 (mtm) cc_final: 0.7407 (ttm) REVERT: G 52 PHE cc_start: 0.7784 (m-80) cc_final: 0.7048 (m-10) REVERT: G 67 HIS cc_start: 0.7517 (m90) cc_final: 0.7038 (m-70) REVERT: G 118 THR cc_start: 0.8597 (m) cc_final: 0.8174 (p) REVERT: G 128 HIS cc_start: 0.5124 (t70) cc_final: 0.4739 (t-90) REVERT: I 51 PHE cc_start: 0.6295 (t80) cc_final: 0.5513 (t80) REVERT: J 31 TYR cc_start: 0.7589 (t80) cc_final: 0.7367 (t80) REVERT: J 34 MET cc_start: 0.9120 (mmm) cc_final: 0.8596 (mmm) REVERT: J 76 ASN cc_start: 0.8710 (m-40) cc_final: 0.8249 (m-40) REVERT: J 81 LEU cc_start: 0.8190 (tt) cc_final: 0.7919 (tt) REVERT: K 40 PHE cc_start: 0.8515 (m-80) cc_final: 0.7745 (m-10) REVERT: K 48 LEU cc_start: 0.9526 (tp) cc_final: 0.9218 (tp) REVERT: K 78 ASP cc_start: 0.8602 (t0) cc_final: 0.8181 (t0) REVERT: K 91 TYR cc_start: 0.8484 (p90) cc_final: 0.7824 (p90) REVERT: L 46 LEU cc_start: 0.9105 (tp) cc_final: 0.8591 (tt) REVERT: M 13 GLN cc_start: 0.9745 (mt0) cc_final: 0.9362 (mt0) REVERT: M 34 MET cc_start: 0.8095 (tpt) cc_final: 0.7882 (tpt) REVERT: M 37 PHE cc_start: 0.8722 (m-80) cc_final: 0.8271 (m-10) REVERT: O 285 PHE cc_start: 0.9578 (t80) cc_final: 0.9197 (t80) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.3418 time to fit residues: 179.1464 Evaluate side-chains 251 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 HIS G 83 HIS G 138 HIS I 65 HIS I 72 HIS ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN ** M 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 14838 Z= 0.444 Angle : 0.848 15.529 20064 Z= 0.457 Chirality : 0.047 0.430 2135 Planarity : 0.007 0.126 2599 Dihedral : 5.461 32.531 1939 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 27.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.13 % Favored : 97.70 % Rotamer: Outliers : 0.06 % Allowed : 5.00 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.08 (0.20), residues: 1741 helix: -0.83 (0.20), residues: 547 sheet: 1.07 (0.20), residues: 631 loop : -0.34 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 109 HIS 0.019 0.003 HIS J 128 PHE 0.026 0.003 PHE E 119 TYR 0.018 0.002 TYR O 78 ARG 0.009 0.001 ARG M 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8249 (m-80) cc_final: 0.7310 (m-10) REVERT: A 66 PHE cc_start: 0.6080 (t80) cc_final: 0.4770 (t80) REVERT: A 74 LEU cc_start: 0.7733 (tt) cc_final: 0.7525 (tp) REVERT: B 45 LEU cc_start: 0.9556 (tp) cc_final: 0.9334 (tp) REVERT: B 51 PHE cc_start: 0.6986 (t80) cc_final: 0.6672 (t80) REVERT: C 50 LEU cc_start: 0.9170 (pp) cc_final: 0.8890 (pp) REVERT: C 57 HIS cc_start: 0.7793 (m90) cc_final: 0.7095 (m90) REVERT: C 127 PHE cc_start: 0.8602 (p90) cc_final: 0.8280 (p90) REVERT: D 37 MET cc_start: 0.7507 (tpt) cc_final: 0.7141 (tpt) REVERT: D 92 LEU cc_start: 0.9216 (mt) cc_final: 0.8853 (pt) REVERT: E 15 LEU cc_start: 0.8672 (tp) cc_final: 0.8457 (tt) REVERT: E 53 HIS cc_start: 0.7809 (t-90) cc_final: 0.7517 (t-90) REVERT: F 34 MET cc_start: 0.7025 (tpt) cc_final: 0.6119 (tpt) REVERT: F 37 PHE cc_start: 0.8153 (m-80) cc_final: 0.7603 (m-10) REVERT: F 49 LEU cc_start: 0.7679 (mp) cc_final: 0.6011 (mt) REVERT: G 44 MET cc_start: 0.8404 (mtm) cc_final: 0.7708 (ttm) REVERT: G 60 LEU cc_start: 0.9209 (tp) cc_final: 0.8975 (tt) REVERT: G 67 HIS cc_start: 0.8102 (m90) cc_final: 0.7452 (m-70) REVERT: G 118 THR cc_start: 0.8938 (m) cc_final: 0.8465 (p) REVERT: G 139 PHE cc_start: 0.7803 (p90) cc_final: 0.7425 (p90) REVERT: I 45 LEU cc_start: 0.9293 (tp) cc_final: 0.9085 (tp) REVERT: J 56 PHE cc_start: 0.5744 (t80) cc_final: 0.5485 (t80) REVERT: J 60 TYR cc_start: 0.8033 (m-80) cc_final: 0.7814 (m-80) REVERT: K 40 PHE cc_start: 0.8581 (m-10) cc_final: 0.7835 (m-10) REVERT: K 91 TYR cc_start: 0.8671 (p90) cc_final: 0.7948 (p90) REVERT: L 46 LEU cc_start: 0.9204 (tp) cc_final: 0.8721 (tp) REVERT: M 34 MET cc_start: 0.8335 (tpt) cc_final: 0.7540 (tpt) REVERT: O 285 PHE cc_start: 0.9644 (t80) cc_final: 0.9316 (t80) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.3234 time to fit residues: 130.9627 Evaluate side-chains 225 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 157 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS E 120 HIS F 13 GLN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 ASN M 119 HIS O 37 ASN ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14838 Z= 0.226 Angle : 0.671 15.736 20064 Z= 0.357 Chirality : 0.046 0.235 2135 Planarity : 0.005 0.051 2599 Dihedral : 5.075 28.684 1939 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.13 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % 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: 0.29 (0.20), residues: 1741 helix: -0.40 (0.21), residues: 551 sheet: 1.21 (0.21), residues: 630 loop : -0.18 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 109 HIS 0.019 0.002 HIS F 107 PHE 0.019 0.002 PHE D 54 TYR 0.022 0.001 TYR A 41 ARG 0.012 0.001 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8155 (m-80) cc_final: 0.7864 (m-10) REVERT: A 66 PHE cc_start: 0.5840 (t80) cc_final: 0.4542 (t80) REVERT: B 45 LEU cc_start: 0.9558 (tp) cc_final: 0.9333 (tp) REVERT: B 92 LEU cc_start: 0.9215 (mt) cc_final: 0.8973 (mp) REVERT: C 19 LEU cc_start: 0.8944 (mm) cc_final: 0.8679 (mm) REVERT: C 56 PHE cc_start: 0.6427 (t80) cc_final: 0.6101 (t80) REVERT: C 127 PHE cc_start: 0.8323 (p90) cc_final: 0.8014 (p90) REVERT: D 54 PHE cc_start: 0.6825 (t80) cc_final: 0.6499 (t80) REVERT: D 92 LEU cc_start: 0.9075 (mt) cc_final: 0.8777 (pt) REVERT: E 15 LEU cc_start: 0.8636 (tp) cc_final: 0.8419 (tt) REVERT: F 34 MET cc_start: 0.6917 (tpt) cc_final: 0.6632 (tpt) REVERT: F 49 LEU cc_start: 0.7470 (mp) cc_final: 0.5558 (mt) REVERT: F 73 MET cc_start: 0.8105 (ptm) cc_final: 0.7756 (ptm) REVERT: G 37 ASP cc_start: 0.8827 (t0) cc_final: 0.8618 (t0) REVERT: G 44 MET cc_start: 0.8412 (mtm) cc_final: 0.7817 (ttm) REVERT: G 52 PHE cc_start: 0.7862 (m-80) cc_final: 0.7411 (m-10) REVERT: G 67 HIS cc_start: 0.8030 (m90) cc_final: 0.7258 (m-70) REVERT: G 118 THR cc_start: 0.8766 (m) cc_final: 0.8285 (p) REVERT: J 14 LYS cc_start: 0.9377 (tttt) cc_final: 0.9121 (tttt) REVERT: J 31 TYR cc_start: 0.7849 (t80) cc_final: 0.7630 (t80) REVERT: J 56 PHE cc_start: 0.5744 (t80) cc_final: 0.5295 (t80) REVERT: J 60 TYR cc_start: 0.7903 (m-80) cc_final: 0.7664 (m-80) REVERT: K 40 PHE cc_start: 0.8372 (m-80) cc_final: 0.8014 (m-10) REVERT: K 48 LEU cc_start: 0.9508 (tp) cc_final: 0.9193 (tp) REVERT: K 91 TYR cc_start: 0.8691 (p90) cc_final: 0.7989 (p90) REVERT: L 46 LEU cc_start: 0.9228 (tp) cc_final: 0.8786 (tp) REVERT: M 44 ASN cc_start: 0.8656 (m-40) cc_final: 0.8436 (m110) REVERT: M 45 LEU cc_start: 0.9480 (tp) cc_final: 0.9217 (tp) REVERT: O 285 PHE cc_start: 0.9620 (t80) cc_final: 0.9242 (t80) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3129 time to fit residues: 129.3268 Evaluate side-chains 230 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN G 135 GLN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.7474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 14838 Z= 0.316 Angle : 0.706 12.968 20064 Z= 0.380 Chirality : 0.045 0.236 2135 Planarity : 0.005 0.056 2599 Dihedral : 5.244 31.137 1939 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.53 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.33 (0.20), residues: 1741 helix: -0.40 (0.21), residues: 552 sheet: 1.30 (0.21), residues: 641 loop : -0.25 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP O 262 HIS 0.029 0.002 HIS D 122 PHE 0.017 0.002 PHE K 59 TYR 0.024 0.002 TYR O 214 ARG 0.031 0.001 ARG J 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8365 (m-80) cc_final: 0.7553 (m-10) REVERT: A 66 PHE cc_start: 0.6045 (t80) cc_final: 0.4898 (t80) REVERT: B 45 LEU cc_start: 0.9584 (tp) cc_final: 0.9358 (tp) REVERT: B 92 LEU cc_start: 0.9219 (mt) cc_final: 0.9009 (mp) REVERT: C 19 LEU cc_start: 0.8955 (mm) cc_final: 0.8751 (mm) REVERT: C 56 PHE cc_start: 0.6611 (t80) cc_final: 0.6163 (t80) REVERT: C 127 PHE cc_start: 0.8499 (p90) cc_final: 0.8158 (p90) REVERT: D 37 MET cc_start: 0.7470 (tpt) cc_final: 0.7189 (tpt) REVERT: D 92 LEU cc_start: 0.9168 (mt) cc_final: 0.8817 (pt) REVERT: D 122 HIS cc_start: 0.7354 (t70) cc_final: 0.6226 (t70) REVERT: F 34 MET cc_start: 0.7215 (tpt) cc_final: 0.6265 (tpt) REVERT: F 37 PHE cc_start: 0.7533 (m-10) cc_final: 0.7191 (m-10) REVERT: F 49 LEU cc_start: 0.7609 (mp) cc_final: 0.6284 (mt) REVERT: G 44 MET cc_start: 0.8398 (mtm) cc_final: 0.7959 (ttt) REVERT: G 60 LEU cc_start: 0.9299 (tt) cc_final: 0.9086 (tt) REVERT: G 67 HIS cc_start: 0.8200 (m90) cc_final: 0.7241 (m-70) REVERT: G 118 THR cc_start: 0.8813 (m) cc_final: 0.8393 (p) REVERT: J 56 PHE cc_start: 0.6274 (t80) cc_final: 0.5562 (t80) REVERT: J 60 TYR cc_start: 0.7985 (m-80) cc_final: 0.7742 (m-80) REVERT: K 17 LEU cc_start: 0.9392 (tp) cc_final: 0.9176 (tt) REVERT: K 48 LEU cc_start: 0.9398 (tp) cc_final: 0.9057 (tp) REVERT: K 91 TYR cc_start: 0.8743 (p90) cc_final: 0.8006 (p90) REVERT: L 46 LEU cc_start: 0.9162 (tp) cc_final: 0.8945 (tp) REVERT: M 45 LEU cc_start: 0.9449 (tp) cc_final: 0.9167 (tp) REVERT: O 285 PHE cc_start: 0.9619 (t80) cc_final: 0.9290 (t80) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.3122 time to fit residues: 117.9729 Evaluate side-chains 213 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 138 optimal weight: 0.0970 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS ** I 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.7578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14838 Z= 0.197 Angle : 0.637 11.058 20064 Z= 0.340 Chirality : 0.046 0.234 2135 Planarity : 0.004 0.052 2599 Dihedral : 5.016 34.103 1939 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.24 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.50 (0.20), residues: 1741 helix: -0.18 (0.21), residues: 552 sheet: 1.34 (0.21), residues: 621 loop : -0.11 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 262 HIS 0.019 0.001 HIS D 122 PHE 0.016 0.002 PHE B 51 TYR 0.018 0.001 TYR L 83 ARG 0.016 0.001 ARG J 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8113 (m-80) cc_final: 0.7399 (m-10) REVERT: A 66 PHE cc_start: 0.6036 (t80) cc_final: 0.4954 (t80) REVERT: B 45 LEU cc_start: 0.9554 (tp) cc_final: 0.9309 (tp) REVERT: B 50 ASP cc_start: 0.8985 (p0) cc_final: 0.8640 (m-30) REVERT: B 92 LEU cc_start: 0.9149 (mt) cc_final: 0.8902 (mp) REVERT: C 19 LEU cc_start: 0.8957 (mm) cc_final: 0.8694 (mm) REVERT: C 27 ASP cc_start: 0.9492 (t0) cc_final: 0.9201 (t0) REVERT: C 127 PHE cc_start: 0.8392 (p90) cc_final: 0.8018 (p90) REVERT: D 92 LEU cc_start: 0.9084 (mt) cc_final: 0.8764 (pt) REVERT: E 74 MET cc_start: 0.7138 (mpp) cc_final: 0.6807 (mpp) REVERT: F 34 MET cc_start: 0.7297 (tpt) cc_final: 0.6929 (tpt) REVERT: F 37 PHE cc_start: 0.7593 (m-10) cc_final: 0.7107 (m-10) REVERT: F 49 LEU cc_start: 0.7507 (mp) cc_final: 0.6298 (mt) REVERT: G 44 MET cc_start: 0.8380 (mtm) cc_final: 0.7988 (ttt) REVERT: G 67 HIS cc_start: 0.7863 (m90) cc_final: 0.7259 (m-70) REVERT: G 118 THR cc_start: 0.8749 (m) cc_final: 0.8311 (p) REVERT: J 31 TYR cc_start: 0.7608 (t80) cc_final: 0.7389 (t80) REVERT: J 56 PHE cc_start: 0.6257 (t80) cc_final: 0.5737 (t80) REVERT: J 60 TYR cc_start: 0.7927 (m-80) cc_final: 0.7711 (m-80) REVERT: J 93 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7706 (ttp80) REVERT: K 91 TYR cc_start: 0.8722 (p90) cc_final: 0.8022 (p90) REVERT: M 13 GLN cc_start: 0.9739 (mt0) cc_final: 0.9515 (mp10) REVERT: M 45 LEU cc_start: 0.9454 (tp) cc_final: 0.9243 (tp) REVERT: M 104 ARG cc_start: 0.8847 (mmt-90) cc_final: 0.8228 (mmt180) REVERT: O 285 PHE cc_start: 0.9619 (t80) cc_final: 0.9264 (t80) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.3168 time to fit residues: 121.7886 Evaluate side-chains 225 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 122 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN E 53 HIS ** I 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.7790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14838 Z= 0.195 Angle : 0.629 10.761 20064 Z= 0.339 Chirality : 0.045 0.251 2135 Planarity : 0.004 0.053 2599 Dihedral : 4.895 32.205 1939 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.24 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.66 (0.21), residues: 1741 helix: -0.04 (0.21), residues: 563 sheet: 1.35 (0.21), residues: 638 loop : 0.04 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 262 HIS 0.018 0.001 HIS D 122 PHE 0.022 0.002 PHE G 66 TYR 0.024 0.001 TYR D 29 ARG 0.007 0.001 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8099 (m-80) cc_final: 0.7378 (m-10) REVERT: A 66 PHE cc_start: 0.6046 (t80) cc_final: 0.4881 (t80) REVERT: B 29 MET cc_start: 0.8911 (mpp) cc_final: 0.8710 (mmt) REVERT: B 45 LEU cc_start: 0.9473 (tp) cc_final: 0.9271 (tp) REVERT: B 92 LEU cc_start: 0.9124 (mt) cc_final: 0.8912 (mp) REVERT: C 19 LEU cc_start: 0.8976 (mm) cc_final: 0.8696 (mm) REVERT: C 27 ASP cc_start: 0.9505 (t0) cc_final: 0.9226 (t0) REVERT: C 127 PHE cc_start: 0.8313 (p90) cc_final: 0.7951 (p90) REVERT: D 92 LEU cc_start: 0.9040 (mt) cc_final: 0.8773 (pt) REVERT: E 51 ASP cc_start: 0.8863 (m-30) cc_final: 0.8472 (m-30) REVERT: E 74 MET cc_start: 0.7187 (mpp) cc_final: 0.6887 (mpp) REVERT: F 34 MET cc_start: 0.7520 (tpt) cc_final: 0.6434 (tpt) REVERT: F 49 LEU cc_start: 0.7526 (mp) cc_final: 0.6534 (mt) REVERT: F 67 ASN cc_start: 0.8468 (p0) cc_final: 0.7879 (t0) REVERT: F 73 MET cc_start: 0.8167 (ptm) cc_final: 0.7799 (ptm) REVERT: G 44 MET cc_start: 0.8334 (mtm) cc_final: 0.7948 (ttt) REVERT: G 60 LEU cc_start: 0.9247 (tt) cc_final: 0.8885 (tt) REVERT: G 67 HIS cc_start: 0.7275 (m90) cc_final: 0.6648 (m-70) REVERT: G 118 THR cc_start: 0.8769 (m) cc_final: 0.8404 (p) REVERT: I 45 LEU cc_start: 0.9281 (tp) cc_final: 0.9048 (tp) REVERT: J 50 LEU cc_start: 0.8528 (tp) cc_final: 0.8048 (tp) REVERT: J 56 PHE cc_start: 0.6274 (t80) cc_final: 0.5428 (t80) REVERT: J 61 PHE cc_start: 0.8057 (m-80) cc_final: 0.7665 (m-10) REVERT: J 93 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7619 (ttp80) REVERT: K 17 LEU cc_start: 0.9364 (tp) cc_final: 0.9159 (tt) REVERT: K 37 MET cc_start: 0.7908 (tpt) cc_final: 0.7553 (tpt) REVERT: K 48 LEU cc_start: 0.9573 (tp) cc_final: 0.9345 (tp) REVERT: K 91 TYR cc_start: 0.8653 (p90) cc_final: 0.7952 (p90) REVERT: L 46 LEU cc_start: 0.9192 (tp) cc_final: 0.8791 (mp) REVERT: M 45 LEU cc_start: 0.9447 (tp) cc_final: 0.9045 (tp) REVERT: M 104 ARG cc_start: 0.8877 (mmt-90) cc_final: 0.8277 (mmt180) REVERT: O 285 PHE cc_start: 0.9616 (t80) cc_final: 0.9251 (t80) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3274 time to fit residues: 125.8773 Evaluate side-chains 220 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN E 53 HIS ** I 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.7996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14838 Z= 0.206 Angle : 0.639 11.725 20064 Z= 0.341 Chirality : 0.045 0.227 2135 Planarity : 0.004 0.056 2599 Dihedral : 4.883 30.728 1939 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.07 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.72 (0.21), residues: 1741 helix: 0.02 (0.21), residues: 563 sheet: 1.33 (0.21), residues: 638 loop : 0.12 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 262 HIS 0.033 0.002 HIS D 122 PHE 0.018 0.002 PHE K 40 TYR 0.014 0.001 TYR F 55 ARG 0.007 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8074 (m-80) cc_final: 0.7277 (m-10) REVERT: A 66 PHE cc_start: 0.5993 (t80) cc_final: 0.4923 (t80) REVERT: B 29 MET cc_start: 0.8858 (mpp) cc_final: 0.8336 (mpp) REVERT: B 51 PHE cc_start: 0.7396 (t80) cc_final: 0.6958 (t80) REVERT: C 19 LEU cc_start: 0.8994 (mm) cc_final: 0.8725 (mm) REVERT: C 27 ASP cc_start: 0.9532 (t0) cc_final: 0.9281 (t0) REVERT: C 127 PHE cc_start: 0.8326 (p90) cc_final: 0.7658 (p90) REVERT: D 92 LEU cc_start: 0.9054 (mt) cc_final: 0.8718 (pt) REVERT: E 74 MET cc_start: 0.7185 (mpp) cc_final: 0.6858 (mpp) REVERT: F 34 MET cc_start: 0.7431 (tpt) cc_final: 0.6913 (tpt) REVERT: F 37 PHE cc_start: 0.7675 (m-10) cc_final: 0.7372 (m-10) REVERT: F 49 LEU cc_start: 0.7576 (mp) cc_final: 0.5762 (mt) REVERT: F 73 MET cc_start: 0.8141 (ptm) cc_final: 0.7833 (ptm) REVERT: G 44 MET cc_start: 0.8331 (mtm) cc_final: 0.8099 (ttt) REVERT: G 60 LEU cc_start: 0.9212 (tt) cc_final: 0.8898 (tt) REVERT: G 67 HIS cc_start: 0.7014 (m90) cc_final: 0.6799 (m-70) REVERT: G 118 THR cc_start: 0.8746 (m) cc_final: 0.8368 (p) REVERT: I 121 PHE cc_start: 0.7888 (p90) cc_final: 0.7387 (p90) REVERT: J 19 LEU cc_start: 0.9527 (tp) cc_final: 0.9312 (tt) REVERT: J 50 LEU cc_start: 0.8465 (tp) cc_final: 0.8049 (tp) REVERT: J 56 PHE cc_start: 0.6516 (t80) cc_final: 0.5454 (t80) REVERT: J 61 PHE cc_start: 0.7989 (m-80) cc_final: 0.7620 (m-10) REVERT: J 93 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7686 (ttp80) REVERT: J 105 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.8129 (mmm-85) REVERT: K 37 MET cc_start: 0.7655 (tpt) cc_final: 0.7300 (tpt) REVERT: K 48 LEU cc_start: 0.9581 (tp) cc_final: 0.9240 (tp) REVERT: K 91 TYR cc_start: 0.8647 (p90) cc_final: 0.7953 (p90) REVERT: L 46 LEU cc_start: 0.9145 (tp) cc_final: 0.8604 (tp) REVERT: M 45 LEU cc_start: 0.9341 (tp) cc_final: 0.9030 (tp) REVERT: O 285 PHE cc_start: 0.9628 (t80) cc_final: 0.9275 (t80) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.3116 time to fit residues: 115.2730 Evaluate side-chains 214 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 93 optimal weight: 0.1980 chunk 67 optimal weight: 0.9980 chunk 122 optimal weight: 0.0980 chunk 47 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 102 optimal weight: 0.0870 overall best weight: 0.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS ** I 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.8103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14838 Z= 0.186 Angle : 0.654 10.012 20064 Z= 0.350 Chirality : 0.046 0.232 2135 Planarity : 0.004 0.056 2599 Dihedral : 4.823 29.885 1939 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.35 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % 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: 0.71 (0.21), residues: 1741 helix: -0.11 (0.21), residues: 563 sheet: 1.41 (0.21), residues: 628 loop : 0.17 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 109 HIS 0.025 0.001 HIS D 122 PHE 0.027 0.002 PHE G 66 TYR 0.015 0.001 TYR F 55 ARG 0.006 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8605 (ptt) cc_final: 0.8275 (ptm) REVERT: A 52 PHE cc_start: 0.7929 (m-80) cc_final: 0.7148 (m-10) REVERT: A 66 PHE cc_start: 0.5813 (t80) cc_final: 0.4807 (t80) REVERT: B 29 MET cc_start: 0.8881 (mpp) cc_final: 0.8427 (mpp) REVERT: B 50 ASP cc_start: 0.8730 (p0) cc_final: 0.8481 (p0) REVERT: B 51 PHE cc_start: 0.7284 (t80) cc_final: 0.6885 (t80) REVERT: C 19 LEU cc_start: 0.8850 (mm) cc_final: 0.8595 (mm) REVERT: C 27 ASP cc_start: 0.9532 (t0) cc_final: 0.9270 (t0) REVERT: C 127 PHE cc_start: 0.8455 (p90) cc_final: 0.8003 (p90) REVERT: D 92 LEU cc_start: 0.9009 (mt) cc_final: 0.8666 (pt) REVERT: E 74 MET cc_start: 0.7056 (mpp) cc_final: 0.6798 (mpp) REVERT: F 34 MET cc_start: 0.7389 (tpt) cc_final: 0.6308 (tpt) REVERT: F 49 LEU cc_start: 0.7523 (mp) cc_final: 0.6021 (mt) REVERT: F 67 ASN cc_start: 0.8385 (t0) cc_final: 0.7304 (p0) REVERT: G 44 MET cc_start: 0.8260 (mtm) cc_final: 0.7985 (ttm) REVERT: G 60 LEU cc_start: 0.9227 (tt) cc_final: 0.8815 (tt) REVERT: G 64 LEU cc_start: 0.7826 (pt) cc_final: 0.7422 (mp) REVERT: G 67 HIS cc_start: 0.7116 (m90) cc_final: 0.6547 (m-70) REVERT: G 118 THR cc_start: 0.8694 (m) cc_final: 0.8281 (p) REVERT: I 45 LEU cc_start: 0.9182 (tp) cc_final: 0.8910 (tp) REVERT: I 121 PHE cc_start: 0.7581 (p90) cc_final: 0.7325 (p90) REVERT: J 19 LEU cc_start: 0.9523 (tp) cc_final: 0.9266 (tt) REVERT: J 50 LEU cc_start: 0.8397 (tp) cc_final: 0.8034 (tp) REVERT: J 56 PHE cc_start: 0.6534 (t80) cc_final: 0.5381 (t80) REVERT: J 93 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7861 (ttp80) REVERT: K 32 MET cc_start: 0.9064 (mtm) cc_final: 0.8810 (ptm) REVERT: K 37 MET cc_start: 0.7600 (tpt) cc_final: 0.7257 (tpt) REVERT: K 48 LEU cc_start: 0.9572 (tp) cc_final: 0.9066 (tp) REVERT: K 91 TYR cc_start: 0.8574 (p90) cc_final: 0.7914 (p90) REVERT: L 38 PHE cc_start: 0.8679 (m-10) cc_final: 0.8202 (m-10) REVERT: M 9 LYS cc_start: 0.9596 (mtmm) cc_final: 0.9386 (ptpt) REVERT: M 45 LEU cc_start: 0.9316 (tp) cc_final: 0.9033 (tp) REVERT: O 285 PHE cc_start: 0.9620 (t80) cc_final: 0.9233 (t80) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3102 time to fit residues: 120.4358 Evaluate side-chains 224 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 114 optimal weight: 0.0970 chunk 172 optimal weight: 0.8980 chunk 158 optimal weight: 0.0170 chunk 137 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.8210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14838 Z= 0.184 Angle : 0.651 9.969 20064 Z= 0.351 Chirality : 0.045 0.237 2135 Planarity : 0.004 0.057 2599 Dihedral : 4.764 29.302 1939 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.18 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % 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: 0.73 (0.21), residues: 1741 helix: -0.06 (0.21), residues: 563 sheet: 1.46 (0.22), residues: 614 loop : 0.13 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 107 HIS 0.019 0.001 HIS D 122 PHE 0.022 0.002 PHE K 40 TYR 0.026 0.001 TYR J 31 ARG 0.010 0.000 ARG B 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.7846 (m-80) cc_final: 0.7119 (m-10) REVERT: A 66 PHE cc_start: 0.5974 (t80) cc_final: 0.4878 (t80) REVERT: B 29 MET cc_start: 0.8860 (mpp) cc_final: 0.8438 (mpp) REVERT: B 50 ASP cc_start: 0.8693 (p0) cc_final: 0.8448 (p0) REVERT: B 51 PHE cc_start: 0.7299 (t80) cc_final: 0.6911 (t80) REVERT: C 19 LEU cc_start: 0.8867 (mm) cc_final: 0.8602 (mm) REVERT: C 27 ASP cc_start: 0.9544 (t0) cc_final: 0.9282 (t0) REVERT: C 98 LEU cc_start: 0.9024 (mp) cc_final: 0.8737 (mt) REVERT: C 127 PHE cc_start: 0.8447 (p90) cc_final: 0.8053 (p90) REVERT: D 37 MET cc_start: 0.7180 (tpt) cc_final: 0.6976 (tpp) REVERT: D 92 LEU cc_start: 0.9066 (mt) cc_final: 0.8717 (pt) REVERT: E 74 MET cc_start: 0.7246 (mpp) cc_final: 0.6941 (mpp) REVERT: F 34 MET cc_start: 0.7403 (tpt) cc_final: 0.6813 (tpt) REVERT: F 37 PHE cc_start: 0.7329 (m-10) cc_final: 0.7021 (m-10) REVERT: F 49 LEU cc_start: 0.7517 (mp) cc_final: 0.5737 (mt) REVERT: G 44 MET cc_start: 0.8387 (mtm) cc_final: 0.8005 (ttt) REVERT: G 60 LEU cc_start: 0.9204 (tt) cc_final: 0.8799 (tt) REVERT: G 64 LEU cc_start: 0.7963 (pt) cc_final: 0.7546 (mp) REVERT: G 67 HIS cc_start: 0.6884 (m90) cc_final: 0.6674 (m-70) REVERT: G 118 THR cc_start: 0.8695 (m) cc_final: 0.8252 (p) REVERT: I 45 LEU cc_start: 0.9225 (tp) cc_final: 0.8860 (tp) REVERT: J 50 LEU cc_start: 0.8384 (tp) cc_final: 0.7932 (tp) REVERT: J 56 PHE cc_start: 0.6304 (t80) cc_final: 0.4965 (t80) REVERT: J 61 PHE cc_start: 0.8010 (m-80) cc_final: 0.7309 (m-80) REVERT: J 93 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7610 (ttp80) REVERT: K 37 MET cc_start: 0.7548 (tpt) cc_final: 0.7245 (tpt) REVERT: K 48 LEU cc_start: 0.9534 (tp) cc_final: 0.8958 (tp) REVERT: K 91 TYR cc_start: 0.8527 (p90) cc_final: 0.7858 (p90) REVERT: K 92 LEU cc_start: 0.8537 (mt) cc_final: 0.8292 (mt) REVERT: M 45 LEU cc_start: 0.9283 (tp) cc_final: 0.8935 (tp) REVERT: O 285 PHE cc_start: 0.9610 (t80) cc_final: 0.9187 (t80) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2953 time to fit residues: 111.2191 Evaluate side-chains 226 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS C 18 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS ** I 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.040166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.032839 restraints weight = 153817.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.033588 restraints weight = 115255.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034222 restraints weight = 92701.129| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.8363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14838 Z= 0.191 Angle : 0.640 10.050 20064 Z= 0.345 Chirality : 0.045 0.233 2135 Planarity : 0.004 0.058 2599 Dihedral : 4.717 28.779 1939 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.30 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % 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: 0.81 (0.21), residues: 1741 helix: -0.02 (0.21), residues: 564 sheet: 1.52 (0.22), residues: 618 loop : 0.20 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 127 HIS 0.017 0.001 HIS D 122 PHE 0.026 0.002 PHE G 66 TYR 0.023 0.001 TYR O 214 ARG 0.007 0.000 ARG B 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3467.83 seconds wall clock time: 63 minutes 45.50 seconds (3825.50 seconds total)