Starting phenix.real_space_refine (version: dev) on Sun Feb 26 20:34:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/02_2023/6w4o_21535.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/02_2023/6w4o_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_21535/02_2023/6w4o_21535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/02_2023/6w4o_21535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/02_2023/6w4o_21535.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4o_21535/02_2023/6w4o_21535.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 8.80, per 1000 atoms: 0.61 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: 5.94 Conformation dependent library (CDL) restraints added in 2.2 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: 0.87 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: 4.73 Time building geometry restraints manager: 6.33 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 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. 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 14.850 Check model and map are aligned: 0.240 Process input model: 41.340 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 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 : 0.774 13.525 20064 Z= 0.501 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 % 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 *********************** 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 : 1.946 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 outliers start: 14 outliers final: 6 residues processed: 660 average time/residue: 0.3664 time to fit residues: 322.0986 Evaluate side-chains 281 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 275 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2379 time to fit residues: 4.6186 ------------------------------------------------------------------------------- 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: 0.8980 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 135 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 157 optimal weight: 0.0980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 GLN ** 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: 0.7278 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 14838 Z= 0.256 Angle : 0.726 12.855 20064 Z= 0.382 Chirality : 0.049 0.236 2135 Planarity : 0.005 0.069 2599 Dihedral : 4.869 30.846 1939 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.72 % Favored : 98.05 % Rotamer Outliers : 0.06 % 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: -0.19 (0.19), residues: 1741 helix: -1.07 (0.19), residues: 529 sheet: 1.01 (0.20), residues: 591 loop : -0.17 (0.26), residues: 621 *********************** 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 396 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 395 time to evaluate : 1.872 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 outliers start: 1 outliers final: 0 residues processed: 396 average time/residue: 0.3548 time to fit residues: 189.1965 Evaluate side-chains 250 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.796 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3770 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 0.0270 chunk 130 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 HIS C 96 GLN ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 14838 Z= 0.289 Angle : 0.705 13.877 20064 Z= 0.375 Chirality : 0.046 0.257 2135 Planarity : 0.006 0.084 2599 Dihedral : 4.952 30.182 1939 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.24 % Favored : 97.59 % Rotamer Outliers : 0.06 % 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: 0.18 (0.20), residues: 1741 helix: -0.63 (0.20), residues: 543 sheet: 1.14 (0.20), residues: 628 loop : -0.07 (0.27), residues: 570 *********************** 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 337 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 336 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 337 average time/residue: 0.3400 time to fit residues: 156.9042 Evaluate side-chains 239 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.757 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1683 time to fit residues: 2.5404 ------------------------------------------------------------------------------- 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: 6.9990 chunk 118 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN C 96 GLN D 70 ASN ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS M 13 GLN ** M 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 ASN ** 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: 0.7479 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 14838 Z= 0.219 Angle : 0.664 13.110 20064 Z= 0.351 Chirality : 0.046 0.278 2135 Planarity : 0.005 0.059 2599 Dihedral : 4.850 27.684 1939 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.01 % Favored : 97.82 % Rotamer Outliers : 0.06 % 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: 0.42 (0.20), residues: 1741 helix: -0.40 (0.21), residues: 539 sheet: 1.22 (0.21), residues: 636 loop : 0.10 (0.27), residues: 566 *********************** 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 328 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 1.951 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 outliers start: 1 outliers final: 1 residues processed: 328 average time/residue: 0.3289 time to fit residues: 148.7570 Evaluate side-chains 248 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1398 time to fit residues: 2.5608 ------------------------------------------------------------------------------- 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: 0.9990 chunk 2 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 HIS ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 14838 Z= 0.208 Angle : 0.664 11.755 20064 Z= 0.349 Chirality : 0.046 0.240 2135 Planarity : 0.004 0.046 2599 Dihedral : 4.855 27.567 1939 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.24 % Favored : 97.59 % Rotamer Outliers : 0.06 % 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: 0.63 (0.20), residues: 1741 helix: -0.20 (0.21), residues: 537 sheet: 1.34 (0.21), residues: 633 loop : 0.16 (0.27), residues: 571 *********************** 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 321 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 320 time to evaluate : 1.899 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 outliers start: 1 outliers final: 1 residues processed: 321 average time/residue: 0.3421 time to fit residues: 150.6256 Evaluate side-chains 235 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1635 time to fit residues: 2.6609 ------------------------------------------------------------------------------- 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: 7.9990 chunk 150 optimal weight: 0.0970 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 138 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS F 117 HIS G 138 HIS ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 GLN ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 14838 Z= 0.196 Angle : 0.668 11.348 20064 Z= 0.352 Chirality : 0.047 0.240 2135 Planarity : 0.004 0.047 2599 Dihedral : 4.780 25.755 1939 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.24 % Favored : 97.59 % Rotamer Outliers : 0.13 % 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: 0.63 (0.20), residues: 1741 helix: -0.20 (0.21), residues: 546 sheet: 1.49 (0.22), residues: 598 loop : 0.07 (0.26), residues: 597 *********************** 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 320 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 318 time to evaluate : 1.829 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 outliers start: 2 outliers final: 1 residues processed: 319 average time/residue: 0.3257 time to fit residues: 144.2535 Evaluate side-chains 240 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1633 time to fit residues: 2.6963 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 0.2980 chunk 95 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS F 117 HIS ** J 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 14838 Z= 0.199 Angle : 0.658 11.005 20064 Z= 0.351 Chirality : 0.046 0.229 2135 Planarity : 0.004 0.046 2599 Dihedral : 4.712 26.543 1939 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.07 % Favored : 97.76 % Rotamer Outliers : 0.00 % 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: 0.68 (0.20), residues: 1741 helix: -0.12 (0.21), residues: 554 sheet: 1.50 (0.21), residues: 615 loop : 0.03 (0.27), residues: 572 *********************** 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 312 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.824 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 outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.3262 time to fit residues: 141.3752 Evaluate side-chains 225 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3945 ------------------------------------------------------------------------------- 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: 9.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS F 117 HIS ** J 123 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: 0.7522 moved from start: 0.7326 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= 0.213 Angle : 0.677 10.913 20064 Z= 0.364 Chirality : 0.047 0.230 2135 Planarity : 0.004 0.051 2599 Dihedral : 4.788 25.538 1939 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.30 % Favored : 97.53 % Rotamer Outliers : 0.00 % 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: 0.71 (0.20), residues: 1741 helix: -0.08 (0.21), residues: 556 sheet: 1.60 (0.21), residues: 614 loop : -0.07 (0.27), residues: 571 *********************** 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 290 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.737 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 outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.3193 time to fit residues: 129.2759 Evaluate side-chains 223 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4690 ------------------------------------------------------------------------------- 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: 3.9990 chunk 145 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 chunk 122 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 146 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.7495 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= 0.194 Angle : 0.670 11.249 20064 Z= 0.359 Chirality : 0.047 0.240 2135 Planarity : 0.004 0.058 2599 Dihedral : 4.735 25.765 1939 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.24 % Favored : 97.59 % Rotamer Outliers : 0.00 % 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: 0.70 (0.20), residues: 1741 helix: -0.10 (0.21), residues: 550 sheet: 1.52 (0.21), residues: 618 loop : -0.00 (0.27), residues: 573 *********************** 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 288 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.825 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 outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3293 time to fit residues: 132.4841 Evaluate side-chains 229 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5239 ------------------------------------------------------------------------------- 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: 1.9990 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS G 83 HIS ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.7881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 14838 Z= 0.266 Angle : 0.714 11.132 20064 Z= 0.385 Chirality : 0.046 0.235 2135 Planarity : 0.005 0.044 2599 Dihedral : 4.907 27.789 1939 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.53 % Favored : 97.30 % Rotamer Outliers : 0.00 % 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: 0.62 (0.20), residues: 1741 helix: -0.13 (0.21), residues: 559 sheet: 1.55 (0.21), residues: 612 loop : -0.17 (0.27), residues: 570 ********************** 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 : 1.930 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 outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.3186 time to fit residues: 121.1241 Evaluate side-chains 212 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3954 ------------------------------------------------------------------------------- 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: 0.9980 chunk 42 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 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 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS G 59 ASN ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.040976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.033643 restraints weight = 148827.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.034347 restraints weight = 114776.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.034933 restraints weight = 94034.413| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.8157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14838 Z= 0.232 Angle : 0.689 11.278 20064 Z= 0.369 Chirality : 0.046 0.241 2135 Planarity : 0.004 0.043 2599 Dihedral : 4.922 27.013 1939 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.47 % Favored : 97.36 % Rotamer Outliers : 0.00 % 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: 0.61 (0.20), residues: 1741 helix: -0.11 (0.21), residues: 557 sheet: 1.47 (0.21), residues: 622 loop : -0.14 (0.27), residues: 562 =============================================================================== Job complete usr+sys time: 3539.70 seconds wall clock time: 65 minutes 43.81 seconds (3943.81 seconds total)