Starting phenix.real_space_refine on Thu Dec 14 19:32:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/12_2023/8f2r_28825.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/12_2023/8f2r_28825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/12_2023/8f2r_28825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/12_2023/8f2r_28825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/12_2023/8f2r_28825.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2r_28825/12_2023/8f2r_28825.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 9189 2.51 5 N 2499 2.21 5 O 2748 1.98 5 H 14772 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 66": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "G ASP 136": "OD1" <-> "OD2" Residue "G GLU 138": "OE1" <-> "OE2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H ASP 57": "OD1" <-> "OD2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "I ASP 75": "OD1" <-> "OD2" Residue "I GLU 80": "OE1" <-> "OE2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I ASP 127": "OD1" <-> "OD2" Residue "I ASP 137": "OD1" <-> "OD2" Residue "I GLU 176": "OE1" <-> "OE2" Residue "I ASP 190": "OD1" <-> "OD2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ASP 67": "OD1" <-> "OD2" Residue "J PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 122": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "J ASP 199": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 29276 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2940 Classifications: {'peptide': 187} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "B" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3240 Classifications: {'peptide': 199} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 192} Chain: "C" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3095 Classifications: {'peptide': 195} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "D" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3093 Classifications: {'peptide': 199} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "E" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3239 Classifications: {'peptide': 205} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "F" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1239 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "G" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3186 Classifications: {'peptide': 200} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "H" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2928 Classifications: {'peptide': 179} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "I" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3104 Classifications: {'peptide': 198} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "J" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3212 Classifications: {'peptide': 198} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 192} Time building chain proxies: 13.11, per 1000 atoms: 0.45 Number of scatterers: 29276 At special positions: 0 Unit cell: (121.408, 132.248, 132.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 O 2748 8.00 N 2499 7.00 C 9189 6.00 H 14772 1.00 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: 23.44 Conformation dependent library (CDL) restraints added in 3.1 seconds 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3524 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 5 sheets defined 64.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.805A pdb=" N LEU A 6 " --> pdb=" O ALA A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 24 Processing helix chain 'A' and resid 31 through 40 Processing helix chain 'A' and resid 44 through 64 Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 68 through 82 Processing helix chain 'A' and resid 87 through 113 removed outlier: 7.412A pdb=" N THR A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'B' and resid 6 through 14 Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 20 through 38 removed outlier: 4.400A pdb=" N ARG B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.997A pdb=" N TYR B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 76 Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 168 through 188 removed outlier: 3.933A pdb=" N MET B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 21 through 38 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 55 through 76 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 93 through 117 removed outlier: 5.040A pdb=" N ASN C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 117 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 195 removed outlier: 4.209A pdb=" N LEU C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 12 through 24 removed outlier: 4.230A pdb=" N SER D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 42 Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 61 through 83 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 99 through 124 removed outlier: 3.606A pdb=" N CYS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Proline residue: D 116 - end of helix Processing helix chain 'D' and resid 178 through 199 removed outlier: 3.635A pdb=" N SER D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 44 through 60 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 78 through 99 removed outlier: 3.726A pdb=" N LEU E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 119 through 132 Processing helix chain 'E' and resid 133 through 143 removed outlier: 4.065A pdb=" N LEU E 137 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 removed outlier: 4.257A pdb=" N ALA E 147 " --> pdb=" O GLN E 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 144 through 147' Processing helix chain 'E' and resid 193 through 222 removed outlier: 3.638A pdb=" N ARG E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 removed outlier: 4.105A pdb=" N VAL F 15 " --> pdb=" O LYS F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 85 Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.732A pdb=" N GLY G 16 " --> pdb=" O PRO G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 43 Processing helix chain 'G' and resid 46 through 62 Processing helix chain 'G' and resid 64 through 86 removed outlier: 4.831A pdb=" N VAL G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 79 - end of helix Processing helix chain 'G' and resid 88 through 100 Processing helix chain 'G' and resid 102 through 115 Processing helix chain 'G' and resid 116 through 126 Processing helix chain 'G' and resid 179 through 198 Processing helix chain 'H' and resid 7 through 15 removed outlier: 3.581A pdb=" N ARG H 11 " --> pdb=" O PRO H 8 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS H 14 " --> pdb=" O ARG H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 18 No H-bonds generated for 'chain 'H' and resid 16 through 18' Processing helix chain 'H' and resid 19 through 32 removed outlier: 3.516A pdb=" N LEU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 42 Processing helix chain 'H' and resid 47 through 68 removed outlier: 3.918A pdb=" N ALA H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 78 Processing helix chain 'H' and resid 83 through 96 Processing helix chain 'H' and resid 97 through 111 removed outlier: 3.749A pdb=" N ILE H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 183 removed outlier: 3.702A pdb=" N VAL H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN H 181 " --> pdb=" O LYS H 177 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 182 " --> pdb=" O VAL H 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 13 Processing helix chain 'I' and resid 14 through 18 Processing helix chain 'I' and resid 20 through 34 removed outlier: 3.706A pdb=" N VAL I 24 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 51 removed outlier: 4.157A pdb=" N LYS I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 75 Processing helix chain 'I' and resid 78 through 83 Processing helix chain 'I' and resid 91 through 117 removed outlier: 4.004A pdb=" N LEU I 97 " --> pdb=" O ASN I 93 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 161 Processing helix chain 'I' and resid 174 through 198 removed outlier: 4.622A pdb=" N ARG I 187 " --> pdb=" O ASP I 183 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE I 188 " --> pdb=" O GLY I 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 25 Processing helix chain 'J' and resid 29 through 41 removed outlier: 3.514A pdb=" N LEU J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 62 Processing helix chain 'J' and resid 64 through 85 Processing helix chain 'J' and resid 88 through 100 Processing helix chain 'J' and resid 102 through 126 removed outlier: 5.911A pdb=" N GLN J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU J 119 " --> pdb=" O SER J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 201 Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 163 removed outlier: 3.576A pdb=" N GLY A 121 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLY A 150 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU A 119 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TRP A 124 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER I 136 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 126 " --> pdb=" O THR I 134 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 130 " --> pdb=" O VAL I 130 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL I 130 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER A 132 " --> pdb=" O TRP I 128 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TRP I 128 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU I 123 " --> pdb=" O GLN I 154 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN I 154 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP I 125 " --> pdb=" O LYS I 152 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL I 144 " --> pdb=" O LYS I 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 161 through 167 removed outlier: 5.704A pdb=" N ASN B 155 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR B 124 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TRP B 129 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER H 130 " --> pdb=" O TRP B 129 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 131 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL H 124 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER B 137 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TRP H 122 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP H 146 " --> pdb=" O GLN H 118 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE H 120 " --> pdb=" O HIS H 144 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS H 144 " --> pdb=" O PHE H 120 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP H 122 " --> pdb=" O SER H 142 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER H 142 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL H 124 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU H 140 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU H 126 " --> pdb=" O MET H 138 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET H 138 " --> pdb=" O LEU H 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 165 through 170 removed outlier: 6.143A pdb=" N GLN C 156 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE C 125 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP C 130 " --> pdb=" O HIS J 147 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS J 147 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU C 132 " --> pdb=" O MET J 145 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU J 141 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR C 138 " --> pdb=" O TRP J 139 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP J 139 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY J 163 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL J 137 " --> pdb=" O GLN J 161 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLN J 161 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TRP J 139 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL J 159 " --> pdb=" O TRP J 139 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU J 141 " --> pdb=" O GLN J 157 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN J 157 " --> pdb=" O LEU J 141 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA J 158 " --> pdb=" O PHE J 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 170 through 177 removed outlier: 3.650A pdb=" N GLY D 133 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA D 162 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU D 131 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TRP D 136 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER F 32 " --> pdb=" O TRP D 136 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D 138 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU F 26 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER D 144 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TRP F 24 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU F 19 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA F 50 " --> pdb=" O LEU F 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 187 through 192 removed outlier: 6.741A pdb=" N SER E 175 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL E 159 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU E 177 " --> pdb=" O TRP E 157 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP E 157 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLN E 179 " --> pdb=" O PHE E 155 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE E 155 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS E 181 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP E 157 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER G 147 " --> pdb=" O TRP E 157 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL E 159 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU G 134 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS G 165 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP G 136 " --> pdb=" O VAL G 163 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2844 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: 10.41 Time building geometry restraints manager: 24.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14745 1.03 - 1.22: 28 1.22 - 1.42: 5937 1.42 - 1.62: 8696 1.62 - 1.81: 109 Bond restraints: 29515 Sorted by residual: bond pdb=" CB PRO H 71 " pdb=" CG PRO H 71 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.84e+00 bond pdb=" CG GLN I 114 " pdb=" CD GLN I 114 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" N LEU E 149 " pdb=" CA LEU E 149 " ideal model delta sigma weight residual 1.454 1.474 -0.021 1.74e-02 3.30e+03 1.44e+00 bond pdb=" CG PRO H 71 " pdb=" CD PRO H 71 " ideal model delta sigma weight residual 1.503 1.464 0.039 3.40e-02 8.65e+02 1.33e+00 bond pdb=" CB ASP F 51 " pdb=" CG ASP F 51 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.33e+00 ... (remaining 29510 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.46: 273 105.46 - 112.63: 35078 112.63 - 119.80: 7892 119.80 - 126.96: 10157 126.96 - 134.13: 163 Bond angle restraints: 53563 Sorted by residual: angle pdb=" CA PRO H 71 " pdb=" N PRO H 71 " pdb=" CD PRO H 71 " ideal model delta sigma weight residual 112.00 106.50 5.50 1.40e+00 5.10e-01 1.54e+01 angle pdb=" N PRO H 71 " pdb=" CD PRO H 71 " pdb=" CG PRO H 71 " ideal model delta sigma weight residual 103.20 98.30 4.90 1.50e+00 4.44e-01 1.07e+01 angle pdb=" N ASN C 109 " pdb=" CA ASN C 109 " pdb=" C ASN C 109 " ideal model delta sigma weight residual 111.82 115.57 -3.75 1.16e+00 7.43e-01 1.05e+01 angle pdb=" CA TYR F 40 " pdb=" CB TYR F 40 " pdb=" CG TYR F 40 " ideal model delta sigma weight residual 113.90 119.56 -5.66 1.80e+00 3.09e-01 9.87e+00 angle pdb=" N MET D 128 " pdb=" CA MET D 128 " pdb=" C MET D 128 " ideal model delta sigma weight residual 109.39 114.18 -4.79 1.59e+00 3.96e-01 9.08e+00 ... (remaining 53558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12234 17.81 - 35.62: 807 35.62 - 53.42: 207 53.42 - 71.23: 164 71.23 - 89.04: 24 Dihedral angle restraints: 13436 sinusoidal: 7326 harmonic: 6110 Sorted by residual: dihedral pdb=" CA CYS C 170 " pdb=" C CYS C 170 " pdb=" N SER C 171 " pdb=" CA SER C 171 " ideal model delta harmonic sigma weight residual 180.00 152.18 27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ASP E 63 " pdb=" C ASP E 63 " pdb=" N CYS E 64 " pdb=" CA CYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ILE A 138 " pdb=" C ILE A 138 " pdb=" N HIS A 139 " pdb=" CA HIS A 139 " ideal model delta harmonic sigma weight residual 180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 13433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1714 0.043 - 0.087: 455 0.087 - 0.130: 112 0.130 - 0.174: 25 0.174 - 0.217: 3 Chirality restraints: 2309 Sorted by residual: chirality pdb=" CA ARG B 141 " pdb=" N ARG B 141 " pdb=" C ARG B 141 " pdb=" CB ARG B 141 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TYR C 145 " pdb=" N TYR C 145 " pdb=" C TYR C 145 " pdb=" CB TYR C 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CA ILE A 145 " pdb=" N ILE A 145 " pdb=" C ILE A 145 " pdb=" CB ILE A 145 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 2306 not shown) Planarity restraints: 4311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 170 " -0.203 9.50e-02 1.11e+02 7.87e-02 4.08e+01 pdb=" NE ARG E 170 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG E 170 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG E 170 " 0.084 2.00e-02 2.50e+03 pdb=" NH2 ARG E 170 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG E 170 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG E 170 " -0.079 2.00e-02 2.50e+03 pdb="HH21 ARG E 170 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 170 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 110 " -0.122 9.50e-02 1.11e+02 5.79e-02 3.98e+01 pdb=" NE ARG I 110 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG I 110 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG I 110 " -0.045 2.00e-02 2.50e+03 pdb=" NH2 ARG I 110 " 0.071 2.00e-02 2.50e+03 pdb="HH11 ARG I 110 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG I 110 " 0.053 2.00e-02 2.50e+03 pdb="HH21 ARG I 110 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG I 110 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 125 " 0.144 9.50e-02 1.11e+02 6.17e-02 3.65e+01 pdb=" NE ARG A 125 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 125 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 125 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 125 " -0.075 2.00e-02 2.50e+03 pdb="HH11 ARG A 125 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 125 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 125 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 125 " 0.076 2.00e-02 2.50e+03 ... (remaining 4308 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 750 2.12 - 2.74: 53464 2.74 - 3.36: 83524 3.36 - 3.98: 102357 3.98 - 4.60: 163404 Nonbonded interactions: 403499 Sorted by model distance: nonbonded pdb=" HH TYR D 140 " pdb=" OE1 GLU D 151 " model vdw 1.504 1.850 nonbonded pdb=" OE1 GLU A 162 " pdb=" HG1 THR F 16 " model vdw 1.510 1.850 nonbonded pdb=" OE1 GLU H 49 " pdb=" H GLU H 49 " model vdw 1.515 1.850 nonbonded pdb=" OE1 GLN E 120 " pdb=" H GLN E 120 " model vdw 1.520 1.850 nonbonded pdb=" OE1 GLN F 18 " pdb=" H GLN F 18 " model vdw 1.565 1.850 ... (remaining 403494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.420 Extract box with map and model: 11.210 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 90.820 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 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 0.068 14743 Z= 0.259 Angle : 0.797 6.379 19911 Z= 0.482 Chirality : 0.043 0.217 2309 Planarity : 0.010 0.123 2547 Dihedral : 15.266 89.040 5566 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.20 % Favored : 97.63 % Rotamer: Outliers : 0.12 % Allowed : 11.27 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.18), residues: 1817 helix: 0.07 (0.14), residues: 1093 sheet: 0.77 (0.28), residues: 287 loop : -0.03 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP E 148 HIS 0.009 0.002 HIS J 181 PHE 0.021 0.003 PHE G 96 TYR 0.031 0.005 TYR C 134 ARG 0.024 0.003 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 2.335 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 outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.7672 time to fit residues: 203.2656 Evaluate side-chains 157 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14743 Z= 0.225 Angle : 0.573 5.456 19911 Z= 0.308 Chirality : 0.037 0.188 2309 Planarity : 0.004 0.069 2547 Dihedral : 4.689 22.444 1945 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.38 % Favored : 98.51 % Rotamer: Outliers : 1.11 % Allowed : 10.77 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 1817 helix: 1.53 (0.15), residues: 1099 sheet: 0.56 (0.28), residues: 296 loop : 0.43 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 115 HIS 0.006 0.001 HIS J 147 PHE 0.016 0.002 PHE C 11 TYR 0.020 0.002 TYR F 40 ARG 0.005 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 2.285 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 outliers start: 18 outliers final: 13 residues processed: 182 average time/residue: 0.6868 time to fit residues: 174.5664 Evaluate side-chains 168 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 2.144 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3017 time to fit residues: 9.9682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 25 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14743 Z= 0.204 Angle : 0.518 6.162 19911 Z= 0.274 Chirality : 0.036 0.166 2309 Planarity : 0.004 0.050 2547 Dihedral : 4.291 23.119 1945 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.76 % Favored : 98.18 % Rotamer: Outliers : 1.05 % Allowed : 11.21 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.20), residues: 1817 helix: 1.92 (0.15), residues: 1104 sheet: 0.58 (0.28), residues: 291 loop : 0.32 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 14 HIS 0.007 0.001 HIS J 147 PHE 0.015 0.001 PHE G 141 TYR 0.019 0.001 TYR F 40 ARG 0.003 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 2.442 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 outliers start: 17 outliers final: 8 residues processed: 175 average time/residue: 0.7446 time to fit residues: 181.2912 Evaluate side-chains 159 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 2.618 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4555 time to fit residues: 11.2759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 10.0000 chunk 121 optimal weight: 0.4980 chunk 83 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14743 Z= 0.174 Angle : 0.492 5.908 19911 Z= 0.259 Chirality : 0.035 0.161 2309 Planarity : 0.004 0.045 2547 Dihedral : 4.088 29.661 1945 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.38 % Favored : 98.57 % Rotamer: Outliers : 0.80 % Allowed : 11.52 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.20), residues: 1817 helix: 2.18 (0.16), residues: 1104 sheet: 0.47 (0.27), residues: 291 loop : 0.20 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 46 HIS 0.008 0.001 HIS H 53 PHE 0.014 0.001 PHE G 141 TYR 0.017 0.001 TYR F 40 ARG 0.005 0.000 ARG D 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 2.493 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 outliers start: 13 outliers final: 8 residues processed: 171 average time/residue: 0.7574 time to fit residues: 178.7434 Evaluate side-chains 164 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 2.283 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.5327 time to fit residues: 9.4361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 ASN J 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14743 Z= 0.189 Angle : 0.486 5.115 19911 Z= 0.257 Chirality : 0.035 0.157 2309 Planarity : 0.004 0.043 2547 Dihedral : 3.978 25.304 1945 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.60 % Favored : 98.35 % Rotamer: Outliers : 0.87 % Allowed : 11.21 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.20), residues: 1817 helix: 2.25 (0.16), residues: 1109 sheet: 0.44 (0.27), residues: 291 loop : -0.02 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 46 HIS 0.007 0.001 HIS J 147 PHE 0.014 0.001 PHE G 141 TYR 0.018 0.001 TYR F 40 ARG 0.003 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 2.257 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 outliers start: 14 outliers final: 5 residues processed: 168 average time/residue: 0.7469 time to fit residues: 174.0261 Evaluate side-chains 157 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 2.209 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3163 time to fit residues: 5.8447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.0470 chunk 154 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 chunk 42 optimal weight: 0.0770 chunk 171 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN B 181 GLN H 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14743 Z= 0.136 Angle : 0.462 5.347 19911 Z= 0.241 Chirality : 0.035 0.152 2309 Planarity : 0.004 0.045 2547 Dihedral : 3.790 23.081 1945 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.60 % Favored : 98.35 % Rotamer: Outliers : 0.43 % Allowed : 11.76 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.20), residues: 1817 helix: 2.50 (0.16), residues: 1109 sheet: 0.55 (0.27), residues: 291 loop : 0.01 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 46 HIS 0.004 0.001 HIS J 147 PHE 0.013 0.001 PHE G 141 TYR 0.013 0.001 TYR F 40 ARG 0.005 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 168 time to evaluate : 2.776 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 outliers start: 7 outliers final: 4 residues processed: 173 average time/residue: 0.7554 time to fit residues: 179.8631 Evaluate side-chains 156 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 2.288 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5957 time to fit residues: 6.3610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 170 optimal weight: 0.2980 chunk 106 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14743 Z= 0.249 Angle : 0.520 5.577 19911 Z= 0.276 Chirality : 0.036 0.147 2309 Planarity : 0.004 0.045 2547 Dihedral : 3.920 25.534 1945 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.96 % Rotamer: Outliers : 0.43 % Allowed : 12.57 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.20), residues: 1817 helix: 2.27 (0.16), residues: 1111 sheet: 0.36 (0.27), residues: 292 loop : -0.28 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 148 HIS 0.008 0.001 HIS B 153 PHE 0.015 0.001 PHE E 155 TYR 0.019 0.001 TYR F 40 ARG 0.005 0.001 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 2.323 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 outliers start: 7 outliers final: 5 residues processed: 164 average time/residue: 0.7779 time to fit residues: 174.5727 Evaluate side-chains 158 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 2.231 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6146 time to fit residues: 7.3301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS I 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14743 Z= 0.194 Angle : 0.488 5.688 19911 Z= 0.258 Chirality : 0.035 0.140 2309 Planarity : 0.004 0.044 2547 Dihedral : 3.827 25.738 1945 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 0.19 % Allowed : 13.07 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1817 helix: 2.43 (0.16), residues: 1104 sheet: 0.40 (0.27), residues: 291 loop : -0.22 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 46 HIS 0.006 0.001 HIS J 147 PHE 0.013 0.001 PHE F 71 TYR 0.015 0.001 TYR F 40 ARG 0.005 0.000 ARG I 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 2.315 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 outliers start: 3 outliers final: 1 residues processed: 161 average time/residue: 0.7607 time to fit residues: 168.4931 Evaluate side-chains 153 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3166 time to fit residues: 3.2646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 143 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14743 Z= 0.264 Angle : 0.530 5.976 19911 Z= 0.282 Chirality : 0.036 0.149 2309 Planarity : 0.004 0.046 2547 Dihedral : 3.933 26.265 1945 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 0.25 % Allowed : 13.07 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.20), residues: 1817 helix: 2.31 (0.16), residues: 1104 sheet: 0.17 (0.27), residues: 292 loop : -0.37 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 46 HIS 0.009 0.001 HIS B 153 PHE 0.015 0.002 PHE F 71 TYR 0.019 0.001 TYR F 40 ARG 0.009 0.001 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 2.240 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 outliers start: 4 outliers final: 1 residues processed: 157 average time/residue: 0.8074 time to fit residues: 171.9070 Evaluate side-chains 150 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 2.494 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3119 time to fit residues: 3.7424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 134 GLN E 94 GLN E 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14743 Z= 0.281 Angle : 0.548 5.935 19911 Z= 0.291 Chirality : 0.037 0.219 2309 Planarity : 0.005 0.068 2547 Dihedral : 4.039 26.785 1945 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.69 % Rotamer: Outliers : 0.06 % Allowed : 13.19 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.20), residues: 1817 helix: 2.25 (0.16), residues: 1106 sheet: 0.10 (0.28), residues: 295 loop : -0.47 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 46 HIS 0.009 0.002 HIS H 53 PHE 0.017 0.002 PHE F 71 TYR 0.017 0.001 TYR F 40 ARG 0.007 0.001 ARG E 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.514 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 outliers start: 1 outliers final: 1 residues processed: 147 average time/residue: 0.7338 time to fit residues: 151.9995 Evaluate side-chains 144 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3178 time to fit residues: 3.6311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 74.0275 > 50: distance: 109 - 160: 31.785 distance: 123 - 179: 21.157 distance: 132 - 145: 35.070 distance: 133 - 199: 27.883 distance: 145 - 146: 10.986 distance: 146 - 147: 36.983 distance: 146 - 155: 20.120 distance: 147 - 148: 16.025 distance: 147 - 160: 24.278 distance: 148 - 216: 57.928 distance: 149 - 156: 7.172 distance: 149 - 157: 42.221 distance: 150 - 151: 12.648 distance: 150 - 158: 21.749 distance: 150 - 159: 16.046 distance: 151 - 152: 39.837 distance: 160 - 161: 40.570 distance: 160 - 168: 10.485 distance: 161 - 162: 56.617 distance: 161 - 164: 20.271 distance: 161 - 169: 41.290 distance: 162 - 163: 42.487 distance: 162 - 179: 34.032 distance: 164 - 165: 25.395 distance: 164 - 166: 24.351 distance: 164 - 170: 33.075 distance: 165 - 167: 40.607 distance: 165 - 171: 47.125 distance: 179 - 180: 25.596 distance: 179 - 190: 47.597 distance: 180 - 181: 49.318 distance: 180 - 183: 49.552 distance: 180 - 191: 29.885 distance: 181 - 182: 18.675 distance: 181 - 199: 38.293 distance: 183 - 192: 18.742 distance: 183 - 193: 39.088 distance: 184 - 186: 39.729 distance: 186 - 188: 10.672 distance: 187 - 189: 34.556 distance: 187 - 196: 18.652 distance: 188 - 189: 44.883 distance: 188 - 197: 21.421 distance: 189 - 198: 6.146 distance: 199 - 200: 14.876 distance: 199 - 208: 47.192 distance: 200 - 201: 55.817 distance: 200 - 203: 23.184 distance: 200 - 209: 45.935 distance: 201 - 216: 56.346 distance: 203 - 204: 53.276 distance: 203 - 210: 57.107 distance: 203 - 211: 39.671 distance: 204 - 205: 39.413 distance: 204 - 212: 42.102 distance: 204 - 213: 56.181 distance: 205 - 206: 39.207 distance: 205 - 207: 40.178 distance: 216 - 217: 68.711 distance: 216 - 225: 39.905 distance: 217 - 218: 56.444 distance: 217 - 220: 56.736 distance: 217 - 226: 57.459 distance: 220 - 221: 45.431 distance: 220 - 227: 40.211 distance: 220 - 228: 39.953 distance: 221 - 222: 21.078 distance: 221 - 229: 44.058 distance: 221 - 230: 24.636 distance: 222 - 224: 39.610 distance: 224 - 231: 40.327 distance: 233 - 234: 38.648 distance: 234 - 235: 56.251 distance: 234 - 237: 56.569 distance: 234 - 242: 23.283 distance: 235 - 236: 57.579 distance: 235 - 252: 40.637 distance: 237 - 238: 48.240 distance: 237 - 244: 39.120 distance: 238 - 239: 11.673 distance: 238 - 240: 44.558 distance: 238 - 245: 17.016 distance: 239 - 246: 22.309 distance: 239 - 247: 21.407 distance: 239 - 248: 22.959 distance: 240 - 249: 22.770 distance: 240 - 251: 29.620 distance: 252 - 253: 45.402 distance: 252 - 260: 27.355 distance: 253 - 254: 24.170 distance: 253 - 256: 4.298 distance: 253 - 261: 16.805 distance: 254 - 266: 18.259 distance: 256 - 257: 26.196 distance: 256 - 262: 47.702 distance: 256 - 263: 27.849 distance: 257 - 258: 40.157 distance: 257 - 259: 40.557 distance: 259 - 264: 30.818 distance: 259 - 265: 39.864 distance: 266 - 267: 21.365 distance: 266 - 275: 58.560 distance: 270 - 271: 30.469 distance: 270 - 278: 24.781 distance: 271 - 272: 10.436 distance: 271 - 279: 19.223 distance: 271 - 280: 50.241 distance: 272 - 273: 19.890 distance: 274 - 281: 56.857 distance: 283 - 284: 16.377 distance: 283 - 291: 39.309 distance: 284 - 285: 39.292 distance: 284 - 287: 39.703 distance: 284 - 292: 35.514 distance: 285 - 286: 3.538 distance: 287 - 288: 8.930 distance: 287 - 293: 37.824 distance: 288 - 289: 28.746 distance: 288 - 290: 30.277 distance: 288 - 295: 42.019 distance: 289 - 296: 17.615 distance: 289 - 297: 40.729 distance: 290 - 299: 3.008 distance: 302 - 303: 40.986 distance: 302 - 310: 40.611 distance: 303 - 311: 55.554 distance: 304 - 316: 34.501 distance: 305 - 353: 38.151 distance: 306 - 307: 48.142 distance: 306 - 312: 40.891 distance: 306 - 313: 21.247 distance: 307 - 308: 21.433 distance: 307 - 309: 24.182 distance: 309 - 314: 5.080 distance: 309 - 315: 5.224