Starting phenix.real_space_refine on Sat Aug 23 13:35:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce8_16601/08_2025/8ce8_16601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce8_16601/08_2025/8ce8_16601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ce8_16601/08_2025/8ce8_16601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce8_16601/08_2025/8ce8_16601.map" model { file = "/net/cci-nas-00/data/ceres_data/8ce8_16601/08_2025/8ce8_16601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce8_16601/08_2025/8ce8_16601.cif" } resolution = 3.81 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 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= 0.005 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 8276 2.51 5 N 2193 2.21 5 O 2142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12674 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "C" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1930 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "D" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "a" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "c" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1930 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "d" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "E" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1236 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Time building chain proxies: 2.74, per 1000 atoms: 0.22 Number of scatterers: 12674 At special positions: 0 Unit cell: (90.48, 120.93, 127.89, 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 63 16.00 O 2142 8.00 N 2193 7.00 C 8276 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 473.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2992 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 69.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.933A pdb=" N TYR A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.664A pdb=" N ALA A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.836A pdb=" N VAL A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.816A pdb=" N GLN A 177 " --> pdb=" O GLN A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 17 removed outlier: 3.545A pdb=" N PHE B 7 " --> pdb=" O PHE B 3 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 21 Processing helix chain 'B' and resid 22 through 40 removed outlier: 4.002A pdb=" N PHE B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 42 through 66 Proline residue: B 51 - end of helix Processing helix chain 'B' and resid 66 through 77 removed outlier: 4.263A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.716A pdb=" N GLN B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 120 removed outlier: 3.634A pdb=" N VAL B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Proline residue: B 113 - end of helix Processing helix chain 'B' and resid 122 through 151 Proline residue: B 138 - end of helix Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 158 through 169 removed outlier: 4.110A pdb=" N SER B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Proline residue: B 167 - end of helix Processing helix chain 'B' and resid 169 through 185 removed outlier: 3.545A pdb=" N MET B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 220 Proline residue: B 208 - end of helix removed outlier: 4.074A pdb=" N ALA B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 10 through 42 Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.690A pdb=" N SER C 53 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 50 through 54' Processing helix chain 'C' and resid 55 through 83 removed outlier: 4.080A pdb=" N LEU C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 3.601A pdb=" N TRP C 66 " --> pdb=" O PRO C 62 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 120 removed outlier: 3.801A pdb=" N ASN C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 126 through 149 removed outlier: 3.719A pdb=" N PHE C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 181 Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 199 through 229 removed outlier: 3.644A pdb=" N ARG C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 removed outlier: 3.801A pdb=" N SER C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.835A pdb=" N PHE D 12 " --> pdb=" O TRP D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 69 Proline residue: D 31 - end of helix removed outlier: 3.762A pdb=" N HIS D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 50 Processing helix chain 'a' and resid 70 through 75 Processing helix chain 'a' and resid 92 through 100 removed outlier: 3.951A pdb=" N TYR a 100 " --> pdb=" O ASN a 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 116 removed outlier: 3.794A pdb=" N ALA a 116 " --> pdb=" O ALA a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 129 Processing helix chain 'a' and resid 130 through 141 removed outlier: 3.863A pdb=" N VAL a 137 " --> pdb=" O GLN a 133 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA a 138 " --> pdb=" O GLN a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 144 No H-bonds generated for 'chain 'a' and resid 142 through 144' Processing helix chain 'a' and resid 160 through 177 removed outlier: 3.868A pdb=" N GLN a 177 " --> pdb=" O GLN a 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 17 removed outlier: 3.604A pdb=" N PHE b 7 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS b 17 " --> pdb=" O VAL b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 40 removed outlier: 4.046A pdb=" N ALA b 22 " --> pdb=" O SER b 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN b 23 " --> pdb=" O ALA b 19 " (cutoff:3.500A) Proline residue: b 24 - end of helix removed outlier: 3.756A pdb=" N PHE b 35 " --> pdb=" O VAL b 31 " (cutoff:3.500A) Proline residue: b 36 - end of helix Processing helix chain 'b' and resid 42 through 66 Proline residue: b 51 - end of helix Processing helix chain 'b' and resid 67 through 69 No H-bonds generated for 'chain 'b' and resid 67 through 69' Processing helix chain 'b' and resid 70 through 77 removed outlier: 3.708A pdb=" N LEU b 74 " --> pdb=" O PHE b 70 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN b 75 " --> pdb=" O ARG b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 84 removed outlier: 3.991A pdb=" N GLN b 81 " --> pdb=" O GLY b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 119 removed outlier: 3.640A pdb=" N VAL b 92 " --> pdb=" O PRO b 88 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU b 106 " --> pdb=" O MET b 102 " (cutoff:3.500A) Proline residue: b 107 - end of helix Proline residue: b 113 - end of helix Processing helix chain 'b' and resid 122 through 151 Proline residue: b 138 - end of helix Proline residue: b 146 - end of helix Processing helix chain 'b' and resid 158 through 185 removed outlier: 4.087A pdb=" N SER b 162 " --> pdb=" O GLY b 158 " (cutoff:3.500A) Proline residue: b 167 - end of helix Proline residue: b 171 - end of helix removed outlier: 3.574A pdb=" N MET b 185 " --> pdb=" O ASP b 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 220 Proline residue: b 208 - end of helix removed outlier: 4.409A pdb=" N ALA b 213 " --> pdb=" O PHE b 209 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE b 219 " --> pdb=" O LEU b 215 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN b 220 " --> pdb=" O ARG b 216 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 9 Processing helix chain 'c' and resid 10 through 41 Proline residue: c 23 - end of helix Processing helix chain 'c' and resid 50 through 54 removed outlier: 3.600A pdb=" N SER c 53 " --> pdb=" O GLN c 50 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR c 54 " --> pdb=" O GLY c 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 50 through 54' Processing helix chain 'c' and resid 55 through 83 removed outlier: 3.956A pdb=" N LEU c 59 " --> pdb=" O ARG c 55 " (cutoff:3.500A) Proline residue: c 62 - end of helix removed outlier: 3.540A pdb=" N TRP c 66 " --> pdb=" O PRO c 62 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER c 67 " --> pdb=" O ALA c 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR c 71 " --> pdb=" O SER c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 86 through 120 removed outlier: 3.642A pdb=" N ASN c 90 " --> pdb=" O MET c 86 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA c 94 " --> pdb=" O ASN c 90 " (cutoff:3.500A) Proline residue: c 98 - end of helix Proline residue: c 117 - end of helix Processing helix chain 'c' and resid 126 through 149 removed outlier: 3.710A pdb=" N PHE c 149 " --> pdb=" O LEU c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 151 through 185 Proline residue: c 171 - end of helix Processing helix chain 'c' and resid 198 through 229 removed outlier: 3.934A pdb=" N LEU c 202 " --> pdb=" O MET c 198 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 242 removed outlier: 3.967A pdb=" N SER c 236 " --> pdb=" O ARG c 232 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 12 removed outlier: 3.949A pdb=" N PHE d 12 " --> pdb=" O TRP d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 69 removed outlier: 4.401A pdb=" N VAL d 21 " --> pdb=" O TYR d 17 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP d 22 " --> pdb=" O ALA d 18 " (cutoff:3.500A) Proline residue: d 31 - end of helix Processing helix chain 'E' and resid 3 through 32 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 150 through 155 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 26 removed outlier: 6.807A pdb=" N LEU A 18 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLU A 12 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N SER A 20 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 10 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU A 22 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 4 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 9 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA A 57 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.256A pdb=" N LEU A 79 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASP A 153 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE A 81 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TRP A 150 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N THR A 184 " --> pdb=" O TRP A 150 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 152 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 199 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 17 through 22 removed outlier: 5.871A pdb=" N SER a 20 " --> pdb=" O CYS a 11 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N CYS a 11 " --> pdb=" O SER a 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU a 22 " --> pdb=" O LEU a 9 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU a 4 " --> pdb=" O LEU a 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 17 through 22 removed outlier: 5.871A pdb=" N SER a 20 " --> pdb=" O CYS a 11 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N CYS a 11 " --> pdb=" O SER a 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU a 22 " --> pdb=" O LEU a 9 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU a 9 " --> pdb=" O ALA a 57 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA a 57 " --> pdb=" O LEU a 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 32 through 34 Processing sheet with id=AA6, first strand: chain 'a' and resid 78 through 81 removed outlier: 6.204A pdb=" N LEU a 79 " --> pdb=" O ILE a 151 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP a 153 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE a 81 " --> pdb=" O ASP a 153 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TRP a 150 " --> pdb=" O ILE a 182 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR a 184 " --> pdb=" O TRP a 150 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU a 152 " --> pdb=" O THR a 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AA8, first strand: chain 'E' and resid 37 through 38 removed outlier: 8.447A pdb=" N GLY E 108 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA E 128 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL E 110 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL E 126 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN E 112 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ILE E 121 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP E 92 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA E 123 " --> pdb=" O ASP E 92 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER E 94 " --> pdb=" O ALA E 123 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU E 125 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N GLU E 96 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 10.921A pdb=" N LEU E 127 " --> pdb=" O GLU E 96 " (cutoff:3.500A) 779 hydrogen bonds defined for protein. 2301 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: 1.97 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1969 1.32 - 1.45: 3561 1.45 - 1.57: 7340 1.57 - 1.70: 0 1.70 - 1.83: 119 Bond restraints: 12989 Sorted by residual: bond pdb=" CA HIS B 17 " pdb=" C HIS B 17 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.23e-02 6.61e+03 2.01e+01 bond pdb=" C ILE c 22 " pdb=" N PRO c 23 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 6.01e+00 bond pdb=" C HIS B 17 " pdb=" O HIS B 17 " ideal model delta sigma weight residual 1.236 1.206 0.030 1.22e-02 6.72e+03 5.93e+00 bond pdb=" CG1 ILE b 217 " pdb=" CD1 ILE b 217 " ideal model delta sigma weight residual 1.513 1.420 0.093 3.90e-02 6.57e+02 5.65e+00 bond pdb=" CA GLU A 12 " pdb=" CB GLU A 12 " ideal model delta sigma weight residual 1.528 1.562 -0.034 1.51e-02 4.39e+03 5.02e+00 ... (remaining 12984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 17127 3.01 - 6.02: 479 6.02 - 9.03: 81 9.03 - 12.05: 16 12.05 - 15.06: 8 Bond angle restraints: 17711 Sorted by residual: angle pdb=" N HIS B 17 " pdb=" CA HIS B 17 " pdb=" C HIS B 17 " ideal model delta sigma weight residual 108.73 96.94 11.79 1.63e+00 3.76e-01 5.23e+01 angle pdb=" CA GLN c 16 " pdb=" CB GLN c 16 " pdb=" CG GLN c 16 " ideal model delta sigma weight residual 114.10 127.84 -13.74 2.00e+00 2.50e-01 4.72e+01 angle pdb=" N GLN c 16 " pdb=" CA GLN c 16 " pdb=" CB GLN c 16 " ideal model delta sigma weight residual 110.39 120.02 -9.63 1.66e+00 3.63e-01 3.37e+01 angle pdb=" C ASN E 33 " pdb=" N ILE E 34 " pdb=" CA ILE E 34 " ideal model delta sigma weight residual 121.97 132.11 -10.14 1.80e+00 3.09e-01 3.17e+01 angle pdb=" CA MET d 27 " pdb=" CB MET d 27 " pdb=" CG MET d 27 " ideal model delta sigma weight residual 114.10 124.43 -10.33 2.00e+00 2.50e-01 2.67e+01 ... (remaining 17706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6641 17.99 - 35.97: 790 35.97 - 53.96: 150 53.96 - 71.94: 24 71.94 - 89.93: 6 Dihedral angle restraints: 7611 sinusoidal: 2977 harmonic: 4634 Sorted by residual: dihedral pdb=" CA ASN C 181 " pdb=" C ASN C 181 " pdb=" N THR C 182 " pdb=" CA THR C 182 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA TYR E 85 " pdb=" C TYR E 85 " pdb=" N ASP E 86 " pdb=" CA ASP E 86 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA LEU a 110 " pdb=" C LEU a 110 " pdb=" N GLU a 111 " pdb=" CA GLU a 111 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 7608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1686 0.072 - 0.145: 329 0.145 - 0.217: 38 0.217 - 0.290: 5 0.290 - 0.362: 1 Chirality restraints: 2059 Sorted by residual: chirality pdb=" CG LEU a 52 " pdb=" CB LEU a 52 " pdb=" CD1 LEU a 52 " pdb=" CD2 LEU a 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CG LEU a 45 " pdb=" CB LEU a 45 " pdb=" CD1 LEU a 45 " pdb=" CD2 LEU a 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA TRP B 55 " pdb=" N TRP B 55 " pdb=" C TRP B 55 " pdb=" CB TRP B 55 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2056 not shown) Planarity restraints: 2203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE b 35 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO b 36 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO b 36 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO b 36 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 89 " 0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO B 90 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN a 27 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" CG ASN a 27 " -0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN a 27 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN a 27 " 0.022 2.00e-02 2.50e+03 ... (remaining 2200 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2846 2.79 - 3.32: 12231 3.32 - 3.85: 21279 3.85 - 4.37: 24130 4.37 - 4.90: 41299 Nonbonded interactions: 101785 Sorted by model distance: nonbonded pdb=" O VAL B 159 " pdb=" OG SER B 162 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR a 92 " pdb=" OE1 GLU a 95 " model vdw 2.297 3.040 nonbonded pdb=" OD1 ASP E 86 " pdb=" N GLY E 89 " model vdw 2.330 3.120 nonbonded pdb=" OH TYR c 54 " pdb=" O SER c 193 " model vdw 2.333 3.040 nonbonded pdb=" OH TYR C 54 " pdb=" O SER C 193 " model vdw 2.338 3.040 ... (remaining 101780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 : 0.006 0.093 12989 Z= 0.277 Angle : 1.203 15.058 17711 Z= 0.605 Chirality : 0.057 0.362 2059 Planarity : 0.010 0.110 2203 Dihedral : 15.729 89.929 4619 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 0.61 % Allowed : 15.37 % Favored : 84.02 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.20), residues: 1602 helix: -0.06 (0.15), residues: 999 sheet: 0.39 (0.60), residues: 81 loop : -0.88 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG a 54 TYR 0.042 0.004 TYR c 58 PHE 0.038 0.003 PHE C 43 TRP 0.052 0.003 TRP c 123 HIS 0.019 0.002 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00635 (12989) covalent geometry : angle 1.20272 (17711) hydrogen bonds : bond 0.12369 ( 774) hydrogen bonds : angle 6.34996 ( 2301) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.6900 (t-170) REVERT: C 96 MET cc_start: 0.7059 (mtm) cc_final: 0.6787 (mtm) REVERT: C 195 ASP cc_start: 0.7587 (t0) cc_final: 0.7364 (p0) REVERT: C 207 PHE cc_start: 0.8135 (t80) cc_final: 0.7797 (t80) REVERT: D 53 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8295 (tm-30) REVERT: b 156 ARG cc_start: 0.6303 (ttm-80) cc_final: 0.5864 (ttt90) REVERT: d 59 ARG cc_start: 0.7872 (mmp80) cc_final: 0.7348 (ttp80) outliers start: 8 outliers final: 3 residues processed: 261 average time/residue: 0.1045 time to fit residues: 38.5636 Evaluate side-chains 220 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 216 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain c residue 147 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 133 GLN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 185 GLN D 38 HIS D 66 GLN a 101 HIS c 50 GLN c 169 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.167965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135962 restraints weight = 17586.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.136069 restraints weight = 14536.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136750 restraints weight = 12455.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137341 restraints weight = 10673.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137563 restraints weight = 9450.084| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12989 Z= 0.163 Angle : 0.712 7.092 17711 Z= 0.355 Chirality : 0.043 0.170 2059 Planarity : 0.007 0.087 2203 Dihedral : 5.707 53.958 1756 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 3.27 % Allowed : 14.23 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.20), residues: 1602 helix: 0.80 (0.16), residues: 1021 sheet: 0.62 (0.60), residues: 81 loop : -0.81 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 59 TYR 0.017 0.002 TYR E 154 PHE 0.013 0.001 PHE b 175 TRP 0.035 0.002 TRP C 66 HIS 0.008 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00396 (12989) covalent geometry : angle 0.71236 (17711) hydrogen bonds : bond 0.03916 ( 774) hydrogen bonds : angle 4.84823 ( 2301) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6514 (t-170) REVERT: C 96 MET cc_start: 0.7491 (mtm) cc_final: 0.6879 (mtm) REVERT: C 207 PHE cc_start: 0.8257 (t80) cc_final: 0.7965 (t80) REVERT: D 53 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8273 (tm-30) REVERT: a 88 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8202 (mmtm) REVERT: b 156 ARG cc_start: 0.6361 (ttm-80) cc_final: 0.5816 (ttt90) REVERT: c 49 GLN cc_start: 0.6926 (mp10) cc_final: 0.6596 (mp10) REVERT: c 50 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6605 (mm-40) REVERT: d 59 ARG cc_start: 0.7872 (mmp80) cc_final: 0.7298 (ttp80) REVERT: E 65 MET cc_start: 0.6622 (mtp) cc_final: 0.6347 (mtm) outliers start: 43 outliers final: 22 residues processed: 272 average time/residue: 0.0917 time to fit residues: 36.3115 Evaluate side-chains 238 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain b residue 104 THR Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain c residue 17 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 50 GLN Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 147 HIS Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 139 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 15 optimal weight: 0.0670 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 35 optimal weight: 0.0020 chunk 150 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.8132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN a 27 ASN ** c 90 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.164903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131765 restraints weight = 17797.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132804 restraints weight = 12339.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133378 restraints weight = 9703.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.133608 restraints weight = 8844.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133882 restraints weight = 8738.771| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12989 Z= 0.164 Angle : 0.687 7.697 17711 Z= 0.338 Chirality : 0.043 0.159 2059 Planarity : 0.006 0.078 2203 Dihedral : 5.357 53.130 1754 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.06 % Favored : 97.88 % Rotamer: Outliers : 3.35 % Allowed : 15.98 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.21), residues: 1602 helix: 1.23 (0.16), residues: 1024 sheet: 0.69 (0.60), residues: 81 loop : -0.62 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 59 TYR 0.012 0.001 TYR A 100 PHE 0.022 0.001 PHE c 137 TRP 0.037 0.002 TRP C 66 HIS 0.005 0.001 HIS a 174 Details of bonding type rmsd covalent geometry : bond 0.00410 (12989) covalent geometry : angle 0.68689 (17711) hydrogen bonds : bond 0.03710 ( 774) hydrogen bonds : angle 4.64360 ( 2301) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6610 (t-170) REVERT: B 200 LEU cc_start: 0.8725 (tp) cc_final: 0.8472 (tt) REVERT: C 21 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8112 (t80) REVERT: C 96 MET cc_start: 0.7596 (mtm) cc_final: 0.6969 (mtm) REVERT: C 181 ASN cc_start: 0.8247 (m110) cc_final: 0.7670 (t0) REVERT: C 185 GLN cc_start: 0.8413 (tp-100) cc_final: 0.8176 (tp40) REVERT: C 207 PHE cc_start: 0.8359 (t80) cc_final: 0.8048 (t80) REVERT: D 53 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8291 (tm-30) REVERT: a 94 LEU cc_start: 0.8138 (tt) cc_final: 0.7906 (tt) REVERT: a 127 ASN cc_start: 0.7879 (p0) cc_final: 0.7545 (p0) REVERT: b 156 ARG cc_start: 0.6336 (ttm-80) cc_final: 0.5792 (ttt90) REVERT: d 27 MET cc_start: 0.6204 (tpt) cc_final: 0.5858 (tpt) REVERT: E 65 MET cc_start: 0.6538 (mtp) cc_final: 0.6092 (mtm) outliers start: 44 outliers final: 26 residues processed: 256 average time/residue: 0.0873 time to fit residues: 32.3898 Evaluate side-chains 239 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 147 HIS Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 238 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 63 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.162487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.130101 restraints weight = 17838.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129523 restraints weight = 16151.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129410 restraints weight = 14627.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130260 restraints weight = 13656.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130408 restraints weight = 11405.152| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12989 Z= 0.167 Angle : 0.672 7.567 17711 Z= 0.329 Chirality : 0.043 0.189 2059 Planarity : 0.006 0.071 2203 Dihedral : 5.173 51.969 1754 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 3.58 % Allowed : 17.12 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1602 helix: 1.52 (0.16), residues: 1022 sheet: 0.58 (0.61), residues: 81 loop : -0.55 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.013 0.002 TYR C 15 PHE 0.025 0.001 PHE c 137 TRP 0.047 0.002 TRP c 234 HIS 0.005 0.001 HIS a 174 Details of bonding type rmsd covalent geometry : bond 0.00417 (12989) covalent geometry : angle 0.67212 (17711) hydrogen bonds : bond 0.03555 ( 774) hydrogen bonds : angle 4.50953 ( 2301) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6719 (t-170) REVERT: B 200 LEU cc_start: 0.8731 (tp) cc_final: 0.8519 (tt) REVERT: C 21 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8030 (t80) REVERT: C 96 MET cc_start: 0.7758 (mtm) cc_final: 0.7171 (mtm) REVERT: C 198 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8198 (ttm) REVERT: C 207 PHE cc_start: 0.8462 (t80) cc_final: 0.8086 (t80) REVERT: C 229 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8112 (mm-30) REVERT: D 53 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8321 (tm-30) REVERT: a 127 ASN cc_start: 0.8144 (p0) cc_final: 0.7770 (p0) REVERT: a 154 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: b 137 THR cc_start: 0.8959 (p) cc_final: 0.8723 (p) REVERT: b 156 ARG cc_start: 0.6555 (ttm-80) cc_final: 0.5861 (ttt90) REVERT: c 85 GLN cc_start: 0.7164 (mt0) cc_final: 0.6722 (mm110) REVERT: E 65 MET cc_start: 0.6760 (mtp) cc_final: 0.6342 (mtm) outliers start: 47 outliers final: 32 residues processed: 258 average time/residue: 0.0923 time to fit residues: 34.7439 Evaluate side-chains 252 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 168 VAL Chi-restraints excluded: chain c residue 217 THR Chi-restraints excluded: chain c residue 238 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 150 optimal weight: 40.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 185 GLN D 43 HIS a 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.156428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124793 restraints weight = 18226.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123762 restraints weight = 19853.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124609 restraints weight = 18767.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124798 restraints weight = 16089.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124904 restraints weight = 13922.463| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12989 Z= 0.221 Angle : 0.732 8.377 17711 Z= 0.357 Chirality : 0.045 0.156 2059 Planarity : 0.006 0.070 2203 Dihedral : 5.047 49.449 1752 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 5.10 % Allowed : 18.72 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.21), residues: 1602 helix: 1.41 (0.16), residues: 1050 sheet: 0.43 (0.59), residues: 83 loop : -0.85 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 59 TYR 0.017 0.002 TYR c 139 PHE 0.014 0.002 PHE B 7 TRP 0.051 0.002 TRP c 234 HIS 0.007 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00548 (12989) covalent geometry : angle 0.73224 (17711) hydrogen bonds : bond 0.03877 ( 774) hydrogen bonds : angle 4.61423 ( 2301) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 232 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6958 (t-170) REVERT: B 200 LEU cc_start: 0.8847 (tp) cc_final: 0.8618 (tt) REVERT: C 21 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.7977 (t80) REVERT: C 96 MET cc_start: 0.7754 (mtm) cc_final: 0.7185 (mtm) REVERT: C 198 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8029 (ttm) REVERT: C 207 PHE cc_start: 0.8371 (t80) cc_final: 0.8059 (t80) REVERT: D 27 MET cc_start: 0.6472 (tpp) cc_final: 0.6156 (tpp) REVERT: D 53 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8301 (tm-30) REVERT: a 127 ASN cc_start: 0.8080 (p0) cc_final: 0.7692 (p0) REVERT: b 106 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7775 (tp) REVERT: b 150 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7787 (mp) REVERT: b 156 ARG cc_start: 0.6701 (ttm-80) cc_final: 0.5680 (ttt-90) REVERT: c 85 GLN cc_start: 0.7511 (mt0) cc_final: 0.7031 (mm110) REVERT: E 16 LEU cc_start: 0.8270 (mm) cc_final: 0.7985 (mm) REVERT: E 65 MET cc_start: 0.6823 (mtp) cc_final: 0.6517 (mtm) REVERT: E 143 MET cc_start: -0.0083 (OUTLIER) cc_final: -0.1026 (mpp) outliers start: 67 outliers final: 42 residues processed: 278 average time/residue: 0.0898 time to fit residues: 36.5198 Evaluate side-chains 265 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 38 SER Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 217 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 143 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 77 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.160914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122937 restraints weight = 17928.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125559 restraints weight = 11767.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127250 restraints weight = 8898.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.128407 restraints weight = 7469.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128985 restraints weight = 6679.569| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12989 Z= 0.144 Angle : 0.653 8.208 17711 Z= 0.318 Chirality : 0.042 0.219 2059 Planarity : 0.005 0.064 2203 Dihedral : 4.855 49.507 1752 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 3.88 % Allowed : 20.55 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.21), residues: 1602 helix: 1.76 (0.16), residues: 1032 sheet: 0.42 (0.59), residues: 83 loop : -0.64 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 48 TYR 0.016 0.002 TYR C 15 PHE 0.015 0.001 PHE C 43 TRP 0.039 0.002 TRP c 234 HIS 0.004 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00356 (12989) covalent geometry : angle 0.65336 (17711) hydrogen bonds : bond 0.03440 ( 774) hydrogen bonds : angle 4.37046 ( 2301) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8898 (p) cc_final: 0.8637 (t) REVERT: B 17 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6857 (t-170) REVERT: B 200 LEU cc_start: 0.8814 (tp) cc_final: 0.8581 (tt) REVERT: C 21 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8043 (t80) REVERT: C 74 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7396 (mtp) REVERT: C 96 MET cc_start: 0.7724 (mtm) cc_final: 0.7185 (mtm) REVERT: C 207 PHE cc_start: 0.8320 (t80) cc_final: 0.8037 (t80) REVERT: C 229 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7938 (mm-30) REVERT: D 53 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8241 (tm-30) REVERT: a 97 LEU cc_start: 0.8961 (tp) cc_final: 0.8750 (tp) REVERT: a 127 ASN cc_start: 0.7900 (p0) cc_final: 0.7483 (p0) REVERT: b 106 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7782 (tp) REVERT: b 150 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7869 (mp) REVERT: b 156 ARG cc_start: 0.6746 (ttm-80) cc_final: 0.5933 (ttt90) REVERT: c 21 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8014 (t80) REVERT: c 85 GLN cc_start: 0.7370 (mt0) cc_final: 0.6960 (mm110) REVERT: E 16 LEU cc_start: 0.8281 (mm) cc_final: 0.8018 (mm) REVERT: E 143 MET cc_start: -0.0325 (OUTLIER) cc_final: -0.0752 (mpp) outliers start: 51 outliers final: 28 residues processed: 271 average time/residue: 0.0891 time to fit residues: 35.6953 Evaluate side-chains 252 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 143 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 102 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.161891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126022 restraints weight = 17752.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128158 restraints weight = 12383.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129670 restraints weight = 9798.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130375 restraints weight = 8397.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130893 restraints weight = 7658.710| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12989 Z= 0.139 Angle : 0.669 8.223 17711 Z= 0.325 Chirality : 0.042 0.230 2059 Planarity : 0.005 0.063 2203 Dihedral : 4.752 48.841 1752 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.00 % Favored : 97.94 % Rotamer: Outliers : 3.12 % Allowed : 21.92 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.21), residues: 1602 helix: 1.80 (0.16), residues: 1044 sheet: 0.41 (0.59), residues: 83 loop : -0.67 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 48 TYR 0.015 0.001 TYR C 58 PHE 0.015 0.001 PHE C 43 TRP 0.060 0.002 TRP C 234 HIS 0.003 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00341 (12989) covalent geometry : angle 0.66869 (17711) hydrogen bonds : bond 0.03301 ( 774) hydrogen bonds : angle 4.25900 ( 2301) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8923 (p) cc_final: 0.8661 (t) REVERT: B 17 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6865 (t-170) REVERT: C 21 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8113 (t80) REVERT: C 74 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7385 (mtp) REVERT: C 96 MET cc_start: 0.7807 (mtm) cc_final: 0.7244 (mtm) REVERT: C 198 MET cc_start: 0.8414 (tmm) cc_final: 0.8053 (tmm) REVERT: C 207 PHE cc_start: 0.8268 (t80) cc_final: 0.8004 (t80) REVERT: C 229 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8033 (mm-30) REVERT: D 53 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8264 (tm-30) REVERT: a 74 TYR cc_start: 0.8472 (t80) cc_final: 0.8236 (t80) REVERT: a 97 LEU cc_start: 0.8917 (tp) cc_final: 0.8715 (tp) REVERT: a 127 ASN cc_start: 0.7891 (p0) cc_final: 0.7493 (p0) REVERT: a 154 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: b 106 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7683 (tp) REVERT: b 150 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7897 (mp) REVERT: b 156 ARG cc_start: 0.6725 (ttm-80) cc_final: 0.5767 (ttt-90) REVERT: c 85 GLN cc_start: 0.7262 (mt0) cc_final: 0.6872 (mm110) REVERT: E 16 LEU cc_start: 0.8379 (mm) cc_final: 0.8071 (mm) outliers start: 41 outliers final: 26 residues processed: 255 average time/residue: 0.1116 time to fit residues: 42.0003 Evaluate side-chains 242 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 108 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 187 GLN ** E 120 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 = 0.3961 r_free = 0.3961 target = 0.162858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129978 restraints weight = 17836.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129885 restraints weight = 17046.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132004 restraints weight = 13733.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132321 restraints weight = 10179.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132219 restraints weight = 9331.554| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12989 Z= 0.132 Angle : 0.663 9.345 17711 Z= 0.321 Chirality : 0.041 0.248 2059 Planarity : 0.005 0.063 2203 Dihedral : 4.544 48.494 1750 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.00 % Favored : 97.94 % Rotamer: Outliers : 2.97 % Allowed : 22.15 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.21), residues: 1602 helix: 1.84 (0.16), residues: 1058 sheet: 0.37 (0.59), residues: 83 loop : -0.83 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 166 TYR 0.020 0.001 TYR c 58 PHE 0.015 0.001 PHE C 43 TRP 0.074 0.002 TRP C 234 HIS 0.003 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00323 (12989) covalent geometry : angle 0.66328 (17711) hydrogen bonds : bond 0.03229 ( 774) hydrogen bonds : angle 4.20926 ( 2301) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8959 (p) cc_final: 0.8688 (t) REVERT: B 17 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6843 (t-170) REVERT: C 15 TYR cc_start: 0.9028 (t80) cc_final: 0.8685 (t80) REVERT: C 21 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8130 (t80) REVERT: C 74 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7378 (mtp) REVERT: C 96 MET cc_start: 0.7859 (mtm) cc_final: 0.7290 (mtm) REVERT: C 198 MET cc_start: 0.8473 (tmm) cc_final: 0.8094 (tmm) REVERT: C 207 PHE cc_start: 0.8278 (t80) cc_final: 0.7957 (t80) REVERT: C 229 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8034 (mm-30) REVERT: D 53 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8274 (tm-30) REVERT: a 74 TYR cc_start: 0.8492 (t80) cc_final: 0.8228 (t80) REVERT: a 97 LEU cc_start: 0.8850 (tp) cc_final: 0.8601 (tp) REVERT: a 127 ASN cc_start: 0.7952 (p0) cc_final: 0.7550 (p0) REVERT: a 154 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: b 106 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7613 (tp) REVERT: b 150 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7852 (mp) REVERT: b 156 ARG cc_start: 0.6692 (ttm-80) cc_final: 0.5655 (ttt-90) REVERT: c 21 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7982 (t80) REVERT: c 85 GLN cc_start: 0.7343 (mt0) cc_final: 0.6899 (mm110) REVERT: c 154 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7302 (tt) REVERT: d 10 GLU cc_start: 0.7447 (tp30) cc_final: 0.7185 (tp30) REVERT: E 16 LEU cc_start: 0.8464 (mm) cc_final: 0.8167 (mm) outliers start: 39 outliers final: 26 residues processed: 246 average time/residue: 0.1175 time to fit residues: 42.4070 Evaluate side-chains 244 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.161193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130299 restraints weight = 17920.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129643 restraints weight = 19396.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130926 restraints weight = 17236.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131088 restraints weight = 13908.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.131303 restraints weight = 12617.688| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12989 Z= 0.150 Angle : 0.679 9.061 17711 Z= 0.328 Chirality : 0.042 0.246 2059 Planarity : 0.005 0.062 2203 Dihedral : 4.513 47.855 1750 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 3.12 % Allowed : 22.22 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.21), residues: 1602 helix: 1.95 (0.16), residues: 1034 sheet: -0.06 (0.54), residues: 93 loop : -0.50 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 166 TYR 0.017 0.002 TYR C 48 PHE 0.016 0.001 PHE C 43 TRP 0.075 0.002 TRP C 234 HIS 0.004 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00372 (12989) covalent geometry : angle 0.67928 (17711) hydrogen bonds : bond 0.03329 ( 774) hydrogen bonds : angle 4.21813 ( 2301) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8886 (p) cc_final: 0.8637 (t) REVERT: B 17 HIS cc_start: 0.7216 (OUTLIER) cc_final: 0.6861 (t-170) REVERT: C 21 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8087 (t80) REVERT: C 54 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6786 (t80) REVERT: C 74 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7350 (mtp) REVERT: C 96 MET cc_start: 0.7884 (mtm) cc_final: 0.7340 (mtm) REVERT: C 207 PHE cc_start: 0.8110 (t80) cc_final: 0.7851 (t80) REVERT: D 54 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.8046 (tpp80) REVERT: a 97 LEU cc_start: 0.8949 (tp) cc_final: 0.8732 (tp) REVERT: a 127 ASN cc_start: 0.7764 (p0) cc_final: 0.7328 (p0) REVERT: a 154 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: b 106 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7734 (tp) REVERT: b 140 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7037 (tt) REVERT: b 150 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7875 (mp) REVERT: c 154 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7529 (tt) REVERT: d 10 GLU cc_start: 0.7401 (tp30) cc_final: 0.7130 (tp30) REVERT: E 16 LEU cc_start: 0.8321 (mm) cc_final: 0.8119 (pp) REVERT: E 65 MET cc_start: 0.6407 (mtm) cc_final: 0.6113 (ptp) outliers start: 41 outliers final: 27 residues processed: 245 average time/residue: 0.1085 time to fit residues: 39.4108 Evaluate side-chains 247 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 91 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 112 optimal weight: 0.0370 chunk 21 optimal weight: 0.3980 chunk 146 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.158963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127115 restraints weight = 18167.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126812 restraints weight = 20662.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127921 restraints weight = 17614.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128073 restraints weight = 14274.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128311 restraints weight = 12695.412| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12989 Z= 0.181 Angle : 0.720 9.573 17711 Z= 0.347 Chirality : 0.043 0.234 2059 Planarity : 0.005 0.061 2203 Dihedral : 4.583 47.260 1750 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 3.50 % Allowed : 22.37 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.21), residues: 1602 helix: 2.04 (0.16), residues: 1014 sheet: -0.15 (0.55), residues: 93 loop : -0.38 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 166 TYR 0.017 0.002 TYR C 58 PHE 0.021 0.001 PHE d 5 TRP 0.060 0.002 TRP C 234 HIS 0.005 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00450 (12989) covalent geometry : angle 0.72027 (17711) hydrogen bonds : bond 0.03609 ( 774) hydrogen bonds : angle 4.33472 ( 2301) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6901 (pp20) REVERT: A 89 THR cc_start: 0.8934 (p) cc_final: 0.8677 (t) REVERT: B 17 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6905 (t-170) REVERT: C 21 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8007 (t80) REVERT: C 74 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7387 (mtp) REVERT: C 96 MET cc_start: 0.7863 (mtm) cc_final: 0.7356 (mtm) REVERT: C 207 PHE cc_start: 0.8150 (t80) cc_final: 0.7897 (t80) REVERT: D 53 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8334 (tm-30) REVERT: D 54 ARG cc_start: 0.8460 (tpp-160) cc_final: 0.8099 (tpp80) REVERT: a 3 MET cc_start: 0.6950 (pmm) cc_final: 0.5998 (ptp) REVERT: a 97 LEU cc_start: 0.9015 (tp) cc_final: 0.8784 (tp) REVERT: a 127 ASN cc_start: 0.7807 (p0) cc_final: 0.7344 (p0) REVERT: a 154 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: b 106 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7740 (tp) REVERT: b 117 MET cc_start: 0.7288 (ttm) cc_final: 0.7052 (ttt) REVERT: b 140 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7121 (tt) REVERT: b 150 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7891 (mp) REVERT: c 21 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8022 (t80) REVERT: d 10 GLU cc_start: 0.7452 (tp30) cc_final: 0.7147 (tp30) REVERT: E 16 LEU cc_start: 0.8332 (mm) cc_final: 0.8022 (mm) REVERT: E 65 MET cc_start: 0.6406 (mtm) cc_final: 0.6106 (ptp) outliers start: 46 outliers final: 29 residues processed: 255 average time/residue: 0.1137 time to fit residues: 42.9204 Evaluate side-chains 254 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 156 optimal weight: 40.0000 chunk 155 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.160216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128627 restraints weight = 18120.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128269 restraints weight = 18474.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129555 restraints weight = 16541.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129781 restraints weight = 12797.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129846 restraints weight = 11809.584| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12989 Z= 0.155 Angle : 0.690 8.949 17711 Z= 0.334 Chirality : 0.042 0.191 2059 Planarity : 0.005 0.062 2203 Dihedral : 4.538 47.248 1750 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 2.89 % Allowed : 23.59 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.21), residues: 1602 helix: 2.09 (0.16), residues: 1014 sheet: -0.16 (0.55), residues: 93 loop : -0.30 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 128 TYR 0.017 0.001 TYR C 48 PHE 0.022 0.001 PHE d 5 TRP 0.050 0.002 TRP C 66 HIS 0.004 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00385 (12989) covalent geometry : angle 0.69017 (17711) hydrogen bonds : bond 0.03390 ( 774) hydrogen bonds : angle 4.26524 ( 2301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1823.33 seconds wall clock time: 32 minutes 14.61 seconds (1934.61 seconds total)