Starting phenix.real_space_refine on Wed May 14 23:07:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce8_16601/05_2025/8ce8_16601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce8_16601/05_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_16601/05_2025/8ce8_16601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce8_16601/05_2025/8ce8_16601.map" model { file = "/net/cci-nas-00/data/ceres_data/8ce8_16601/05_2025/8ce8_16601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce8_16601/05_2025/8ce8_16601.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.63, per 1000 atoms: 0.60 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: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.30 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: 3.47 Time building geometry restraints manager: 3.64 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: 0.660 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.790 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- 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 : 6.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (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 TRP 0.052 0.003 TRP c 123 HIS 0.019 0.002 HIS D 38 PHE 0.038 0.003 PHE C 43 TYR 0.042 0.004 TYR c 58 ARG 0.018 0.001 ARG a 54 Details of bonding type rmsd hydrogen bonds : bond 0.12369 ( 774) hydrogen bonds : angle 6.34996 ( 2301) covalent geometry : bond 0.00635 (12989) covalent geometry : angle 1.20272 (17711) *********************** 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 : 1.379 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: 0.2588 time to fit residues: 95.1962 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 : 1.379 ------------------------------------------------------------------------------- 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 132 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN D 38 HIS D 66 GLN a 101 HIS c 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.163336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126488 restraints weight = 17766.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129251 restraints weight = 11383.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130774 restraints weight = 8502.600| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12989 Z= 0.211 Angle : 0.750 7.410 17711 Z= 0.376 Chirality : 0.044 0.172 2059 Planarity : 0.007 0.089 2203 Dihedral : 5.713 53.778 1756 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 3.88 % Allowed : 14.38 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1602 helix: 0.77 (0.16), residues: 1019 sheet: 0.56 (0.59), residues: 81 loop : -0.80 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 66 HIS 0.007 0.002 HIS D 38 PHE 0.014 0.002 PHE b 175 TYR 0.016 0.002 TYR E 154 ARG 0.007 0.001 ARG D 59 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 774) hydrogen bonds : angle 4.85732 ( 2301) covalent geometry : bond 0.00518 (12989) covalent geometry : angle 0.74965 (17711) *********************** 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 296 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.6645 (ptp) cc_final: 0.6438 (mtp) REVERT: B 17 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6592 (t-170) REVERT: C 21 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7971 (t80) REVERT: C 96 MET cc_start: 0.7572 (mtm) cc_final: 0.7019 (mtm) REVERT: C 207 PHE cc_start: 0.8330 (t80) cc_final: 0.8068 (t80) REVERT: D 27 MET cc_start: 0.6906 (tmm) cc_final: 0.6563 (tpp) REVERT: D 53 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8328 (tm-30) REVERT: a 88 LYS cc_start: 0.8548 (mmtm) cc_final: 0.8319 (mmtm) REVERT: b 156 ARG cc_start: 0.6471 (ttm-80) cc_final: 0.5850 (ttt90) outliers start: 51 outliers final: 29 residues processed: 277 average time/residue: 0.2427 time to fit residues: 96.6115 Evaluate side-chains 243 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU 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 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 a residue 124 ILE Chi-restraints excluded: chain b residue 38 SER Chi-restraints excluded: chain b residue 104 THR Chi-restraints excluded: chain b residue 217 ILE 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 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 217 THR 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 81 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 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 = 0.164616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133184 restraints weight = 17759.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132769 restraints weight = 12557.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131750 restraints weight = 11365.236| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12989 Z= 0.150 Angle : 0.674 7.547 17711 Z= 0.332 Chirality : 0.042 0.190 2059 Planarity : 0.006 0.076 2203 Dihedral : 5.379 52.800 1754 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.75 % Rotamer: Outliers : 2.97 % Allowed : 17.05 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1602 helix: 1.22 (0.16), residues: 1021 sheet: 0.58 (0.59), residues: 81 loop : -0.64 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 66 HIS 0.004 0.001 HIS a 174 PHE 0.025 0.001 PHE b 3 TYR 0.011 0.002 TYR a 100 ARG 0.003 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 774) hydrogen bonds : angle 4.62361 ( 2301) covalent geometry : bond 0.00371 (12989) covalent geometry : angle 0.67356 (17711) *********************** 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 274 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7111 (OUTLIER) cc_final: 0.6610 (t-170) REVERT: B 200 LEU cc_start: 0.8773 (tp) cc_final: 0.8518 (tt) REVERT: C 21 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8093 (t80) REVERT: C 96 MET cc_start: 0.7573 (mtm) cc_final: 0.6961 (mtm) REVERT: C 181 ASN cc_start: 0.8198 (m110) cc_final: 0.7817 (t0) REVERT: C 185 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8257 (tp40) REVERT: C 207 PHE cc_start: 0.8339 (t80) cc_final: 0.8021 (t80) REVERT: D 53 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8338 (tm-30) REVERT: a 127 ASN cc_start: 0.7845 (p0) cc_final: 0.7502 (p0) REVERT: a 154 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: b 156 ARG cc_start: 0.6345 (ttm-80) cc_final: 0.5803 (ttt90) REVERT: E 143 MET cc_start: 0.0515 (mpp) cc_final: -0.0553 (mtt) outliers start: 39 outliers final: 27 residues processed: 259 average time/residue: 0.2492 time to fit residues: 93.2998 Evaluate side-chains 246 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 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 161 ILE Chi-restraints excluded: chain C residue 182 THR 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 a residue 180 ILE Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 206 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 145 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 238 LEU Chi-restraints excluded: chain E residue 16 LEU 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 0 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 57 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.164768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131747 restraints weight = 17505.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132574 restraints weight = 12130.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133785 restraints weight = 9955.378| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12989 Z= 0.137 Angle : 0.647 9.481 17711 Z= 0.316 Chirality : 0.042 0.148 2059 Planarity : 0.006 0.069 2203 Dihedral : 5.040 52.373 1752 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.75 % Rotamer: Outliers : 3.35 % Allowed : 17.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1602 helix: 1.50 (0.16), residues: 1032 sheet: 0.56 (0.59), residues: 81 loop : -0.63 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP c 234 HIS 0.004 0.001 HIS a 186 PHE 0.014 0.001 PHE b 175 TYR 0.012 0.001 TYR c 58 ARG 0.006 0.000 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 774) hydrogen bonds : angle 4.43286 ( 2301) covalent geometry : bond 0.00336 (12989) covalent geometry : angle 0.64655 (17711) *********************** 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 263 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8586 (mt) REVERT: B 17 HIS cc_start: 0.7114 (OUTLIER) cc_final: 0.6661 (t-170) REVERT: B 200 LEU cc_start: 0.8762 (tp) cc_final: 0.8527 (tt) REVERT: C 21 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8073 (t80) REVERT: C 74 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7157 (mtp) REVERT: C 96 MET cc_start: 0.7647 (mtm) cc_final: 0.7091 (mtm) REVERT: C 198 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8271 (ttm) REVERT: C 207 PHE cc_start: 0.8191 (t80) cc_final: 0.7890 (t80) REVERT: D 27 MET cc_start: 0.5968 (tpp) cc_final: 0.5764 (tpp) REVERT: D 53 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8292 (tm-30) REVERT: a 127 ASN cc_start: 0.7671 (p0) cc_final: 0.7285 (p0) REVERT: a 154 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: b 137 THR cc_start: 0.8915 (p) cc_final: 0.8704 (p) REVERT: b 156 ARG cc_start: 0.6402 (ttm-80) cc_final: 0.5930 (ttt90) REVERT: c 85 GLN cc_start: 0.7087 (mt0) cc_final: 0.6732 (mm110) REVERT: E 143 MET cc_start: 0.0444 (mpp) cc_final: -0.0075 (mtt) outliers start: 44 outliers final: 29 residues processed: 249 average time/residue: 0.2444 time to fit residues: 87.1870 Evaluate side-chains 242 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 29 LEU 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 30 VAL 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 198 MET Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain a residue 18 LEU 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 180 ILE 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 121 THR Chi-restraints excluded: chain c residue 145 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 43 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 154 optimal weight: 40.0000 chunk 63 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 C 185 GLN D 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.163786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132797 restraints weight = 17682.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131916 restraints weight = 19084.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132619 restraints weight = 17721.050| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12989 Z= 0.147 Angle : 0.652 8.062 17711 Z= 0.316 Chirality : 0.042 0.245 2059 Planarity : 0.005 0.066 2203 Dihedral : 4.902 51.284 1752 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 3.65 % Allowed : 17.66 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1602 helix: 1.67 (0.16), residues: 1028 sheet: 0.55 (0.59), residues: 81 loop : -0.64 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP c 234 HIS 0.004 0.001 HIS C 174 PHE 0.015 0.001 PHE b 175 TYR 0.014 0.001 TYR c 58 ARG 0.004 0.000 ARG d 48 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 774) hydrogen bonds : angle 4.38283 ( 2301) covalent geometry : bond 0.00366 (12989) covalent geometry : angle 0.65178 (17711) *********************** 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 274 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.6767 (t-170) REVERT: B 71 ARG cc_start: 0.8328 (tpp80) cc_final: 0.8026 (tpp-160) REVERT: C 21 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.7884 (t80) REVERT: C 66 TRP cc_start: 0.7446 (m100) cc_final: 0.7127 (m100) REVERT: C 74 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7220 (mtp) REVERT: C 198 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8310 (ttm) REVERT: C 207 PHE cc_start: 0.8322 (t80) cc_final: 0.7964 (t80) REVERT: D 27 MET cc_start: 0.6317 (tpp) cc_final: 0.5958 (tpp) REVERT: D 53 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8281 (tm-30) REVERT: a 127 ASN cc_start: 0.7952 (p0) cc_final: 0.7558 (p0) REVERT: a 154 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: b 106 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7652 (tp) REVERT: b 137 THR cc_start: 0.8921 (p) cc_final: 0.8687 (p) REVERT: b 156 ARG cc_start: 0.6608 (ttm-80) cc_final: 0.5699 (ttt-90) REVERT: b 173 LEU cc_start: 0.8599 (tp) cc_final: 0.8279 (tp) REVERT: c 85 GLN cc_start: 0.7094 (mt0) cc_final: 0.6702 (mm110) REVERT: c 118 MET cc_start: 0.7102 (mtt) cc_final: 0.6715 (mtt) REVERT: E 143 MET cc_start: 0.0050 (mpp) cc_final: -0.0270 (mtt) outliers start: 48 outliers final: 32 residues processed: 259 average time/residue: 0.2366 time to fit residues: 88.4783 Evaluate side-chains 252 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR 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 106 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 180 MET 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 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 198 MET 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 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 206 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 145 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 238 LEU Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 100 HIS ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN a 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.160740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129090 restraints weight = 17981.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128267 restraints weight = 22159.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129033 restraints weight = 19744.228| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12989 Z= 0.191 Angle : 0.692 7.891 17711 Z= 0.335 Chirality : 0.044 0.247 2059 Planarity : 0.005 0.066 2203 Dihedral : 4.909 50.162 1752 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 4.41 % Allowed : 19.48 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1602 helix: 1.62 (0.16), residues: 1046 sheet: 0.57 (0.60), residues: 81 loop : -0.87 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP c 234 HIS 0.005 0.001 HIS C 174 PHE 0.017 0.001 PHE b 3 TYR 0.011 0.002 TYR C 15 ARG 0.003 0.000 ARG c 220 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 774) hydrogen bonds : angle 4.42856 ( 2301) covalent geometry : bond 0.00478 (12989) covalent geometry : angle 0.69248 (17711) *********************** 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 287 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 229 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6900 (t-170) REVERT: C 21 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.7991 (t80) REVERT: C 74 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7327 (mtp) REVERT: D 27 MET cc_start: 0.6458 (tpp) cc_final: 0.5997 (tpp) REVERT: D 53 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8249 (tm-30) REVERT: a 3 MET cc_start: 0.7086 (pmm) cc_final: 0.6474 (ptp) REVERT: a 127 ASN cc_start: 0.7912 (p0) cc_final: 0.7500 (p0) REVERT: a 154 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: b 106 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7701 (tp) REVERT: b 156 ARG cc_start: 0.6892 (ttm-80) cc_final: 0.5810 (ttt-90) REVERT: b 173 LEU cc_start: 0.8782 (tp) cc_final: 0.8524 (tp) REVERT: c 14 LEU cc_start: 0.8969 (tp) cc_final: 0.8569 (tt) REVERT: c 85 GLN cc_start: 0.7380 (mt0) cc_final: 0.6960 (mm110) REVERT: E 143 MET cc_start: -0.0033 (mpp) cc_final: -0.0338 (mtt) outliers start: 58 outliers final: 36 residues processed: 268 average time/residue: 0.2498 time to fit residues: 96.2407 Evaluate side-chains 253 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR 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 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 180 MET 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 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 182 THR 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 b residue 103 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER 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 162 LEU Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 147 optimal weight: 50.0000 chunk 79 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** a 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.162308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130537 restraints weight = 17875.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129698 restraints weight = 20881.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130783 restraints weight = 18425.719| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12989 Z= 0.144 Angle : 0.660 8.362 17711 Z= 0.319 Chirality : 0.042 0.197 2059 Planarity : 0.005 0.064 2203 Dihedral : 4.795 49.712 1752 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 3.65 % Allowed : 21.00 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1602 helix: 1.75 (0.16), residues: 1046 sheet: 0.50 (0.59), residues: 81 loop : -0.77 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP c 234 HIS 0.004 0.001 HIS C 174 PHE 0.016 0.001 PHE C 43 TYR 0.017 0.002 TYR c 58 ARG 0.004 0.000 ARG d 48 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 774) hydrogen bonds : angle 4.33210 ( 2301) covalent geometry : bond 0.00358 (12989) covalent geometry : angle 0.65964 (17711) *********************** 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 268 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8942 (p) cc_final: 0.8660 (t) REVERT: A 102 ARG cc_start: 0.7011 (mmt90) cc_final: 0.6585 (mmt-90) REVERT: B 17 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6889 (t-170) REVERT: B 154 LEU cc_start: 0.8412 (mm) cc_final: 0.8059 (mp) REVERT: C 21 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8052 (t80) REVERT: C 74 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7323 (mtp) REVERT: C 207 PHE cc_start: 0.8457 (t80) cc_final: 0.8118 (t80) REVERT: D 53 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8251 (tm-30) REVERT: a 3 MET cc_start: 0.6834 (pmm) cc_final: 0.6283 (ptp) REVERT: a 109 CYS cc_start: 0.5820 (t) cc_final: 0.5151 (p) REVERT: a 127 ASN cc_start: 0.7922 (p0) cc_final: 0.7519 (p0) REVERT: b 106 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7651 (tp) REVERT: b 156 ARG cc_start: 0.6958 (ttm-80) cc_final: 0.5762 (ttt-90) REVERT: b 173 LEU cc_start: 0.8606 (tp) cc_final: 0.8386 (tp) REVERT: c 85 GLN cc_start: 0.7319 (mt0) cc_final: 0.6883 (mm110) REVERT: E 16 LEU cc_start: 0.8149 (mm) cc_final: 0.7845 (mm) outliers start: 48 outliers final: 29 residues processed: 255 average time/residue: 0.2352 time to fit residues: 87.6048 Evaluate side-chains 239 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 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 180 MET 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 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 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 187 GLN Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER 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 162 LEU Chi-restraints excluded: chain c residue 225 ILE Chi-restraints excluded: chain d residue 32 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 89 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 146 optimal weight: 50.0000 chunk 120 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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** ** a 187 GLN ** 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 = 0.3929 r_free = 0.3929 target = 0.159924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127829 restraints weight = 18235.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127546 restraints weight = 13812.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127760 restraints weight = 13113.354| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12989 Z= 0.179 Angle : 0.702 8.851 17711 Z= 0.340 Chirality : 0.043 0.204 2059 Planarity : 0.005 0.063 2203 Dihedral : 4.818 48.659 1752 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 3.81 % Allowed : 20.78 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.21), residues: 1602 helix: 1.74 (0.16), residues: 1048 sheet: 0.41 (0.60), residues: 81 loop : -0.84 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP c 234 HIS 0.005 0.001 HIS C 174 PHE 0.020 0.001 PHE b 3 TYR 0.012 0.001 TYR c 48 ARG 0.005 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 774) hydrogen bonds : angle 4.36854 ( 2301) covalent geometry : bond 0.00443 (12989) covalent geometry : angle 0.70250 (17711) *********************** 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 259 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8908 (p) cc_final: 0.8634 (t) REVERT: B 17 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6911 (t-170) REVERT: B 154 LEU cc_start: 0.8352 (mm) cc_final: 0.8068 (mp) REVERT: C 21 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8049 (t80) REVERT: C 74 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7292 (mtp) REVERT: C 207 PHE cc_start: 0.8352 (t80) cc_final: 0.8063 (t80) REVERT: D 53 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8232 (tm-30) REVERT: a 3 MET cc_start: 0.6818 (pmm) cc_final: 0.6379 (ptp) REVERT: a 74 TYR cc_start: 0.8477 (t80) cc_final: 0.8248 (t80) REVERT: a 109 CYS cc_start: 0.5844 (t) cc_final: 0.5315 (p) REVERT: a 127 ASN cc_start: 0.7852 (p0) cc_final: 0.7441 (p0) REVERT: b 106 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7675 (tp) REVERT: b 140 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7049 (tt) REVERT: b 156 ARG cc_start: 0.6777 (ttm-80) cc_final: 0.5810 (ttt-90) REVERT: c 85 GLN cc_start: 0.7470 (mt0) cc_final: 0.7045 (mm110) REVERT: E 16 LEU cc_start: 0.8168 (mm) cc_final: 0.7822 (mm) outliers start: 50 outliers final: 37 residues processed: 246 average time/residue: 0.2363 time to fit residues: 84.7929 Evaluate side-chains 245 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 54 ILE 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 180 MET 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 82 LEU 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 213 SER Chi-restraints excluded: chain C residue 225 ILE 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 191 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 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 162 LEU Chi-restraints excluded: chain c residue 168 VAL Chi-restraints excluded: chain c residue 225 ILE Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 115 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** a 75 HIS a 187 GLN c 52 ASN ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121799 restraints weight = 18596.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120111 restraints weight = 19226.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120952 restraints weight = 18180.776| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 12989 Z= 0.285 Angle : 0.835 8.916 17711 Z= 0.404 Chirality : 0.048 0.218 2059 Planarity : 0.006 0.063 2203 Dihedral : 5.103 53.040 1752 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 4.11 % Allowed : 20.85 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1602 helix: 1.51 (0.16), residues: 1030 sheet: -0.13 (0.55), residues: 93 loop : -0.77 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 66 HIS 0.009 0.002 HIS C 174 PHE 0.019 0.002 PHE b 175 TYR 0.023 0.002 TYR C 15 ARG 0.006 0.001 ARG C 189 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 774) hydrogen bonds : angle 4.73132 ( 2301) covalent geometry : bond 0.00704 (12989) covalent geometry : angle 0.83450 (17711) *********************** 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 282 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6983 (pp20) REVERT: A 89 THR cc_start: 0.8967 (p) cc_final: 0.8693 (t) REVERT: A 102 ARG cc_start: 0.7178 (mmt90) cc_final: 0.6739 (mmt-90) REVERT: B 17 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.7010 (t-170) REVERT: C 21 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.7927 (t80) REVERT: C 74 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7544 (mtp) REVERT: C 207 PHE cc_start: 0.8381 (t80) cc_final: 0.8152 (t80) REVERT: a 3 MET cc_start: 0.6881 (pmm) cc_final: 0.6572 (ptp) REVERT: a 109 CYS cc_start: 0.5832 (t) cc_final: 0.5381 (p) REVERT: a 127 ASN cc_start: 0.8018 (p0) cc_final: 0.7586 (p0) REVERT: b 44 GLN cc_start: 0.6898 (pp30) cc_final: 0.6655 (pp30) REVERT: b 49 ILE cc_start: 0.8451 (tp) cc_final: 0.7971 (tp) REVERT: b 106 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7948 (tp) REVERT: b 140 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7201 (tt) REVERT: c 21 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8071 (t80) REVERT: c 85 GLN cc_start: 0.7853 (mt0) cc_final: 0.7370 (mm110) REVERT: c 118 MET cc_start: 0.7441 (mtt) cc_final: 0.7015 (mtt) REVERT: E 16 LEU cc_start: 0.8194 (mm) cc_final: 0.7839 (mm) outliers start: 54 outliers final: 35 residues processed: 270 average time/residue: 0.2297 time to fit residues: 90.4667 Evaluate side-chains 258 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 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 54 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 115 VAL 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 30 VAL 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 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 213 SER Chi-restraints excluded: chain C residue 225 ILE 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 191 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 148 VAL 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 162 LEU Chi-restraints excluded: chain c residue 168 VAL Chi-restraints excluded: chain c residue 225 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 150 optimal weight: 40.0000 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 52 ASN ** 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 = 0.3928 r_free = 0.3928 target = 0.160014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127761 restraints weight = 18025.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127612 restraints weight = 17503.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129093 restraints weight = 15291.182| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3968 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= 0.148 Angle : 0.710 9.696 17711 Z= 0.344 Chirality : 0.043 0.279 2059 Planarity : 0.005 0.063 2203 Dihedral : 4.862 47.733 1752 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.75 % Rotamer: Outliers : 2.74 % Allowed : 23.29 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.21), residues: 1602 helix: 1.89 (0.16), residues: 1014 sheet: -0.18 (0.56), residues: 95 loop : -0.57 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 66 HIS 0.003 0.001 HIS C 174 PHE 0.022 0.001 PHE b 3 TYR 0.024 0.002 TYR c 58 ARG 0.008 0.000 ARG C 128 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 774) hydrogen bonds : angle 4.40542 ( 2301) covalent geometry : bond 0.00360 (12989) covalent geometry : angle 0.70959 (17711) ********************** 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 255 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6988 (pp20) REVERT: A 89 THR cc_start: 0.8923 (p) cc_final: 0.8643 (t) REVERT: A 161 VAL cc_start: 0.8816 (m) cc_final: 0.8593 (p) REVERT: B 17 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.6882 (t-170) REVERT: C 21 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8001 (t80) REVERT: C 74 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7305 (mtp) REVERT: C 207 PHE cc_start: 0.8269 (t80) cc_final: 0.8029 (t80) REVERT: D 53 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8286 (tm-30) REVERT: a 3 MET cc_start: 0.6736 (pmm) cc_final: 0.6369 (ptp) REVERT: a 109 CYS cc_start: 0.5720 (t) cc_final: 0.5515 (p) REVERT: a 127 ASN cc_start: 0.7822 (p0) cc_final: 0.7405 (p0) REVERT: b 106 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7821 (tp) REVERT: b 117 MET cc_start: 0.7280 (ttm) cc_final: 0.7016 (ttt) REVERT: b 140 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7082 (tt) REVERT: c 21 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.7842 (t80) REVERT: c 85 GLN cc_start: 0.7633 (mt0) cc_final: 0.7238 (mm110) REVERT: E 16 LEU cc_start: 0.8155 (mm) cc_final: 0.7817 (mm) outliers start: 36 outliers final: 25 residues processed: 246 average time/residue: 0.2308 time to fit residues: 83.4736 Evaluate side-chains 243 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 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 106 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 182 THR 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 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 191 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 c residue 5 LEU Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 168 VAL Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 48 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 149 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** ** 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 = 0.3925 r_free = 0.3925 target = 0.159408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127030 restraints weight = 18038.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126668 restraints weight = 17871.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127971 restraints weight = 14774.113| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12989 Z= 0.155 Angle : 0.713 9.266 17711 Z= 0.346 Chirality : 0.043 0.197 2059 Planarity : 0.005 0.062 2203 Dihedral : 4.723 47.229 1750 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 2.59 % Allowed : 23.36 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.21), residues: 1602 helix: 1.91 (0.16), residues: 1015 sheet: -0.14 (0.56), residues: 93 loop : -0.57 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 66 HIS 0.004 0.001 HIS C 174 PHE 0.020 0.001 PHE b 3 TYR 0.021 0.002 TYR c 58 ARG 0.009 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 774) hydrogen bonds : angle 4.39700 ( 2301) covalent geometry : bond 0.00382 (12989) covalent geometry : angle 0.71318 (17711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.56 seconds wall clock time: 64 minutes 37.91 seconds (3877.91 seconds total)