Starting phenix.real_space_refine on Wed Jul 30 12:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce8_16601/07_2025/8ce8_16601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce8_16601/07_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_16601/07_2025/8ce8_16601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce8_16601/07_2025/8ce8_16601.map" model { file = "/net/cci-nas-00/data/ceres_data/8ce8_16601/07_2025/8ce8_16601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce8_16601/07_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-5711/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: 8.02, per 1000 atoms: 0.63 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: 3.13 Conformation dependent library (CDL) restraints added in 1.8 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: 1.20 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: 3.53 Time building geometry restraints manager: 3.71 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: 0.540 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.950 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.610 ------------------------------------------------------------------------------- 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 : 1.435 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: 0.2646 time to fit residues: 97.2407 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 : 1.413 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.163396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126501 restraints weight = 17748.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129276 restraints weight = 11460.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131042 restraints weight = 8546.583| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1794 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= 0.210 Angle : 0.748 7.003 17711 Z= 0.374 Chirality : 0.044 0.170 2059 Planarity : 0.007 0.089 2203 Dihedral : 5.715 53.780 1756 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 3.81 % Allowed : 14.61 % Favored : 81.58 % 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 0.037 0.002 TRP C 66 HIS 0.007 0.001 HIS D 38 PHE 0.014 0.002 PHE B 7 TYR 0.016 0.002 TYR E 154 ARG 0.008 0.001 ARG D 59 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 774) hydrogen bonds : angle 4.85996 ( 2301) covalent geometry : bond 0.00517 (12989) covalent geometry : angle 0.74824 (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 295 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 245 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.6644 (ptp) cc_final: 0.6438 (mtp) REVERT: B 17 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6580 (t-170) REVERT: C 21 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7967 (t80) REVERT: C 96 MET cc_start: 0.7576 (mtm) cc_final: 0.7018 (mtm) REVERT: C 207 PHE cc_start: 0.8335 (t80) cc_final: 0.8069 (t80) REVERT: D 27 MET cc_start: 0.6906 (tmm) cc_final: 0.6556 (tpp) REVERT: D 53 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8328 (tm-30) REVERT: a 88 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8318 (mmtm) REVERT: b 156 ARG cc_start: 0.6469 (ttm-80) cc_final: 0.5846 (ttt90) outliers start: 50 outliers final: 28 residues processed: 277 average time/residue: 0.2469 time to fit residues: 98.6756 Evaluate side-chains 242 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 155 optimal weight: 0.0970 chunk 82 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4001 r_free = 0.4001 target = 0.166732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133153 restraints weight = 17665.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134019 restraints weight = 12273.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135083 restraints weight = 10356.528| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12989 Z= 0.136 Angle : 0.664 8.094 17711 Z= 0.326 Chirality : 0.042 0.184 2059 Planarity : 0.006 0.075 2203 Dihedral : 5.347 53.111 1754 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 2.89 % Allowed : 16.82 % Favored : 80.29 % 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: 0.97 (0.21), residues: 1602 helix: 1.30 (0.16), residues: 1023 sheet: 0.62 (0.59), residues: 81 loop : -0.64 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 66 HIS 0.004 0.001 HIS a 186 PHE 0.024 0.001 PHE b 3 TYR 0.012 0.001 TYR a 100 ARG 0.003 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 774) hydrogen bonds : angle 4.57115 ( 2301) covalent geometry : bond 0.00330 (12989) covalent geometry : angle 0.66392 (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 275 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6499 (t-170) REVERT: C 21 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8129 (t80) REVERT: C 96 MET cc_start: 0.7683 (mtm) cc_final: 0.7083 (mtm) REVERT: C 181 ASN cc_start: 0.8172 (m110) cc_final: 0.7673 (t0) REVERT: C 185 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8224 (tp40) REVERT: C 207 PHE cc_start: 0.8310 (t80) cc_final: 0.7985 (t80) REVERT: C 229 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8080 (mm-30) REVERT: D 53 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8357 (tm-30) REVERT: a 127 ASN cc_start: 0.7891 (p0) cc_final: 0.7565 (p0) REVERT: a 154 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: b 156 ARG cc_start: 0.6374 (ttm-80) cc_final: 0.5805 (ttt90) REVERT: c 85 GLN cc_start: 0.6954 (mt0) cc_final: 0.6559 (mm110) outliers start: 38 outliers final: 27 residues processed: 260 average time/residue: 0.2468 time to fit residues: 92.8630 Evaluate side-chains 247 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 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 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 147 HIS 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: 0.7980 chunk 48 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** D 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.166156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133564 restraints weight = 17485.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133674 restraints weight = 12794.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134361 restraints weight = 11136.495| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12989 Z= 0.135 Angle : 0.643 7.875 17711 Z= 0.314 Chirality : 0.042 0.146 2059 Planarity : 0.006 0.069 2203 Dihedral : 5.112 52.099 1754 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.82 % Rotamer: Outliers : 3.27 % Allowed : 17.58 % Favored : 79.15 % 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: 1.31 (0.21), residues: 1602 helix: 1.59 (0.16), residues: 1032 sheet: 0.67 (0.60), residues: 81 loop : -0.60 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP c 234 HIS 0.004 0.001 HIS a 186 PHE 0.015 0.001 PHE b 175 TYR 0.013 0.001 TYR c 58 ARG 0.006 0.000 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 774) hydrogen bonds : angle 4.39556 ( 2301) covalent geometry : bond 0.00330 (12989) covalent geometry : angle 0.64305 (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 266 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6657 (t-170) REVERT: B 200 LEU cc_start: 0.8715 (tp) cc_final: 0.8457 (tt) REVERT: C 21 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8038 (t80) REVERT: C 74 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7240 (mtp) REVERT: C 198 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8210 (ttm) REVERT: C 207 PHE cc_start: 0.8178 (t80) cc_final: 0.7882 (t80) REVERT: C 229 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7857 (mm-30) REVERT: D 27 MET cc_start: 0.6032 (tpp) cc_final: 0.5758 (tpp) REVERT: D 53 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8278 (tm-30) REVERT: a 127 ASN cc_start: 0.7674 (p0) cc_final: 0.7291 (p0) REVERT: a 154 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: b 156 ARG cc_start: 0.6352 (ttm-80) cc_final: 0.5700 (ttt-90) REVERT: c 85 GLN cc_start: 0.6960 (mt0) cc_final: 0.6641 (mm110) REVERT: c 154 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7145 (tt) REVERT: E 16 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7804 (mm) REVERT: E 143 MET cc_start: 0.0451 (mpp) cc_final: -0.0107 (mtt) outliers start: 43 outliers final: 29 residues processed: 251 average time/residue: 0.2446 time to fit residues: 89.2867 Evaluate side-chains 247 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 201 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 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 74 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 121 THR 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 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 147 HIS Chi-restraints excluded: chain c residue 154 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 43 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 154 optimal weight: 30.0000 chunk 63 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 D 66 GLN ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133175 restraints weight = 17520.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134122 restraints weight = 14895.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134081 restraints weight = 12258.527| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12989 Z= 0.126 Angle : 0.625 7.783 17711 Z= 0.304 Chirality : 0.041 0.147 2059 Planarity : 0.005 0.065 2203 Dihedral : 4.958 51.767 1754 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.75 % Rotamer: Outliers : 3.58 % Allowed : 18.19 % Favored : 78.23 % 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: 1.49 (0.21), residues: 1602 helix: 1.75 (0.16), residues: 1032 sheet: 0.70 (0.60), residues: 81 loop : -0.59 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP c 234 HIS 0.003 0.001 HIS a 186 PHE 0.015 0.001 PHE C 43 TYR 0.011 0.001 TYR C 15 ARG 0.005 0.000 ARG d 48 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 774) hydrogen bonds : angle 4.28434 ( 2301) covalent geometry : bond 0.00306 (12989) covalent geometry : angle 0.62550 (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 271 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6678 (t-170) REVERT: B 71 ARG cc_start: 0.8228 (tpp80) cc_final: 0.8001 (tpp-160) REVERT: B 200 LEU cc_start: 0.8731 (tp) cc_final: 0.8486 (tt) REVERT: C 21 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7923 (t80) REVERT: C 74 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7167 (mtp) REVERT: C 198 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8076 (ttm) REVERT: C 207 PHE cc_start: 0.8137 (t80) cc_final: 0.7841 (t80) REVERT: C 229 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7729 (mm-30) REVERT: D 27 MET cc_start: 0.5934 (tpp) cc_final: 0.5645 (tpp) REVERT: D 53 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8222 (tm-30) REVERT: a 127 ASN cc_start: 0.7628 (p0) cc_final: 0.7226 (p0) REVERT: a 154 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: b 156 ARG cc_start: 0.6391 (ttm-80) cc_final: 0.5872 (ttt90) REVERT: c 85 GLN cc_start: 0.6926 (mt0) cc_final: 0.6671 (mm110) REVERT: E 16 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7756 (mm) REVERT: E 143 MET cc_start: 0.0080 (mpp) cc_final: -0.0299 (mtt) outliers start: 47 outliers final: 28 residues processed: 256 average time/residue: 0.2434 time to fit residues: 90.4115 Evaluate side-chains 252 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 201 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 106 LEU Chi-restraints excluded: chain B residue 112 SER 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 74 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 147 HIS Chi-restraints excluded: chain c residue 154 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 E residue 16 LEU 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: 0.8980 chunk 140 optimal weight: 9.9990 chunk 106 optimal weight: 0.0570 chunk 130 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.167869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135218 restraints weight = 17586.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135896 restraints weight = 12538.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136884 restraints weight = 10335.989| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12989 Z= 0.125 Angle : 0.635 8.520 17711 Z= 0.307 Chirality : 0.042 0.302 2059 Planarity : 0.005 0.064 2203 Dihedral : 4.764 51.269 1752 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 3.20 % Allowed : 19.03 % Favored : 77.78 % 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: 1.83 (0.16), residues: 1046 sheet: 0.79 (0.60), residues: 81 loop : -0.74 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 234 HIS 0.003 0.001 HIS a 186 PHE 0.015 0.001 PHE C 43 TYR 0.016 0.001 TYR c 58 ARG 0.004 0.000 ARG D 59 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 774) hydrogen bonds : angle 4.19425 ( 2301) covalent geometry : bond 0.00303 (12989) covalent geometry : angle 0.63471 (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 270 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7567 (tt) cc_final: 0.7229 (tt) REVERT: A 102 ARG cc_start: 0.6922 (mmt90) cc_final: 0.6567 (mmt-90) REVERT: B 17 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6780 (t-170) REVERT: C 21 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8024 (t80) REVERT: C 74 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7206 (mtp) REVERT: C 198 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8130 (ttm) REVERT: C 229 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7963 (mm-30) REVERT: D 27 MET cc_start: 0.6230 (tpp) cc_final: 0.5747 (tpp) REVERT: D 53 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8287 (tm-30) REVERT: a 127 ASN cc_start: 0.8052 (p0) cc_final: 0.7685 (p0) REVERT: b 140 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7120 (tt) REVERT: b 150 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8398 (mp) REVERT: c 85 GLN cc_start: 0.6867 (mt0) cc_final: 0.6480 (mm110) REVERT: d 41 MET cc_start: 0.7738 (mtm) cc_final: 0.7509 (mmt) REVERT: E 65 MET cc_start: 0.6547 (mtm) cc_final: 0.6066 (ptp) outliers start: 42 outliers final: 30 residues processed: 257 average time/residue: 0.2487 time to fit residues: 91.2291 Evaluate side-chains 245 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 21 ILE 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 180 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE 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 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 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 147 HIS Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain E residue 16 LEU 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: 3.9990 chunk 84 optimal weight: 6.9990 chunk 147 optimal weight: 50.0000 chunk 79 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 150 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 177 GLN a 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.164110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132471 restraints weight = 17626.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133057 restraints weight = 16625.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134457 restraints weight = 13631.576| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12989 Z= 0.162 Angle : 0.671 7.252 17711 Z= 0.325 Chirality : 0.043 0.272 2059 Planarity : 0.005 0.064 2203 Dihedral : 4.765 50.305 1752 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.00 % Favored : 97.94 % Rotamer: Outliers : 3.81 % Allowed : 18.72 % Favored : 77.47 % 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: 1.51 (0.21), residues: 1602 helix: 1.82 (0.16), residues: 1046 sheet: 0.59 (0.60), residues: 81 loop : -0.75 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 234 HIS 0.004 0.001 HIS C 174 PHE 0.016 0.001 PHE C 43 TYR 0.012 0.001 TYR c 139 ARG 0.008 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 774) hydrogen bonds : angle 4.28600 ( 2301) covalent geometry : bond 0.00404 (12989) covalent geometry : angle 0.67064 (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 269 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6927 (mmt90) cc_final: 0.6539 (mmt-90) REVERT: B 17 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6850 (t-170) REVERT: C 21 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8052 (t80) REVERT: C 74 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7287 (mtp) REVERT: C 198 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8070 (ttm) REVERT: C 207 PHE cc_start: 0.8486 (t80) cc_final: 0.8122 (t80) REVERT: D 54 ARG cc_start: 0.8505 (tpp-160) cc_final: 0.8146 (tpp80) REVERT: a 127 ASN cc_start: 0.7886 (p0) cc_final: 0.7488 (p0) outliers start: 50 outliers final: 35 residues processed: 252 average time/residue: 0.2628 time to fit residues: 95.7166 Evaluate side-chains 249 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 21 ILE 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 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 198 MET Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 186 HIS Chi-restraints excluded: chain a residue 187 GLN Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain E residue 16 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: 0.5980 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 146 optimal weight: 0.0970 chunk 120 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 E 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.165177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133274 restraints weight = 17788.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134176 restraints weight = 16120.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135890 restraints weight = 12907.539| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12989 Z= 0.132 Angle : 0.650 7.818 17711 Z= 0.315 Chirality : 0.042 0.259 2059 Planarity : 0.005 0.063 2203 Dihedral : 4.590 49.946 1750 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 3.27 % Allowed : 19.63 % Favored : 77.09 % 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: 1.59 (0.21), residues: 1602 helix: 1.90 (0.16), residues: 1046 sheet: 0.54 (0.60), residues: 81 loop : -0.76 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP c 234 HIS 0.003 0.001 HIS C 174 PHE 0.016 0.001 PHE C 43 TYR 0.012 0.001 TYR c 48 ARG 0.006 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 774) hydrogen bonds : angle 4.21999 ( 2301) covalent geometry : bond 0.00322 (12989) covalent geometry : angle 0.64954 (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 256 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8918 (p) cc_final: 0.8639 (t) REVERT: A 94 LEU cc_start: 0.7581 (tt) cc_final: 0.7238 (tt) REVERT: B 17 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.6879 (t-170) REVERT: C 16 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: C 21 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8113 (t80) REVERT: C 74 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7305 (mtp) REVERT: C 198 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8151 (ttm) REVERT: C 207 PHE cc_start: 0.8418 (t80) cc_final: 0.8087 (t80) REVERT: C 229 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7983 (mm-30) REVERT: D 53 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8260 (tm-30) REVERT: D 54 ARG cc_start: 0.8505 (tpp-160) cc_final: 0.8090 (tpp80) REVERT: a 127 ASN cc_start: 0.7855 (p0) cc_final: 0.7475 (p0) REVERT: E 65 MET cc_start: 0.6770 (mtm) cc_final: 0.6192 (ptp) outliers start: 43 outliers final: 32 residues processed: 242 average time/residue: 0.2306 time to fit residues: 82.0324 Evaluate side-chains 244 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 16 GLN 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 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 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 186 HIS Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain E residue 16 LEU 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: 0.9990 chunk 29 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS C 16 GLN ** C 147 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 = 0.3913 r_free = 0.3913 target = 0.158414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125105 restraints weight = 18181.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125477 restraints weight = 15873.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125514 restraints weight = 13280.202| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12989 Z= 0.225 Angle : 0.749 10.374 17711 Z= 0.363 Chirality : 0.045 0.181 2059 Planarity : 0.005 0.064 2203 Dihedral : 4.739 48.597 1750 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 3.50 % Allowed : 19.86 % Favored : 76.64 % 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: 1.77 (0.16), residues: 1024 sheet: 0.45 (0.60), residues: 83 loop : -0.65 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 66 HIS 0.007 0.001 HIS C 174 PHE 0.016 0.001 PHE C 43 TYR 0.016 0.002 TYR C 58 ARG 0.006 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 774) hydrogen bonds : angle 4.49363 ( 2301) covalent geometry : bond 0.00553 (12989) covalent geometry : angle 0.74882 (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 272 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7073 (mmt90) cc_final: 0.6641 (mmt-90) REVERT: A 201 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5645 (pp) REVERT: B 17 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.6960 (t-170) REVERT: C 16 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: C 21 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8001 (t80) REVERT: C 74 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7442 (mtp) REVERT: C 207 PHE cc_start: 0.8345 (t80) cc_final: 0.8081 (t80) REVERT: C 229 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8073 (mm-30) REVERT: D 53 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8258 (tm-30) REVERT: D 54 ARG cc_start: 0.8602 (tpp-160) cc_final: 0.8185 (tpp80) REVERT: a 3 MET cc_start: 0.7018 (pmm) cc_final: 0.5988 (ptp) REVERT: a 74 TYR cc_start: 0.8524 (t80) cc_final: 0.8310 (t80) REVERT: a 127 ASN cc_start: 0.7969 (p0) cc_final: 0.7585 (p0) REVERT: b 140 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7159 (tt) REVERT: c 229 GLU cc_start: 0.7310 (mp0) cc_final: 0.7092 (mp0) REVERT: E 143 MET cc_start: -0.1322 (mmt) cc_final: -0.2964 (tpp) outliers start: 46 outliers final: 35 residues processed: 257 average time/residue: 0.2369 time to fit residues: 88.0400 Evaluate side-chains 254 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 161 VAL Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 201 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 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 16 GLN 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 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 186 HIS Chi-restraints excluded: chain b residue 83 MET Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 140 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 162 LEU Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain E residue 16 LEU 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: 0.7980 chunk 46 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.162100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129597 restraints weight = 17809.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129897 restraints weight = 14028.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130371 restraints weight = 12793.754| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12989 Z= 0.137 Angle : 0.673 8.210 17711 Z= 0.327 Chirality : 0.042 0.226 2059 Planarity : 0.005 0.063 2203 Dihedral : 4.602 49.108 1750 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 2.89 % Allowed : 21.16 % Favored : 75.95 % 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: 1.65 (0.21), residues: 1602 helix: 1.94 (0.16), residues: 1028 sheet: 0.49 (0.60), residues: 83 loop : -0.59 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP c 234 HIS 0.003 0.001 HIS C 174 PHE 0.017 0.001 PHE C 43 TYR 0.021 0.002 TYR c 58 ARG 0.005 0.000 ARG b 71 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 774) hydrogen bonds : angle 4.31380 ( 2301) covalent geometry : bond 0.00331 (12989) covalent geometry : angle 0.67294 (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 254 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8920 (p) cc_final: 0.8649 (t) REVERT: A 201 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.5702 (pp) REVERT: B 17 HIS cc_start: 0.7245 (OUTLIER) cc_final: 0.6873 (t-170) REVERT: C 21 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8099 (t80) REVERT: C 74 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7223 (mtp) REVERT: C 207 PHE cc_start: 0.8241 (t80) cc_final: 0.7980 (t80) REVERT: C 229 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8119 (mm-30) REVERT: D 53 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8214 (tm-30) REVERT: D 54 ARG cc_start: 0.8576 (tpp-160) cc_final: 0.8207 (tpp80) REVERT: a 3 MET cc_start: 0.6856 (pmm) cc_final: 0.5806 (ptp) REVERT: a 74 TYR cc_start: 0.8441 (t80) cc_final: 0.8195 (t80) REVERT: a 127 ASN cc_start: 0.7822 (p0) cc_final: 0.7407 (p0) REVERT: b 117 MET cc_start: 0.7275 (ttm) cc_final: 0.7032 (ttt) REVERT: b 140 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7093 (tt) REVERT: E 143 MET cc_start: -0.1326 (mmt) cc_final: -0.2894 (tpp) outliers start: 38 outliers final: 31 residues processed: 244 average time/residue: 0.2424 time to fit residues: 85.9187 Evaluate side-chains 243 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 161 VAL Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 201 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 106 LEU Chi-restraints excluded: chain B residue 112 SER 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 74 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 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 186 HIS Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 140 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 162 LEU Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 139 VAL 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: 0.5980 chunk 25 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3918 r_free = 0.3918 target = 0.158822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127741 restraints weight = 18013.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.126648 restraints weight = 15521.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126232 restraints weight = 16418.695| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12989 Z= 0.195 Angle : 0.730 9.042 17711 Z= 0.355 Chirality : 0.044 0.233 2059 Planarity : 0.005 0.062 2203 Dihedral : 4.645 48.046 1750 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 3.12 % Allowed : 21.16 % Favored : 75.72 % 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: 1.49 (0.21), residues: 1602 helix: 1.81 (0.16), residues: 1026 sheet: 0.39 (0.60), residues: 83 loop : -0.62 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 20 HIS 0.006 0.001 HIS C 174 PHE 0.023 0.001 PHE d 5 TYR 0.025 0.002 TYR C 15 ARG 0.007 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 774) hydrogen bonds : angle 4.43722 ( 2301) covalent geometry : bond 0.00482 (12989) covalent geometry : angle 0.73005 (17711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3969.39 seconds wall clock time: 70 minutes 6.62 seconds (4206.62 seconds total)