Starting phenix.real_space_refine on Thu Feb 15 15:21:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce8_16601/02_2024/8ce8_16601.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce8_16601/02_2024/8ce8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce8_16601/02_2024/8ce8_16601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce8_16601/02_2024/8ce8_16601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce8_16601/02_2024/8ce8_16601.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce8_16601/02_2024/8ce8_16601.pdb" } 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 Residue "A GLU 5": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "a GLU 8": "OE1" <-> "OE2" Residue "a GLU 15": "OE1" <-> "OE2" Residue "a GLU 30": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 154": "OE1" <-> "OE2" Residue "a GLU 176": "OE1" <-> "OE2" Residue "b PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 178": "OE1" <-> "OE2" Residue "c GLU 229": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.39, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.77 Conformation dependent library (CDL) restraints added in 2.3 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: 1.14 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: 3.54 Time building geometry restraints manager: 5.19 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: 96.94 - 104.39: 240 104.39 - 111.85: 6091 111.85 - 119.31: 4832 119.31 - 126.76: 6246 126.76 - 134.22: 302 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 2.440 nonbonded pdb=" OG1 THR a 92 " pdb=" OE1 GLU a 95 " model vdw 2.297 2.440 nonbonded pdb=" OD1 ASP E 86 " pdb=" N GLY E 89 " model vdw 2.330 2.520 nonbonded pdb=" OH TYR c 54 " pdb=" O SER c 193 " model vdw 2.333 2.440 nonbonded pdb=" OH TYR C 54 " pdb=" O SER C 193 " model vdw 2.338 2.440 ... (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 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: 0.010 Normalize map: mean=0, sd=1: 0.940 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: 3.680 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 33.240 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.670 ------------------------------------------------------------------------------- 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= 0.414 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 257 time to evaluate : 1.357 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: 0.2598 time to fit residues: 95.2200 Evaluate side-chains 220 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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: 5.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN D 38 HIS D 66 GLN a 69 GLN a 101 HIS c 169 ASN E 2 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12989 Z= 0.259 Angle : 0.706 7.930 17711 Z= 0.351 Chirality : 0.042 0.174 2059 Planarity : 0.007 0.087 2203 Dihedral : 5.661 53.427 1756 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.75 % Rotamer: Outliers : 3.20 % Allowed : 14.76 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1602 helix: 0.81 (0.16), residues: 1021 sheet: 0.62 (0.60), residues: 81 loop : -0.87 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 66 HIS 0.008 0.001 HIS D 38 PHE 0.013 0.001 PHE b 175 TYR 0.014 0.002 TYR A 100 ARG 0.005 0.000 ARG D 59 *********************** 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 286 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 244 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6552 (t-170) REVERT: C 96 MET cc_start: 0.7502 (mtm) cc_final: 0.6904 (mtm) REVERT: C 207 PHE cc_start: 0.8323 (t80) cc_final: 0.8033 (t80) REVERT: D 53 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8231 (tm-30) REVERT: b 156 ARG cc_start: 0.6278 (ttm-80) cc_final: 0.5783 (ttt90) REVERT: c 190 MET cc_start: 0.5666 (tmm) cc_final: 0.5410 (tmm) REVERT: d 59 ARG cc_start: 0.7866 (mmp80) cc_final: 0.7301 (ttp80) outliers start: 42 outliers final: 26 residues processed: 270 average time/residue: 0.2409 time to fit residues: 93.2786 Evaluate side-chains 239 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU 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 121 THR 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 154 GLU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain c residue 17 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 147 HIS Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 195 ASP Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 2 ASN 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 79 optimal weight: 0.0270 chunk 44 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN D 66 GLN a 27 ASN a 69 GLN a 177 GLN ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12989 Z= 0.303 Angle : 0.709 7.899 17711 Z= 0.349 Chirality : 0.044 0.174 2059 Planarity : 0.006 0.078 2203 Dihedral : 5.399 51.967 1756 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 4.34 % Allowed : 15.53 % Favored : 80.14 % 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: 0.86 (0.21), residues: 1602 helix: 1.19 (0.16), residues: 1021 sheet: 0.64 (0.61), residues: 81 loop : -0.61 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 66 HIS 0.006 0.001 HIS a 174 PHE 0.023 0.002 PHE c 137 TYR 0.012 0.002 TYR c 139 ARG 0.007 0.000 ARG c 55 *********************** 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 289 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 232 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6626 (t-170) REVERT: B 200 LEU cc_start: 0.8767 (tp) cc_final: 0.8518 (tt) REVERT: C 21 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.7951 (t80) REVERT: C 74 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7323 (mtp) REVERT: C 96 MET cc_start: 0.7620 (mtm) cc_final: 0.7045 (mtm) REVERT: C 207 PHE cc_start: 0.8417 (t80) cc_final: 0.8125 (t80) REVERT: D 53 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8247 (tm-30) REVERT: a 42 LYS cc_start: 0.8548 (pttt) cc_final: 0.8189 (ptmt) REVERT: a 88 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7996 (mmtm) REVERT: a 127 ASN cc_start: 0.8068 (p0) cc_final: 0.7686 (p0) REVERT: a 171 MET cc_start: 0.8298 (tpp) cc_final: 0.8038 (tpp) REVERT: b 137 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8725 (p) REVERT: b 156 ARG cc_start: 0.6462 (ttm-80) cc_final: 0.5896 (ttt90) REVERT: c 190 MET cc_start: 0.5445 (tmm) cc_final: 0.5240 (tmm) REVERT: d 27 MET cc_start: 0.6338 (tpt) cc_final: 0.5929 (tpt) outliers start: 57 outliers final: 36 residues processed: 262 average time/residue: 0.2421 time to fit residues: 91.8225 Evaluate side-chains 256 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR 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 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 190 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL 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 47 LEU 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 38 SER Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 217 THR Chi-restraints excluded: chain c residue 238 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 185 GLN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12989 Z= 0.285 Angle : 0.675 7.752 17711 Z= 0.331 Chirality : 0.043 0.184 2059 Planarity : 0.006 0.071 2203 Dihedral : 5.120 51.028 1754 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 4.19 % Allowed : 17.35 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1602 helix: 1.52 (0.16), residues: 1021 sheet: 0.53 (0.60), residues: 81 loop : -0.61 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP c 234 HIS 0.005 0.001 HIS C 174 PHE 0.026 0.001 PHE c 137 TYR 0.015 0.002 TYR c 139 ARG 0.004 0.000 ARG D 59 *********************** 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 285 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 230 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6699 (t-170) REVERT: B 200 LEU cc_start: 0.8790 (tp) cc_final: 0.8530 (tt) REVERT: C 21 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.7985 (t80) REVERT: C 74 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7280 (mtp) REVERT: C 181 ASN cc_start: 0.8250 (m110) cc_final: 0.7744 (t0) REVERT: C 207 PHE cc_start: 0.8446 (t80) cc_final: 0.8130 (t80) REVERT: D 27 MET cc_start: 0.6403 (tpp) cc_final: 0.6110 (tpp) REVERT: D 53 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8235 (tm-30) REVERT: a 88 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8110 (mmtm) REVERT: b 106 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7650 (tp) REVERT: b 137 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8610 (p) REVERT: b 156 ARG cc_start: 0.6598 (ttm-80) cc_final: 0.5964 (ttt90) REVERT: c 85 GLN cc_start: 0.7305 (mt0) cc_final: 0.6888 (mm110) REVERT: d 10 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7605 (tp30) outliers start: 55 outliers final: 40 residues processed: 264 average time/residue: 0.2380 time to fit residues: 90.6757 Evaluate side-chains 261 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 216 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 89 THR 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 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 190 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 38 SER Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 206 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 168 VAL Chi-restraints excluded: chain c residue 238 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 136 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12989 Z= 0.273 Angle : 0.658 6.990 17711 Z= 0.322 Chirality : 0.042 0.169 2059 Planarity : 0.006 0.068 2203 Dihedral : 5.022 50.084 1754 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 4.34 % Allowed : 19.03 % 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: 1.28 (0.21), residues: 1602 helix: 1.61 (0.16), residues: 1026 sheet: 0.39 (0.59), residues: 83 loop : -0.64 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP c 234 HIS 0.005 0.001 HIS C 174 PHE 0.013 0.001 PHE C 43 TYR 0.013 0.002 TYR c 58 ARG 0.004 0.000 ARG D 59 *********************** 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 278 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 221 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6808 (t-170) REVERT: B 200 LEU cc_start: 0.8756 (tp) cc_final: 0.8541 (tt) REVERT: C 21 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.7867 (t80) REVERT: C 207 PHE cc_start: 0.8397 (t80) cc_final: 0.8093 (t80) REVERT: D 27 MET cc_start: 0.6515 (tpp) cc_final: 0.6046 (tpp) REVERT: D 53 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8218 (tm-30) REVERT: a 88 LYS cc_start: 0.8347 (mmtm) cc_final: 0.8113 (mmtm) REVERT: a 127 ASN cc_start: 0.8140 (p0) cc_final: 0.7705 (p0) REVERT: a 171 MET cc_start: 0.8212 (tpp) cc_final: 0.7892 (tpp) REVERT: b 150 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7650 (mp) REVERT: b 156 ARG cc_start: 0.6852 (ttm-80) cc_final: 0.6000 (ttt90) REVERT: c 85 GLN cc_start: 0.7402 (mt0) cc_final: 0.6915 (mm110) REVERT: E 143 MET cc_start: 0.0380 (mpp) cc_final: -0.0673 (mtt) outliers start: 57 outliers final: 43 residues processed: 260 average time/residue: 0.2420 time to fit residues: 90.5746 Evaluate side-chains 254 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 208 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 89 THR 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 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 190 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 38 SER Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 168 VAL Chi-restraints excluded: chain c residue 225 ILE Chi-restraints excluded: chain c residue 238 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 146 optimal weight: 50.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12989 Z= 0.267 Angle : 0.667 8.748 17711 Z= 0.324 Chirality : 0.043 0.348 2059 Planarity : 0.005 0.064 2203 Dihedral : 4.940 49.255 1754 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 4.41 % Allowed : 20.02 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.26 (0.21), residues: 1602 helix: 1.65 (0.16), residues: 1046 sheet: 0.34 (0.60), residues: 83 loop : -0.88 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 234 HIS 0.005 0.001 HIS C 174 PHE 0.016 0.001 PHE b 175 TYR 0.015 0.002 TYR c 58 ARG 0.005 0.000 ARG D 59 *********************** 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 286 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 228 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6839 (t-170) REVERT: C 21 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8039 (t80) REVERT: C 74 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7258 (mtp) REVERT: C 198 MET cc_start: 0.8318 (tmm) cc_final: 0.7923 (tmm) REVERT: C 207 PHE cc_start: 0.8431 (t80) cc_final: 0.8125 (t80) REVERT: D 27 MET cc_start: 0.6498 (tpp) cc_final: 0.5940 (tpp) REVERT: D 53 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8192 (tm-30) REVERT: a 127 ASN cc_start: 0.8179 (p0) cc_final: 0.7718 (p0) REVERT: a 171 MET cc_start: 0.8236 (tpp) cc_final: 0.7833 (tpp) REVERT: b 106 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7573 (tp) REVERT: b 156 ARG cc_start: 0.6916 (ttm-80) cc_final: 0.5979 (ttt90) REVERT: c 85 GLN cc_start: 0.7372 (mt0) cc_final: 0.6923 (mm110) REVERT: E 143 MET cc_start: 0.0223 (mpp) cc_final: -0.0353 (mtt) outliers start: 58 outliers final: 41 residues processed: 269 average time/residue: 0.2394 time to fit residues: 93.2771 Evaluate side-chains 258 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 213 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 89 THR 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 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 173 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 168 VAL Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 151 optimal weight: 30.0000 chunk 94 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 69 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3332 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= 0.215 Angle : 0.649 7.953 17711 Z= 0.315 Chirality : 0.041 0.240 2059 Planarity : 0.005 0.064 2203 Dihedral : 4.850 48.986 1754 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 3.20 % Allowed : 22.07 % Favored : 74.73 % 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: 1.56 (0.21), residues: 1602 helix: 1.89 (0.16), residues: 1030 sheet: 0.32 (0.59), residues: 83 loop : -0.68 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP c 234 HIS 0.004 0.001 HIS a 186 PHE 0.014 0.001 PHE b 175 TYR 0.017 0.001 TYR c 58 ARG 0.004 0.000 ARG D 59 *********************** 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 259 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 217 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6883 (t-170) REVERT: C 21 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8120 (t80) REVERT: C 74 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7297 (mtp) REVERT: C 207 PHE cc_start: 0.8344 (t80) cc_final: 0.8078 (t80) REVERT: D 53 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8154 (tm-30) REVERT: a 127 ASN cc_start: 0.8085 (p0) cc_final: 0.7674 (p0) REVERT: a 171 MET cc_start: 0.8207 (tpp) cc_final: 0.7831 (tpp) REVERT: b 69 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8003 (mp) REVERT: b 106 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7583 (tp) REVERT: b 150 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7691 (mp) REVERT: b 156 ARG cc_start: 0.6972 (ttm-80) cc_final: 0.5706 (ttt-90) REVERT: c 85 GLN cc_start: 0.7270 (mt0) cc_final: 0.6814 (mm110) REVERT: E 143 MET cc_start: -0.0134 (mpp) cc_final: -0.0532 (mtt) outliers start: 42 outliers final: 29 residues processed: 244 average time/residue: 0.2419 time to fit residues: 85.1437 Evaluate side-chains 242 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR 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 170 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 135 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12989 Z= 0.284 Angle : 0.686 7.456 17711 Z= 0.331 Chirality : 0.043 0.214 2059 Planarity : 0.005 0.063 2203 Dihedral : 4.757 47.740 1752 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 3.81 % Allowed : 21.92 % Favored : 74.28 % 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: 1.37 (0.21), residues: 1602 helix: 1.72 (0.16), residues: 1048 sheet: 0.28 (0.60), residues: 83 loop : -0.78 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP c 234 HIS 0.005 0.001 HIS C 174 PHE 0.016 0.001 PHE c 137 TYR 0.013 0.002 TYR c 48 ARG 0.005 0.000 ARG D 59 *********************** 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 275 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7354 (OUTLIER) cc_final: 0.6912 (t-170) REVERT: C 21 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8028 (t80) REVERT: C 74 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7332 (mtp) REVERT: C 207 PHE cc_start: 0.8364 (t80) cc_final: 0.8073 (t80) REVERT: D 54 ARG cc_start: 0.8520 (tpp-160) cc_final: 0.8137 (tpp80) REVERT: a 127 ASN cc_start: 0.8172 (p0) cc_final: 0.7732 (p0) REVERT: a 171 MET cc_start: 0.8253 (tpp) cc_final: 0.7821 (tpp) REVERT: b 106 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7535 (tp) REVERT: b 150 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7742 (mp) REVERT: b 156 ARG cc_start: 0.7064 (ttm-80) cc_final: 0.5891 (ttt90) REVERT: c 85 GLN cc_start: 0.7521 (mt0) cc_final: 0.7012 (mm110) REVERT: c 221 MET cc_start: 0.8424 (tpp) cc_final: 0.8199 (tpp) outliers start: 50 outliers final: 36 residues processed: 259 average time/residue: 0.2464 time to fit residues: 91.3004 Evaluate side-chains 257 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 89 THR 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 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 180 MET Chi-restraints excluded: chain B residue 190 ASP 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 182 THR 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 84 LEU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 225 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 135 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3784 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= 0.316 Angle : 0.710 11.084 17711 Z= 0.343 Chirality : 0.043 0.221 2059 Planarity : 0.005 0.062 2203 Dihedral : 4.817 49.356 1752 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 3.73 % Allowed : 22.68 % Favored : 73.59 % 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: 1.42 (0.21), residues: 1602 helix: 1.75 (0.16), residues: 1032 sheet: 0.24 (0.60), residues: 83 loop : -0.65 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 66 HIS 0.006 0.001 HIS C 174 PHE 0.016 0.001 PHE b 175 TYR 0.020 0.002 TYR c 58 ARG 0.005 0.000 ARG D 59 *********************** 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 267 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 218 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.6945 (t-170) REVERT: C 21 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7990 (t80) REVERT: C 207 PHE cc_start: 0.8362 (t80) cc_final: 0.8099 (t80) REVERT: D 53 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8156 (tm-30) REVERT: a 127 ASN cc_start: 0.8161 (p0) cc_final: 0.7743 (p0) REVERT: a 171 MET cc_start: 0.8298 (tpp) cc_final: 0.7883 (tpp) REVERT: b 106 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7655 (tp) REVERT: b 117 MET cc_start: 0.7367 (ttm) cc_final: 0.7093 (ttt) REVERT: b 140 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7185 (tt) REVERT: b 150 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7830 (mp) REVERT: c 85 GLN cc_start: 0.7647 (mt0) cc_final: 0.7111 (mm110) REVERT: c 90 ASN cc_start: 0.8725 (m-40) cc_final: 0.8445 (m-40) outliers start: 49 outliers final: 39 residues processed: 251 average time/residue: 0.2226 time to fit residues: 82.2932 Evaluate side-chains 257 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 213 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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 89 THR 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 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 180 MET Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain 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 162 LEU Chi-restraints excluded: chain c residue 225 ILE Chi-restraints excluded: chain c residue 238 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 0.0030 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3893 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= 0.216 Angle : 0.658 8.428 17711 Z= 0.320 Chirality : 0.041 0.198 2059 Planarity : 0.005 0.063 2203 Dihedral : 4.669 47.359 1752 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 3.27 % Allowed : 22.91 % Favored : 73.82 % 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: 1.72 (0.21), residues: 1602 helix: 2.01 (0.16), residues: 1016 sheet: -0.21 (0.55), residues: 95 loop : -0.39 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP c 234 HIS 0.004 0.001 HIS a 186 PHE 0.014 0.001 PHE d 5 TYR 0.015 0.002 TYR C 15 ARG 0.006 0.000 ARG B 156 ********************** 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 268 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 225 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6898 (t-170) REVERT: C 21 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8034 (t80) REVERT: C 96 MET cc_start: 0.7455 (mtp) cc_final: 0.7057 (mtm) REVERT: C 207 PHE cc_start: 0.8302 (t80) cc_final: 0.8006 (t80) REVERT: C 229 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8088 (mm-30) REVERT: D 53 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8123 (tm-30) REVERT: a 127 ASN cc_start: 0.8048 (p0) cc_final: 0.7624 (p0) REVERT: b 106 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7648 (tp) REVERT: b 117 MET cc_start: 0.7403 (ttm) cc_final: 0.7128 (ttt) REVERT: b 150 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7782 (mp) REVERT: c 21 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7928 (t80) REVERT: c 85 GLN cc_start: 0.7520 (mt0) cc_final: 0.7027 (mm110) outliers start: 43 outliers final: 32 residues processed: 258 average time/residue: 0.2415 time to fit residues: 91.8304 Evaluate side-chains 251 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 214 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 89 THR Chi-restraints excluded: chain A residue 110 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 104 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 217 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 225 ILE Chi-restraints excluded: chain c residue 238 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 132 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.162118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131698 restraints weight = 17921.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130654 restraints weight = 13629.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.130070 restraints weight = 14249.468| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12989 Z= 0.209 Angle : 0.650 7.646 17711 Z= 0.314 Chirality : 0.041 0.177 2059 Planarity : 0.005 0.063 2203 Dihedral : 4.570 46.808 1752 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 2.97 % Allowed : 23.14 % Favored : 73.90 % 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: 1.85 (0.21), residues: 1602 helix: 2.11 (0.16), residues: 1016 sheet: -0.25 (0.54), residues: 95 loop : -0.29 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 66 HIS 0.004 0.001 HIS a 186 PHE 0.014 0.001 PHE d 5 TYR 0.015 0.001 TYR C 48 ARG 0.005 0.000 ARG d 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2438.76 seconds wall clock time: 45 minutes 7.69 seconds (2707.69 seconds total)