Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 02:17:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7f_12746/04_2023/7o7f_12746_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7f_12746/04_2023/7o7f_12746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7f_12746/04_2023/7o7f_12746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7f_12746/04_2023/7o7f_12746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7f_12746/04_2023/7o7f_12746_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7f_12746/04_2023/7o7f_12746_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 75 5.16 5 C 7113 2.51 5 N 1882 2.21 5 O 2100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "I PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H ASP 93": "OD1" <-> "OD2" Residue "H TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F ASP 107": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11170 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1767 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2440 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 478 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "I" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1654 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 206} Chain: "F" Number of atoms: 1694 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Conformer: "B" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} bond proxies already assigned to first conformer: 1700 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU F 148 " occ=0.73 ... (16 atoms not shown) pdb=" OE2BGLU F 148 " occ=0.27 Time building chain proxies: 6.96, per 1000 atoms: 0.62 Number of scatterers: 11170 At special positions: 0 Unit cell: (95.632, 136.776, 156.792, 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 75 16.00 O 2100 8.00 N 1882 7.00 C 7113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 178 " distance=2.03 Simple disulfide: pdb=" SG CYS I 10 " - pdb=" SG CYS I 34 " distance=2.03 Simple disulfide: pdb=" SG CYS I 11 " - pdb=" SG CYS I 50 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 167 " - pdb=" SG CYS H 222 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 113 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 219 " distance=2.04 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: 4.50 Conformation dependent library (CDL) restraints added in 1.9 seconds 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2662 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 18 sheets defined 30.5% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.831A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.811A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.964A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.871A pdb=" N PHE A 334 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 26 through 57 Proline residue: C 34 - end of helix removed outlier: 3.637A pdb=" N GLY C 47 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 90 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 98 through 131 Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 142 through 166 Proline residue: C 162 - end of helix removed outlier: 3.942A pdb=" N PHE C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 200 removed outlier: 3.690A pdb=" N LYS C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 223 removed outlier: 3.641A pdb=" N ILE C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 259 Proline residue: C 250 - end of helix Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 269 through 298 Proline residue: C 294 - end of helix Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'G' and resid 11 through 26 Processing helix chain 'G' and resid 33 through 50 removed outlier: 3.615A pdb=" N ARG G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 23 No H-bonds generated for 'chain 'I' and resid 21 through 23' Processing helix chain 'I' and resid 56 through 65 Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'F' and resid 105 through 107 No H-bonds generated for 'chain 'F' and resid 105 through 107' Processing helix chain 'F' and resid 147 through 152 Processing helix chain 'F' and resid 208 through 213 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.624A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.606A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.989A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.809A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.878A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.733A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.611A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.780A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 24 through 29 removed outlier: 6.786A pdb=" N VAL I 42 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR I 27 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL I 40 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 22 through 26 Processing sheet with id= K, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.064A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 147 through 151 removed outlier: 5.760A pdb=" N TYR H 202 " --> pdb=" O GLY H 171 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 178 through 181 removed outlier: 4.780A pdb=" N VAL H 220 " --> pdb=" O LEU H 237 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 196 through 198 Processing sheet with id= O, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.729A pdb=" N ALA F 95 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 127 through 129 removed outlier: 5.863A pdb=" N LEU F 62 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU F 71 " --> pdb=" O LEU F 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 139 through 143 Processing sheet with id= R, first strand: chain 'F' and resid 178 through 180 removed outlier: 4.118A pdb=" N TRP F 173 " --> pdb=" O ARG F 180 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1326 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: 3.71 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1808 1.31 - 1.44: 3167 1.44 - 1.57: 6340 1.57 - 1.70: 0 1.70 - 1.83: 105 Bond restraints: 11420 Sorted by residual: bond pdb=" C VAL C 83 " pdb=" O VAL C 83 " ideal model delta sigma weight residual 1.238 1.181 0.057 8.50e-03 1.38e+04 4.58e+01 bond pdb=" N PCA I 0 " pdb=" CD PCA I 0 " ideal model delta sigma weight residual 1.345 1.467 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C THR C 288 " pdb=" O THR C 288 " ideal model delta sigma weight residual 1.237 1.177 0.060 1.17e-02 7.31e+03 2.60e+01 bond pdb=" C LEU C 80 " pdb=" O LEU C 80 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.29e-02 6.01e+03 1.50e+01 bond pdb=" N PRO I 3 " pdb=" CA PRO I 3 " ideal model delta sigma weight residual 1.469 1.424 0.044 1.28e-02 6.10e+03 1.20e+01 ... (remaining 11415 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.41: 272 106.41 - 113.34: 6251 113.34 - 120.26: 4063 120.26 - 127.19: 4766 127.19 - 134.12: 125 Bond angle restraints: 15477 Sorted by residual: angle pdb=" N MET C 287 " pdb=" CA MET C 287 " pdb=" C MET C 287 " ideal model delta sigma weight residual 111.28 104.25 7.03 1.09e+00 8.42e-01 4.16e+01 angle pdb=" CA THR C 288 " pdb=" C THR C 288 " pdb=" O THR C 288 " ideal model delta sigma weight residual 120.55 114.14 6.41 1.06e+00 8.90e-01 3.66e+01 angle pdb=" N THR C 284 " pdb=" CA THR C 284 " pdb=" C THR C 284 " ideal model delta sigma weight residual 111.28 105.08 6.20 1.09e+00 8.42e-01 3.23e+01 angle pdb=" N THR C 288 " pdb=" CA THR C 288 " pdb=" CB THR C 288 " ideal model delta sigma weight residual 110.12 118.24 -8.12 1.47e+00 4.63e-01 3.05e+01 angle pdb=" CA PHE C 41 " pdb=" C PHE C 41 " pdb=" O PHE C 41 " ideal model delta sigma weight residual 120.70 115.27 5.43 1.03e+00 9.43e-01 2.78e+01 ... (remaining 15472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6169 17.93 - 35.87: 522 35.87 - 53.80: 80 53.80 - 71.73: 19 71.73 - 89.67: 16 Dihedral angle restraints: 6806 sinusoidal: 2676 harmonic: 4130 Sorted by residual: dihedral pdb=" CB CYS I 11 " pdb=" SG CYS I 11 " pdb=" SG CYS I 50 " pdb=" CB CYS I 50 " ideal model delta sinusoidal sigma weight residual 93.00 149.38 -56.38 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 152.79 27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA PHE H 51 " pdb=" C PHE H 51 " pdb=" N GLY H 52 " pdb=" CA GLY H 52 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1412 0.046 - 0.091: 234 0.091 - 0.137: 91 0.137 - 0.183: 7 0.183 - 0.228: 3 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CB THR C 288 " pdb=" CA THR C 288 " pdb=" OG1 THR C 288 " pdb=" CG2 THR C 288 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL C 40 " pdb=" CA VAL C 40 " pdb=" CG1 VAL C 40 " pdb=" CG2 VAL C 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA HIS C 289 " pdb=" N HIS C 289 " pdb=" C HIS C 289 " pdb=" CB HIS C 289 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 1744 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 78 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C PHE C 78 " 0.061 2.00e-02 2.50e+03 pdb=" O PHE C 78 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE C 79 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 289 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C HIS C 289 " 0.057 2.00e-02 2.50e+03 pdb=" O HIS C 289 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS C 290 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 80 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C LEU C 80 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU C 80 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 81 " 0.014 2.00e-02 2.50e+03 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 88 2.53 - 3.12: 8789 3.12 - 3.71: 16850 3.71 - 4.31: 24458 4.31 - 4.90: 41752 Nonbonded interactions: 91937 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 1.932 2.440 nonbonded pdb=" OH TYR C 187 " pdb=" O CYS I 34 " model vdw 1.955 2.440 nonbonded pdb=" OG1 THR A 324 " pdb=" OD1 ASN A 331 " model vdw 1.970 2.440 nonbonded pdb=" OG1 THR C 65 " pdb=" OD2 ASP C 125 " model vdw 1.973 2.440 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 1.984 2.440 ... (remaining 91932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.27 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 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: 10.990 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 32.750 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.122 11420 Z= 0.233 Angle : 0.637 9.970 15477 Z= 0.401 Chirality : 0.042 0.228 1747 Planarity : 0.003 0.051 1959 Dihedral : 14.025 89.666 4120 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.48 (0.23), residues: 1405 helix: 1.58 (0.25), residues: 425 sheet: 0.05 (0.27), residues: 378 loop : -0.32 (0.26), residues: 602 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.2792 time to fit residues: 83.6493 Evaluate side-chains 179 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 8.9990 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 244 HIS C 192 ASN C 194 GLN C 293 ASN G 21 GLN F 191 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 11420 Z= 0.249 Angle : 0.575 8.505 15477 Z= 0.305 Chirality : 0.043 0.199 1747 Planarity : 0.004 0.056 1959 Dihedral : 4.513 35.036 1537 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.52 (0.23), residues: 1405 helix: 1.60 (0.25), residues: 418 sheet: 0.10 (0.26), residues: 384 loop : -0.29 (0.26), residues: 603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 1.440 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 200 average time/residue: 0.2797 time to fit residues: 76.3823 Evaluate side-chains 181 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1122 time to fit residues: 3.9677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 11420 Z= 0.266 Angle : 0.571 7.731 15477 Z= 0.303 Chirality : 0.043 0.183 1747 Planarity : 0.004 0.050 1959 Dihedral : 4.533 36.762 1537 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.42 (0.23), residues: 1405 helix: 1.53 (0.26), residues: 417 sheet: 0.18 (0.27), residues: 360 loop : -0.45 (0.25), residues: 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 193 average time/residue: 0.3185 time to fit residues: 85.8743 Evaluate side-chains 173 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1075 time to fit residues: 3.2874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.0010 chunk 94 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 125 optimal weight: 0.0170 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 111 optimal weight: 0.0770 overall best weight: 0.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 11420 Z= 0.151 Angle : 0.527 13.170 15477 Z= 0.274 Chirality : 0.041 0.159 1747 Planarity : 0.004 0.051 1959 Dihedral : 4.231 31.371 1537 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.54 (0.23), residues: 1405 helix: 1.61 (0.26), residues: 418 sheet: 0.18 (0.26), residues: 367 loop : -0.31 (0.26), residues: 620 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 206 average time/residue: 0.2708 time to fit residues: 76.4839 Evaluate side-chains 183 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1037 time to fit residues: 3.2229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 11420 Z= 0.263 Angle : 0.573 10.802 15477 Z= 0.298 Chirality : 0.042 0.172 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.365 33.908 1537 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.45 (0.23), residues: 1405 helix: 1.39 (0.25), residues: 426 sheet: 0.27 (0.26), residues: 372 loop : -0.39 (0.26), residues: 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.368 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 187 average time/residue: 0.2864 time to fit residues: 73.3419 Evaluate side-chains 174 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1104 time to fit residues: 2.6660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 11420 Z= 0.212 Angle : 0.550 9.926 15477 Z= 0.286 Chirality : 0.041 0.157 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.307 32.694 1537 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.48 (0.23), residues: 1405 helix: 1.50 (0.26), residues: 420 sheet: 0.23 (0.27), residues: 366 loop : -0.37 (0.26), residues: 619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 1.372 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 188 average time/residue: 0.2745 time to fit residues: 70.4589 Evaluate side-chains 179 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1109 time to fit residues: 3.2914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.0000 chunk 74 optimal weight: 0.3980 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 11420 Z= 0.200 Angle : 0.555 9.482 15477 Z= 0.289 Chirality : 0.041 0.208 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.261 31.209 1537 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.47 (0.23), residues: 1405 helix: 1.51 (0.26), residues: 420 sheet: 0.22 (0.26), residues: 366 loop : -0.40 (0.25), residues: 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 1.223 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 181 average time/residue: 0.2922 time to fit residues: 71.7472 Evaluate side-chains 173 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1579 time to fit residues: 3.4382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 11420 Z= 0.259 Angle : 0.589 10.696 15477 Z= 0.306 Chirality : 0.042 0.181 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.405 32.753 1537 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.34 (0.23), residues: 1405 helix: 1.36 (0.26), residues: 421 sheet: 0.14 (0.26), residues: 376 loop : -0.44 (0.26), residues: 608 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 1.454 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 175 average time/residue: 0.2905 time to fit residues: 69.5159 Evaluate side-chains 171 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 166 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1079 time to fit residues: 2.8622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.2980 chunk 116 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 0.1980 chunk 117 optimal weight: 0.3980 chunk 81 optimal weight: 0.6980 chunk 131 optimal weight: 0.0050 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 11420 Z= 0.158 Angle : 0.553 9.553 15477 Z= 0.286 Chirality : 0.041 0.187 1747 Planarity : 0.004 0.054 1959 Dihedral : 4.176 27.907 1537 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.51 (0.23), residues: 1405 helix: 1.55 (0.26), residues: 421 sheet: 0.16 (0.26), residues: 373 loop : -0.30 (0.26), residues: 611 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 1.368 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 179 average time/residue: 0.2986 time to fit residues: 72.3972 Evaluate side-chains 170 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1166 time to fit residues: 2.1997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 7.9990 chunk 62 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.0670 chunk 116 optimal weight: 10.0000 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 ASN G 21 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 11420 Z= 0.156 Angle : 0.553 10.289 15477 Z= 0.284 Chirality : 0.041 0.177 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.076 25.841 1537 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.54 (0.23), residues: 1405 helix: 1.48 (0.26), residues: 429 sheet: 0.23 (0.25), residues: 384 loop : -0.29 (0.26), residues: 592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.350 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.2854 time to fit residues: 67.8277 Evaluate side-chains 162 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.198127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.164708 restraints weight = 27223.825| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 5.39 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 11420 Z= 0.227 Angle : 0.573 9.338 15477 Z= 0.296 Chirality : 0.042 0.180 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.190 28.253 1537 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.49 (0.23), residues: 1405 helix: 1.46 (0.26), residues: 424 sheet: 0.22 (0.26), residues: 384 loop : -0.34 (0.26), residues: 597 =============================================================================== Job complete usr+sys time: 2581.25 seconds wall clock time: 47 minutes 47.91 seconds (2867.91 seconds total)