Starting phenix.real_space_refine on Sat Apr 6 11:02:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyh_35822/04_2024/8iyh_35822_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyh_35822/04_2024/8iyh_35822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyh_35822/04_2024/8iyh_35822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyh_35822/04_2024/8iyh_35822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyh_35822/04_2024/8iyh_35822_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyh_35822/04_2024/8iyh_35822_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.039 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 48 5.16 5 C 5108 2.51 5 N 1392 2.21 5 O 1487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "H GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2410 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1538 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2001 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 485 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 215 Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 400 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.74, per 1000 atoms: 0.59 Number of scatterers: 8035 At special positions: 0 Unit cell: (89.995, 117.432, 133.895, 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 48 16.00 O 1487 8.00 N 1392 7.00 C 5108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 183 " distance=2.37 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 266 " distance=2.03 Simple disulfide: pdb=" SG CYS D 100 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 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: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 14 sheets defined 34.5% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 4 through 25 Processing helix chain 'A' and resid 30 through 36 removed outlier: 6.067A pdb=" N ASN A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 32 removed outlier: 3.767A pdb=" N LYS B 32 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 246 through 255 Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.841A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 297 through 311 removed outlier: 4.178A pdb=" N LYS B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'D' and resid 25 through 53 Proline residue: D 31 - end of helix removed outlier: 3.961A pdb=" N LEU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 88 Proline residue: D 81 - end of helix Processing helix chain 'D' and resid 97 through 129 removed outlier: 3.502A pdb=" N PHE D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 138 Processing helix chain 'D' and resid 141 through 157 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 188 through 217 removed outlier: 3.796A pdb=" N PHE D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Proline residue: D 200 - end of helix Processing helix chain 'D' and resid 225 through 261 removed outlier: 4.256A pdb=" N ILE D 230 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 266 through 294 removed outlier: 3.820A pdb=" N ARG D 270 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER D 271 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 280 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN D 286 " --> pdb=" O THR D 283 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 289 " --> pdb=" O ASN D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 58 through 63 removed outlier: 6.925A pdb=" N ALA A 73 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET A 61 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 71 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N TRP A 63 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 69 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS A 91 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP A 83 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS A 89 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.981A pdb=" N GLY A 115 " --> pdb=" O MET A 101 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS A 103 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 113 " --> pdb=" O CYS A 103 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR A 105 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR A 111 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 116 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 137 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASN A 125 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 135 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 146 through 151 removed outlier: 6.773A pdb=" N SER A 160 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS A 149 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 158 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE A 151 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLN A 156 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASP A 170 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLN A 176 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 187 through 192 removed outlier: 6.525A pdb=" N GLY A 202 " --> pdb=" O MET A 188 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A 190 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 200 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU A 192 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A 198 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A 220 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP A 212 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS A 218 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.735A pdb=" N GLY A 244 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 232 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 242 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE A 234 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA A 240 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 262 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP A 254 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU A 260 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 273 through 278 removed outlier: 6.262A pdb=" N GLY A 288 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 276 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 286 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A 278 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 284 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 306 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASP A 298 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A 304 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.475A pdb=" N ILE A 338 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR A 50 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 336 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 319 through 323 removed outlier: 7.304A pdb=" N ILE B 265 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N HIS B 322 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 267 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS B 196 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU B 36 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG B 198 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 38 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 200 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLY B 40 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 186 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 11 through 13 Processing sheet with id= J, first strand: chain 'D' and resid 169 through 171 Processing sheet with id= K, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.556A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.506A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL H 149 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU H 246 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.898A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 993 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: 2.60 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1399 1.32 - 1.45: 2223 1.45 - 1.57: 4518 1.57 - 1.69: 1 1.69 - 1.81: 64 Bond restraints: 8205 Sorted by residual: bond pdb=" N PHE D 186 " pdb=" CA PHE D 186 " ideal model delta sigma weight residual 1.455 1.528 -0.073 1.23e-02 6.61e+03 3.50e+01 bond pdb=" CA PHE D 186 " pdb=" C PHE D 186 " ideal model delta sigma weight residual 1.522 1.581 -0.060 1.22e-02 6.72e+03 2.39e+01 bond pdb=" C20 FI7 D 401 " pdb=" N19 FI7 D 401 " ideal model delta sigma weight residual 1.396 1.327 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C22 FI7 D 401 " pdb=" O23 FI7 D 401 " ideal model delta sigma weight residual 1.269 1.203 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C LYS B 24 " pdb=" O LYS B 24 " ideal model delta sigma weight residual 1.236 1.201 0.036 1.15e-02 7.56e+03 9.75e+00 ... (remaining 8200 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.42: 185 106.42 - 113.57: 4475 113.57 - 120.72: 3545 120.72 - 127.87: 2910 127.87 - 135.02: 76 Bond angle restraints: 11191 Sorted by residual: angle pdb=" CA PHE D 186 " pdb=" C PHE D 186 " pdb=" O PHE D 186 " ideal model delta sigma weight residual 120.70 112.56 8.14 1.08e+00 8.57e-01 5.68e+01 angle pdb=" N HIS D 184 " pdb=" CA HIS D 184 " pdb=" C HIS D 184 " ideal model delta sigma weight residual 113.19 120.64 -7.45 1.19e+00 7.06e-01 3.92e+01 angle pdb=" N PHE D 186 " pdb=" CA PHE D 186 " pdb=" C PHE D 186 " ideal model delta sigma weight residual 109.40 119.18 -9.78 1.63e+00 3.76e-01 3.60e+01 angle pdb=" O LEU B 23 " pdb=" C LEU B 23 " pdb=" N LYS B 24 " ideal model delta sigma weight residual 122.07 116.90 5.17 1.03e+00 9.43e-01 2.52e+01 angle pdb=" CA LEU B 23 " pdb=" C LEU B 23 " pdb=" N LYS B 24 " ideal model delta sigma weight residual 117.07 122.14 -5.07 1.14e+00 7.69e-01 1.98e+01 ... (remaining 11186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4372 17.56 - 35.11: 339 35.11 - 52.67: 70 52.67 - 70.22: 10 70.22 - 87.78: 3 Dihedral angle restraints: 4794 sinusoidal: 1561 harmonic: 3233 Sorted by residual: dihedral pdb=" CB CYS D 18 " pdb=" SG CYS D 18 " pdb=" SG CYS D 183 " pdb=" CB CYS D 183 " ideal model delta sinusoidal sigma weight residual 93.00 53.07 39.93 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA VAL D 29 " pdb=" C VAL D 29 " pdb=" N LEU D 30 " pdb=" CA LEU D 30 " ideal model delta harmonic sigma weight residual -180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 938 0.044 - 0.088: 263 0.088 - 0.132: 91 0.132 - 0.177: 8 0.177 - 0.221: 3 Chirality restraints: 1303 Sorted by residual: chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ILE D 242 " pdb=" N ILE D 242 " pdb=" C ILE D 242 " pdb=" CB ILE D 242 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE D 13 " pdb=" N ILE D 13 " pdb=" C ILE D 13 " pdb=" CB ILE D 13 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 1300 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 FI7 D 401 " 0.064 2.00e-02 2.50e+03 5.71e-02 5.72e+01 pdb=" C05 FI7 D 401 " -0.021 2.00e-02 2.50e+03 pdb=" C07 FI7 D 401 " -0.063 2.00e-02 2.50e+03 pdb=" C08 FI7 D 401 " 0.091 2.00e-02 2.50e+03 pdb=" N06 FI7 D 401 " -0.075 2.00e-02 2.50e+03 pdb=" N15 FI7 D 401 " -0.013 2.00e-02 2.50e+03 pdb=" O16 FI7 D 401 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 FI7 D 401 " 0.081 2.00e-02 2.50e+03 4.11e-02 3.38e+01 pdb=" C08 FI7 D 401 " -0.040 2.00e-02 2.50e+03 pdb=" C09 FI7 D 401 " -0.032 2.00e-02 2.50e+03 pdb=" C10 FI7 D 401 " -0.010 2.00e-02 2.50e+03 pdb=" C11 FI7 D 401 " -0.001 2.00e-02 2.50e+03 pdb=" C13 FI7 D 401 " -0.014 2.00e-02 2.50e+03 pdb=" N14 FI7 D 401 " -0.036 2.00e-02 2.50e+03 pdb=" O12 FI7 D 401 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 232 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C PHE D 232 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE D 232 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE D 233 " -0.022 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 749 2.74 - 3.28: 8124 3.28 - 3.82: 13026 3.82 - 4.36: 15165 4.36 - 4.90: 27525 Nonbonded interactions: 64589 Sorted by model distance: nonbonded pdb=" OD1 ASP A 27 " pdb=" OG SER G 31 " model vdw 2.204 2.440 nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.212 2.440 nonbonded pdb=" O GLY D 44 " pdb=" OH TYR D 295 " model vdw 2.213 2.440 nonbonded pdb=" NZ LYS G 32 " pdb=" OD2 ASP G 36 " model vdw 2.273 2.520 nonbonded pdb=" OG SER A 281 " pdb=" OD2 ASP G 48 " model vdw 2.278 2.440 ... (remaining 64584 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=1.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.000 Extract box with map and model: 5.500 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.480 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 0.073 8205 Z= 0.289 Angle : 0.723 9.780 11191 Z= 0.432 Chirality : 0.046 0.221 1303 Planarity : 0.005 0.075 1440 Dihedral : 13.480 87.775 2689 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 15.16 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.53 (0.26), residues: 1099 helix: 0.81 (0.28), residues: 372 sheet: 0.26 (0.31), residues: 273 loop : 0.21 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 82 HIS 0.004 0.001 HIS D 184 PHE 0.015 0.001 PHE D 232 TYR 0.010 0.001 TYR H 190 ARG 0.006 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.848 Fit side-chains REVERT: A 46 ARG cc_start: 0.7274 (mtm110) cc_final: 0.7028 (ttp80) REVERT: B 24 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6812 (pttm) REVERT: B 26 ASP cc_start: 0.8047 (t0) cc_final: 0.7726 (t0) REVERT: B 210 LYS cc_start: 0.7393 (ptmm) cc_final: 0.6892 (pttm) REVERT: B 273 ASP cc_start: 0.7963 (m-30) cc_final: 0.7631 (p0) REVERT: D 84 MET cc_start: 0.6521 (tpt) cc_final: 0.6267 (tpt) REVERT: D 225 LYS cc_start: 0.6333 (mmtp) cc_final: 0.6041 (mttt) outliers start: 8 outliers final: 1 residues processed: 136 average time/residue: 0.2160 time to fit residues: 39.3136 Evaluate side-chains 110 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain D residue 232 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS D 112 GLN G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8205 Z= 0.263 Angle : 0.577 6.947 11191 Z= 0.307 Chirality : 0.045 0.166 1303 Planarity : 0.005 0.052 1440 Dihedral : 6.176 55.928 1217 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.19 % Allowed : 13.13 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.50 (0.25), residues: 1099 helix: 0.84 (0.27), residues: 374 sheet: 0.09 (0.30), residues: 287 loop : 0.27 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 169 HIS 0.005 0.001 HIS A 91 PHE 0.022 0.002 PHE H 68 TYR 0.016 0.001 TYR H 190 ARG 0.005 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 0.903 Fit side-chains REVERT: A 46 ARG cc_start: 0.7365 (mtm110) cc_final: 0.7092 (ttp80) REVERT: B 210 LYS cc_start: 0.7395 (ptmm) cc_final: 0.6909 (pttm) REVERT: B 258 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7250 (mtmm) REVERT: B 273 ASP cc_start: 0.7934 (m-30) cc_final: 0.7552 (p0) outliers start: 31 outliers final: 20 residues processed: 134 average time/residue: 0.1993 time to fit residues: 36.7230 Evaluate side-chains 126 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 0.0370 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN G 24 ASN H 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8205 Z= 0.224 Angle : 0.521 8.382 11191 Z= 0.278 Chirality : 0.044 0.164 1303 Planarity : 0.004 0.055 1440 Dihedral : 5.637 53.783 1211 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.06 % Allowed : 14.48 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.25), residues: 1099 helix: 0.94 (0.27), residues: 372 sheet: -0.08 (0.30), residues: 287 loop : 0.32 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE D 232 TYR 0.014 0.001 TYR H 190 ARG 0.005 0.001 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 0.901 Fit side-chains REVERT: A 46 ARG cc_start: 0.7391 (mtm110) cc_final: 0.7078 (ttp80) REVERT: B 26 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7244 (m-30) REVERT: B 210 LYS cc_start: 0.7351 (ptmm) cc_final: 0.6869 (pttm) REVERT: B 258 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7163 (mtmm) REVERT: B 273 ASP cc_start: 0.7905 (m-30) cc_final: 0.7508 (p0) REVERT: D 218 ARG cc_start: 0.7418 (mmm-85) cc_final: 0.7180 (mtp85) outliers start: 30 outliers final: 22 residues processed: 134 average time/residue: 0.2162 time to fit residues: 39.5163 Evaluate side-chains 129 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.0010 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8205 Z= 0.249 Angle : 0.511 7.252 11191 Z= 0.273 Chirality : 0.043 0.163 1303 Planarity : 0.004 0.038 1440 Dihedral : 5.091 43.153 1211 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.01 % Allowed : 14.88 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.25), residues: 1099 helix: 1.08 (0.28), residues: 369 sheet: -0.29 (0.29), residues: 287 loop : 0.24 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.002 PHE A 235 TYR 0.014 0.001 TYR H 190 ARG 0.003 0.001 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 107 time to evaluate : 0.893 Fit side-chains REVERT: B 26 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: B 210 LYS cc_start: 0.7314 (ptmm) cc_final: 0.6838 (pttm) REVERT: B 258 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7131 (mtmm) REVERT: B 273 ASP cc_start: 0.7923 (m-30) cc_final: 0.7511 (p0) REVERT: D 218 ARG cc_start: 0.7366 (mmm-85) cc_final: 0.7149 (mtp85) outliers start: 37 outliers final: 25 residues processed: 135 average time/residue: 0.1897 time to fit residues: 35.5382 Evaluate side-chains 132 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 268 ASN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8205 Z= 0.268 Angle : 0.517 6.686 11191 Z= 0.277 Chirality : 0.043 0.166 1303 Planarity : 0.004 0.040 1440 Dihedral : 4.811 34.855 1211 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.87 % Allowed : 15.70 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.32 (0.25), residues: 1099 helix: 1.11 (0.28), residues: 369 sheet: -0.43 (0.30), residues: 287 loop : 0.09 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.001 PHE A 235 TYR 0.015 0.001 TYR H 190 ARG 0.002 0.000 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 109 time to evaluate : 0.916 Fit side-chains REVERT: B 26 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: B 210 LYS cc_start: 0.7312 (ptmm) cc_final: 0.6839 (pttm) REVERT: B 258 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7132 (mtmm) REVERT: B 273 ASP cc_start: 0.7919 (m-30) cc_final: 0.7522 (p0) REVERT: D 198 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6556 (m-10) REVERT: D 218 ARG cc_start: 0.7365 (mmm-85) cc_final: 0.7132 (mtp85) outliers start: 36 outliers final: 31 residues processed: 134 average time/residue: 0.1879 time to fit residues: 34.9232 Evaluate side-chains 141 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 108 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 26 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8205 Z= 0.200 Angle : 0.481 6.234 11191 Z= 0.257 Chirality : 0.042 0.167 1303 Planarity : 0.004 0.040 1440 Dihedral : 4.315 22.576 1211 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.28 % Allowed : 16.64 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.39 (0.26), residues: 1099 helix: 1.25 (0.28), residues: 367 sheet: -0.45 (0.30), residues: 282 loop : 0.09 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE A 235 TYR 0.014 0.001 TYR H 190 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 112 time to evaluate : 0.821 Fit side-chains REVERT: B 26 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: B 210 LYS cc_start: 0.7294 (ptmm) cc_final: 0.6825 (pttm) REVERT: B 258 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7131 (mtmm) REVERT: B 273 ASP cc_start: 0.7927 (m-30) cc_final: 0.7496 (p0) REVERT: D 120 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8491 (p) REVERT: D 198 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6583 (m-10) REVERT: D 232 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.6963 (t80) REVERT: G 38 MET cc_start: 0.7933 (ttp) cc_final: 0.7668 (ttp) outliers start: 39 outliers final: 26 residues processed: 138 average time/residue: 0.1896 time to fit residues: 36.2275 Evaluate side-chains 140 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7816 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8205 Z= 0.234 Angle : 0.500 8.588 11191 Z= 0.266 Chirality : 0.043 0.172 1303 Planarity : 0.004 0.041 1440 Dihedral : 4.259 26.420 1211 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.87 % Allowed : 17.19 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.33 (0.26), residues: 1099 helix: 1.21 (0.28), residues: 373 sheet: -0.55 (0.30), residues: 287 loop : 0.08 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE A 235 TYR 0.015 0.001 TYR H 190 ARG 0.003 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 0.882 Fit side-chains REVERT: B 26 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: B 210 LYS cc_start: 0.7310 (ptmm) cc_final: 0.6854 (pttm) REVERT: B 258 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7142 (mtmm) REVERT: B 273 ASP cc_start: 0.7945 (m-30) cc_final: 0.7498 (p0) REVERT: D 120 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8496 (p) REVERT: D 198 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6589 (m-10) REVERT: D 218 ARG cc_start: 0.7353 (mmm-85) cc_final: 0.6979 (mtp85) REVERT: D 253 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7429 (ttm170) REVERT: G 38 MET cc_start: 0.7861 (ttp) cc_final: 0.7565 (ttp) outliers start: 36 outliers final: 27 residues processed: 137 average time/residue: 0.2052 time to fit residues: 38.2383 Evaluate side-chains 143 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8205 Z= 0.228 Angle : 0.500 8.081 11191 Z= 0.267 Chirality : 0.043 0.170 1303 Planarity : 0.004 0.041 1440 Dihedral : 4.196 27.803 1211 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.33 % Allowed : 18.00 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.26), residues: 1099 helix: 1.24 (0.28), residues: 372 sheet: -0.52 (0.30), residues: 288 loop : 0.11 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE A 235 TYR 0.014 0.001 TYR H 190 ARG 0.002 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 0.882 Fit side-chains REVERT: A 45 MET cc_start: 0.8367 (ptt) cc_final: 0.7928 (ptt) REVERT: B 26 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7431 (m-30) REVERT: B 210 LYS cc_start: 0.7253 (ptmm) cc_final: 0.6831 (pttm) REVERT: B 258 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7140 (mtmm) REVERT: D 120 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8494 (p) REVERT: D 198 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6585 (m-10) REVERT: D 218 ARG cc_start: 0.7398 (mmm-85) cc_final: 0.7011 (mtp85) REVERT: D 253 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7448 (ttm170) REVERT: G 38 MET cc_start: 0.7860 (ttp) cc_final: 0.7579 (ttp) outliers start: 32 outliers final: 28 residues processed: 133 average time/residue: 0.2141 time to fit residues: 38.4868 Evaluate side-chains 144 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7829 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8205 Z= 0.269 Angle : 0.515 8.102 11191 Z= 0.275 Chirality : 0.043 0.174 1303 Planarity : 0.004 0.040 1440 Dihedral : 4.278 28.484 1211 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.87 % Allowed : 17.46 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.28 (0.26), residues: 1099 helix: 1.20 (0.27), residues: 372 sheet: -0.62 (0.30), residues: 291 loop : 0.07 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE A 235 TYR 0.015 0.001 TYR H 190 ARG 0.003 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 0.841 Fit side-chains REVERT: A 45 MET cc_start: 0.8309 (ptt) cc_final: 0.7795 (ptt) REVERT: A 270 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8664 (pt) REVERT: B 26 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7394 (m-30) REVERT: B 210 LYS cc_start: 0.7267 (ptmm) cc_final: 0.6853 (pttm) REVERT: B 258 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7163 (mtmm) REVERT: D 120 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8509 (p) REVERT: D 198 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6537 (m-10) REVERT: D 218 ARG cc_start: 0.7393 (mmm-85) cc_final: 0.6979 (mtp85) REVERT: D 253 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7462 (ttm170) REVERT: G 38 MET cc_start: 0.7889 (ttp) cc_final: 0.7600 (ttp) outliers start: 36 outliers final: 30 residues processed: 135 average time/residue: 0.1997 time to fit residues: 36.8629 Evaluate side-chains 146 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8205 Z= 0.237 Angle : 0.503 8.033 11191 Z= 0.269 Chirality : 0.043 0.170 1303 Planarity : 0.004 0.040 1440 Dihedral : 4.222 28.705 1211 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.60 % Allowed : 17.59 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.31 (0.26), residues: 1099 helix: 1.21 (0.27), residues: 372 sheet: -0.58 (0.30), residues: 288 loop : 0.07 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE A 235 TYR 0.014 0.001 TYR H 190 ARG 0.005 0.000 ARG B 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 113 time to evaluate : 0.851 Fit side-chains REVERT: A 17 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7661 (tm-30) REVERT: A 45 MET cc_start: 0.8362 (ptt) cc_final: 0.7837 (ptt) REVERT: A 270 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8684 (pt) REVERT: B 26 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: B 210 LYS cc_start: 0.7258 (ptmm) cc_final: 0.6841 (pttm) REVERT: B 258 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7152 (mtmm) REVERT: D 120 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8515 (p) REVERT: D 198 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6529 (m-10) REVERT: D 218 ARG cc_start: 0.7419 (mmm-85) cc_final: 0.6981 (mtp85) REVERT: D 253 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7421 (ttm170) REVERT: G 38 MET cc_start: 0.7876 (ttp) cc_final: 0.7582 (ttp) outliers start: 34 outliers final: 29 residues processed: 134 average time/residue: 0.1961 time to fit residues: 35.9852 Evaluate side-chains 144 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.187165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139652 restraints weight = 8823.981| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.99 r_work: 0.3134 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8205 Z= 0.256 Angle : 0.508 7.900 11191 Z= 0.272 Chirality : 0.043 0.171 1303 Planarity : 0.004 0.040 1440 Dihedral : 4.251 29.119 1211 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.87 % Allowed : 17.32 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.27 (0.26), residues: 1099 helix: 1.22 (0.27), residues: 372 sheet: -0.62 (0.30), residues: 288 loop : 0.04 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE A 235 TYR 0.015 0.001 TYR H 190 ARG 0.004 0.000 ARG B 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1988.48 seconds wall clock time: 36 minutes 49.33 seconds (2209.33 seconds total)