Starting phenix.real_space_refine on Tue Jun 25 18:52:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2k_38015/06_2024/8x2k_38015_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2k_38015/06_2024/8x2k_38015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2k_38015/06_2024/8x2k_38015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2k_38015/06_2024/8x2k_38015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2k_38015/06_2024/8x2k_38015_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2k_38015/06_2024/8x2k_38015_neut_updated.pdb" } resolution = 3.03 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= -0.003 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5440 2.51 5 N 1472 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 258": "OD1" <-> "OD2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8570 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1896 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1795 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'LEU%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1803 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {'5YM': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 5.73, per 1000 atoms: 0.67 Number of scatterers: 8570 At special positions: 0 Unit cell: (88.4, 122.4, 124.95, 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 56 16.00 O 1602 8.00 N 1472 7.00 C 5440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " 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: 3.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 15 sheets defined 33.7% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 43 through 67 Processing helix chain 'A' and resid 74 through 101 Processing helix chain 'A' and resid 106 through 139 removed outlier: 3.620A pdb=" N GLY A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 148 through 166 removed outlier: 3.989A pdb=" N GLY A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 231 removed outlier: 3.973A pdb=" N ALA A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 257 through 268 Proline residue: A 262 - end of helix removed outlier: 4.125A pdb=" N LEU A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 300 removed outlier: 3.805A pdb=" N LEU A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 284 " --> pdb=" O TYR A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Proline residue: A 294 - end of helix removed outlier: 3.860A pdb=" N PHE A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'B' and resid 14 through 37 removed outlier: 3.998A pdb=" N ALA B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 332 through 352 removed outlier: 3.931A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.560A pdb=" N VAL B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 383 " --> pdb=" O CYS B 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.551A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 23 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.581A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 43 through 47 removed outlier: 7.454A pdb=" N ALA B 243 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU B 46 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE B 245 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER B 286 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE B 246 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE B 288 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL B 248 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE B 290 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 212 through 214 Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.940A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.071A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.782A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 180 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 198 through 202 removed outlier: 4.007A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.802A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 284 through 286 Processing sheet with id= I, first strand: chain 'C' and resid 317 through 320 removed outlier: 4.141A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 Processing sheet with id= L, first strand: chain 'E' and resid 49 through 51 Processing sheet with id= M, first strand: chain 'E' and resid 147 through 149 Processing sheet with id= N, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= O, first strand: chain 'E' and resid 226 through 231 removed outlier: 3.604A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 346 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: 2.76 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1392 1.30 - 1.43: 2297 1.43 - 1.56: 4964 1.56 - 1.69: 0 1.69 - 1.82: 81 Bond restraints: 8734 Sorted by residual: bond pdb=" C LEU A 212 " pdb=" O LEU A 212 " ideal model delta sigma weight residual 1.237 1.170 0.066 1.17e-02 7.31e+03 3.23e+01 bond pdb=" C18 5YM A 401 " pdb=" N20 5YM A 401 " ideal model delta sigma weight residual 1.344 1.450 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C TYR A 135 " pdb=" O TYR A 135 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.29e-02 6.01e+03 2.49e+01 bond pdb=" C ILE A 208 " pdb=" O ILE A 208 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.13e-02 7.83e+03 1.97e+01 bond pdb=" C PHE A 263 " pdb=" O PHE A 263 " ideal model delta sigma weight residual 1.236 1.191 0.046 1.15e-02 7.56e+03 1.59e+01 ... (remaining 8729 not shown) Histogram of bond angle deviations from ideal: 95.34 - 103.11: 48 103.11 - 110.88: 3196 110.88 - 118.66: 3748 118.66 - 126.43: 4720 126.43 - 134.21: 130 Bond angle restraints: 11842 Sorted by residual: angle pdb=" N VAL A 160 " pdb=" CA VAL A 160 " pdb=" C VAL A 160 " ideal model delta sigma weight residual 111.81 100.78 11.03 8.60e-01 1.35e+00 1.64e+02 angle pdb=" N THR A 121 " pdb=" CA THR A 121 " pdb=" C THR A 121 " ideal model delta sigma weight residual 114.04 103.06 10.98 1.24e+00 6.50e-01 7.84e+01 angle pdb=" N PRO A 189 " pdb=" CA PRO A 189 " pdb=" CB PRO A 189 " ideal model delta sigma weight residual 103.25 95.34 7.91 1.05e+00 9.07e-01 5.68e+01 angle pdb=" CA LEU A 212 " pdb=" C LEU A 212 " pdb=" O LEU A 212 " ideal model delta sigma weight residual 120.55 113.11 7.44 1.06e+00 8.90e-01 4.93e+01 angle pdb=" N ALA A 129 " pdb=" CA ALA A 129 " pdb=" C ALA A 129 " ideal model delta sigma weight residual 113.12 104.57 8.55 1.25e+00 6.40e-01 4.68e+01 ... (remaining 11837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 5065 33.81 - 67.62: 112 67.62 - 101.43: 10 101.43 - 135.24: 0 135.24 - 169.05: 1 Dihedral angle restraints: 5188 sinusoidal: 1981 harmonic: 3207 Sorted by residual: dihedral pdb=" C TYR A 135 " pdb=" N TYR A 135 " pdb=" CA TYR A 135 " pdb=" CB TYR A 135 " ideal model delta harmonic sigma weight residual -122.60 -109.21 -13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" N20 5YM A 401 " pdb=" C21 5YM A 401 " pdb=" C22 5YM A 401 " pdb=" O23 5YM A 401 " ideal model delta sinusoidal sigma weight residual -61.92 107.13 -169.05 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N ALA A 129 " pdb=" C ALA A 129 " pdb=" CA ALA A 129 " pdb=" CB ALA A 129 " ideal model delta harmonic sigma weight residual 122.90 111.87 11.03 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 5185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1246 0.083 - 0.165: 100 0.165 - 0.247: 13 0.247 - 0.330: 3 0.330 - 0.412: 1 Chirality restraints: 1363 Sorted by residual: chirality pdb=" CB VAL A 205 " pdb=" CA VAL A 205 " pdb=" CG1 VAL A 205 " pdb=" CG2 VAL A 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA VAL A 160 " pdb=" N VAL A 160 " pdb=" C VAL A 160 " pdb=" CB VAL A 160 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ALA A 129 " pdb=" N ALA A 129 " pdb=" C ALA A 129 " pdb=" CB ALA A 129 " both_signs ideal model delta sigma weight residual False 2.48 2.78 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1360 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 200 " -0.026 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ILE A 200 " 0.087 2.00e-02 2.50e+03 pdb=" O ILE A 200 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A 201 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 162 " -0.016 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C GLY A 162 " 0.053 2.00e-02 2.50e+03 pdb=" O GLY A 162 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 163 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 113 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C VAL A 113 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL A 113 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY A 114 " -0.017 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 49 2.51 - 3.11: 6326 3.11 - 3.70: 12309 3.70 - 4.30: 18275 4.30 - 4.90: 31475 Nonbonded interactions: 68434 Sorted by model distance: nonbonded pdb=" OH TYR B 318 " pdb=" OD2 ASP B 343 " model vdw 1.909 2.440 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 1.957 2.440 nonbonded pdb=" O ASP C 228 " pdb=" OG SER C 245 " model vdw 1.979 2.440 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.009 2.440 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.064 2.440 ... (remaining 68429 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: 2.630 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: 7.150 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.090 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.005 0.106 8734 Z= 0.330 Angle : 0.734 11.933 11842 Z= 0.476 Chirality : 0.049 0.412 1363 Planarity : 0.004 0.056 1503 Dihedral : 14.074 169.051 3113 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 0.77 % Allowed : 1.09 % Favored : 98.14 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.94 % 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: -0.74 (0.25), residues: 1089 helix: 0.30 (0.27), residues: 395 sheet: -0.78 (0.30), residues: 278 loop : -0.88 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 339 HIS 0.003 0.001 HIS B 357 PHE 0.029 0.002 PHE A 202 TYR 0.010 0.001 TYR C 105 ARG 0.012 0.001 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 0.974 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: B 238 PHE cc_start: 0.7600 (m-10) cc_final: 0.7388 (m-10) REVERT: C 197 ARG cc_start: 0.6720 (mmt90) cc_final: 0.6392 (mmp80) REVERT: E 180 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7167 (mtt180) outliers start: 7 outliers final: 3 residues processed: 139 average time/residue: 0.2651 time to fit residues: 47.9243 Evaluate side-chains 115 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 0.0870 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN C 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8734 Z= 0.224 Angle : 0.535 6.746 11842 Z= 0.281 Chirality : 0.042 0.161 1363 Planarity : 0.004 0.055 1503 Dihedral : 7.261 178.180 1227 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.77 % Allowed : 7.77 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.26), residues: 1089 helix: 0.76 (0.27), residues: 394 sheet: -0.56 (0.31), residues: 278 loop : -0.76 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 339 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.002 PHE C 199 TYR 0.008 0.001 TYR E 102 ARG 0.004 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.073 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: C 197 ARG cc_start: 0.6751 (mmt90) cc_final: 0.6437 (mmp80) REVERT: E 180 ARG cc_start: 0.7548 (mtm110) cc_final: 0.7178 (mtt180) outliers start: 7 outliers final: 5 residues processed: 123 average time/residue: 0.2672 time to fit residues: 42.7416 Evaluate side-chains 111 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 262 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.0770 chunk 106 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8734 Z= 0.172 Angle : 0.484 6.334 11842 Z= 0.256 Chirality : 0.041 0.150 1363 Planarity : 0.004 0.056 1503 Dihedral : 6.972 178.828 1223 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.42 % Allowed : 9.63 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.06 (0.26), residues: 1089 helix: 1.03 (0.27), residues: 393 sheet: -0.43 (0.31), residues: 283 loop : -0.67 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 339 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE B 222 TYR 0.008 0.001 TYR E 190 ARG 0.003 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.922 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: C 197 ARG cc_start: 0.6683 (mmt90) cc_final: 0.6410 (mmp80) REVERT: E 17 SER cc_start: 0.7819 (m) cc_final: 0.7453 (p) REVERT: E 180 ARG cc_start: 0.7467 (mtm110) cc_final: 0.7060 (mtt180) outliers start: 13 outliers final: 11 residues processed: 119 average time/residue: 0.2473 time to fit residues: 38.9119 Evaluate side-chains 120 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0030 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8734 Z= 0.249 Angle : 0.526 6.671 11842 Z= 0.276 Chirality : 0.042 0.171 1363 Planarity : 0.004 0.056 1503 Dihedral : 7.084 177.999 1223 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.08 % Allowed : 11.93 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.13 (0.26), residues: 1089 helix: 0.98 (0.27), residues: 395 sheet: -0.44 (0.31), residues: 286 loop : -0.74 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 339 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.002 PHE B 222 TYR 0.011 0.001 TYR E 190 ARG 0.003 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.975 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: D 21 MET cc_start: 0.6664 (ttp) cc_final: 0.5872 (tmm) REVERT: E 180 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7112 (mtt180) outliers start: 19 outliers final: 11 residues processed: 115 average time/residue: 0.2521 time to fit residues: 38.5510 Evaluate side-chains 115 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.7947 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8734 Z= 0.312 Angle : 0.564 7.825 11842 Z= 0.295 Chirality : 0.043 0.181 1363 Planarity : 0.004 0.057 1503 Dihedral : 7.234 177.360 1223 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.41 % Allowed : 12.58 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.16 (0.26), residues: 1089 helix: 0.97 (0.27), residues: 386 sheet: -0.39 (0.31), residues: 297 loop : -0.79 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 339 HIS 0.004 0.001 HIS B 357 PHE 0.017 0.002 PHE B 222 TYR 0.012 0.002 TYR E 190 ARG 0.005 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.091 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 262 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7663 (ttm) REVERT: D 21 MET cc_start: 0.6694 (ttp) cc_final: 0.5917 (tmm) REVERT: E 180 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7170 (mtt180) outliers start: 22 outliers final: 16 residues processed: 120 average time/residue: 0.2503 time to fit residues: 39.9066 Evaluate side-chains 119 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 104 optimal weight: 0.0370 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8734 Z= 0.353 Angle : 0.592 7.975 11842 Z= 0.309 Chirality : 0.044 0.188 1363 Planarity : 0.004 0.057 1503 Dihedral : 7.368 177.173 1223 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.52 % Allowed : 14.77 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.30 (0.26), residues: 1089 helix: 0.86 (0.27), residues: 386 sheet: -0.54 (0.31), residues: 296 loop : -0.82 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 339 HIS 0.005 0.001 HIS B 357 PHE 0.017 0.002 PHE B 222 TYR 0.013 0.002 TYR E 190 ARG 0.005 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.966 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 262 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7716 (ttm) REVERT: D 21 MET cc_start: 0.6615 (ttp) cc_final: 0.5885 (tmm) REVERT: E 180 ARG cc_start: 0.7611 (mtm110) cc_final: 0.7210 (mtt180) outliers start: 23 outliers final: 19 residues processed: 120 average time/residue: 0.2473 time to fit residues: 39.3297 Evaluate side-chains 119 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8734 Z= 0.184 Angle : 0.487 6.458 11842 Z= 0.259 Chirality : 0.041 0.179 1363 Planarity : 0.004 0.055 1503 Dihedral : 6.952 172.636 1223 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.75 % Allowed : 15.97 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.08 (0.26), residues: 1089 helix: 1.09 (0.27), residues: 387 sheet: -0.41 (0.30), residues: 300 loop : -0.77 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 339 HIS 0.003 0.001 HIS E 35 PHE 0.021 0.001 PHE A 97 TYR 0.008 0.001 TYR E 102 ARG 0.006 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.932 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 197 ARG cc_start: 0.6742 (mmt90) cc_final: 0.6382 (mmp80) REVERT: C 262 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7606 (ttm) REVERT: D 21 MET cc_start: 0.6601 (ttp) cc_final: 0.5852 (tmm) REVERT: E 17 SER cc_start: 0.7775 (m) cc_final: 0.7386 (p) REVERT: E 180 ARG cc_start: 0.7495 (mtm110) cc_final: 0.7152 (mtt180) outliers start: 16 outliers final: 11 residues processed: 115 average time/residue: 0.2655 time to fit residues: 40.3100 Evaluate side-chains 115 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8734 Z= 0.198 Angle : 0.494 6.449 11842 Z= 0.262 Chirality : 0.041 0.151 1363 Planarity : 0.004 0.055 1503 Dihedral : 6.820 168.196 1223 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.08 % Allowed : 15.86 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.05 (0.26), residues: 1089 helix: 1.14 (0.27), residues: 388 sheet: -0.43 (0.31), residues: 293 loop : -0.74 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 339 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE B 222 TYR 0.009 0.001 TYR E 190 ARG 0.006 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.897 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 262 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7617 (ttm) REVERT: D 21 MET cc_start: 0.6539 (ttp) cc_final: 0.5837 (tmm) REVERT: E 17 SER cc_start: 0.7784 (m) cc_final: 0.7367 (p) REVERT: E 180 ARG cc_start: 0.7480 (mtm110) cc_final: 0.7154 (mtt180) outliers start: 19 outliers final: 15 residues processed: 114 average time/residue: 0.2519 time to fit residues: 37.8807 Evaluate side-chains 118 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0970 chunk 97 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8734 Z= 0.187 Angle : 0.493 7.923 11842 Z= 0.258 Chirality : 0.041 0.151 1363 Planarity : 0.004 0.055 1503 Dihedral : 6.604 159.806 1223 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.41 % Allowed : 15.54 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.02 (0.26), residues: 1089 helix: 1.18 (0.27), residues: 388 sheet: -0.41 (0.31), residues: 287 loop : -0.75 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 339 HIS 0.003 0.001 HIS E 35 PHE 0.036 0.001 PHE A 97 TYR 0.008 0.001 TYR E 190 ARG 0.006 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.918 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 262 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7589 (ttm) REVERT: D 21 MET cc_start: 0.6543 (ttp) cc_final: 0.5900 (tmm) REVERT: E 17 SER cc_start: 0.7785 (m) cc_final: 0.7362 (p) REVERT: E 180 ARG cc_start: 0.7466 (mtm110) cc_final: 0.7151 (mtt180) outliers start: 22 outliers final: 16 residues processed: 117 average time/residue: 0.2528 time to fit residues: 39.0873 Evaluate side-chains 120 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8734 Z= 0.158 Angle : 0.478 7.771 11842 Z= 0.252 Chirality : 0.040 0.136 1363 Planarity : 0.004 0.054 1503 Dihedral : 6.187 143.720 1223 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.19 % Allowed : 15.43 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.13 (0.26), residues: 1089 helix: 1.35 (0.27), residues: 386 sheet: -0.34 (0.31), residues: 290 loop : -0.70 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 339 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 222 TYR 0.008 0.001 TYR E 102 ARG 0.007 0.000 ARG C 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.974 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: D 21 MET cc_start: 0.6578 (ttp) cc_final: 0.5951 (tmm) REVERT: E 17 SER cc_start: 0.7803 (m) cc_final: 0.7410 (p) REVERT: E 180 ARG cc_start: 0.7429 (mtm110) cc_final: 0.7081 (mtt180) outliers start: 20 outliers final: 15 residues processed: 130 average time/residue: 0.2460 time to fit residues: 42.6357 Evaluate side-chains 122 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.155489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111090 restraints weight = 10176.500| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.34 r_work: 0.3156 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8734 Z= 0.279 Angle : 0.561 8.481 11842 Z= 0.290 Chirality : 0.043 0.181 1363 Planarity : 0.004 0.055 1503 Dihedral : 6.280 133.447 1223 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.30 % Allowed : 15.75 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.06 (0.26), residues: 1089 helix: 1.11 (0.27), residues: 388 sheet: -0.35 (0.30), residues: 308 loop : -0.81 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 339 HIS 0.004 0.001 HIS B 357 PHE 0.015 0.002 PHE B 222 TYR 0.012 0.002 TYR E 190 ARG 0.007 0.000 ARG C 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2288.43 seconds wall clock time: 41 minutes 27.62 seconds (2487.62 seconds total)