Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 18:12:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/04_2023/7srr_25402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/04_2023/7srr_25402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/04_2023/7srr_25402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/04_2023/7srr_25402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/04_2023/7srr_25402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/04_2023/7srr_25402_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1944 atoms to isotropic. 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 54 5.16 5 C 5395 2.51 5 N 1411 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 20": "OD1" <-> "OD2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8394 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1713 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2518 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 363 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1704 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2096 Unusual residues: {'7LD': 1} Classifications: {'peptide': 274, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 12, 'TRANS': 261, None: 1} Not linked: pdbres="ILE R 395 " pdbres="7LD R 501 " Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Time building chain proxies: 4.92, per 1000 atoms: 0.59 Number of scatterers: 8394 At special positions: 0 Unit cell: (101.521, 117.139, 131.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1534 8.00 N 1411 7.00 C 5395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 350 " - pdb=" SG CYS R 353 " 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: 3.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 12 sheets defined 32.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 7 through 31 removed outlier: 3.524A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 184 through 203 Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.579A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' 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 helix chain 'R' and resid 57 through 81 removed outlier: 3.998A pdb=" N MET R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE R 65 " --> pdb=" O ILE R 61 " (cutoff:3.500A) Proline residue: R 67 - end of helix removed outlier: 3.552A pdb=" N ILE R 76 " --> pdb=" O ASN R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 106 removed outlier: 3.610A pdb=" N PHE R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET R 94 " --> pdb=" O ASN R 90 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER R 95 " --> pdb=" O TYR R 91 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU R 96 " --> pdb=" O PHE R 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 116 Processing helix chain 'R' and resid 128 through 158 removed outlier: 3.794A pdb=" N LEU R 132 " --> pdb=" O CYS R 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE R 133 " --> pdb=" O PRO R 129 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER R 150 " --> pdb=" O LEU R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 164 Processing helix chain 'R' and resid 169 through 187 Processing helix chain 'R' and resid 189 through 192 No H-bonds generated for 'chain 'R' and resid 189 through 192' Processing helix chain 'R' and resid 217 through 220 No H-bonds generated for 'chain 'R' and resid 217 through 220' Processing helix chain 'R' and resid 227 through 244 removed outlier: 3.509A pdb=" N ILE R 232 " --> pdb=" O THR R 228 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR R 237 " --> pdb=" O MET R 233 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS R 242 " --> pdb=" O PHE R 238 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA R 243 " --> pdb=" O LEU R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 336 removed outlier: 3.760A pdb=" N ALA R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER R 323 " --> pdb=" O GLU R 319 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY R 327 " --> pdb=" O SER R 323 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET R 336 " --> pdb=" O LEU R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 349 Processing helix chain 'R' and resid 355 through 361 Processing helix chain 'R' and resid 365 through 374 removed outlier: 3.691A pdb=" N SER R 372 " --> pdb=" O ILE R 368 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY R 374 " --> pdb=" O TYR R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 379 No H-bonds generated for 'chain 'R' and resid 376 through 379' Processing helix chain 'R' and resid 385 through 394 removed outlier: 4.803A pdb=" N ARG R 393 " --> pdb=" O ASP R 389 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR R 394 " --> pdb=" O ALA R 390 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 7.435A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 109 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.101A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.147A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 7.012A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.686A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.947A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.565A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.821A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.794A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.629A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 148 343 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: 2.57 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2674 1.34 - 1.46: 1849 1.46 - 1.58: 3977 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8579 Sorted by residual: bond pdb=" C14 7LD R 501 " pdb=" C16 7LD R 501 " ideal model delta sigma weight residual 1.525 1.403 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C11 7LD R 501 " pdb=" C9 7LD R 501 " ideal model delta sigma weight residual 1.525 1.406 0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C10 7LD R 501 " pdb=" C14 7LD R 501 " ideal model delta sigma weight residual 1.501 1.398 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C15 7LD R 501 " pdb=" C7 7LD R 501 " ideal model delta sigma weight residual 1.491 1.396 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C3 7LD R 501 " pdb=" C7 7LD R 501 " ideal model delta sigma weight residual 1.414 1.322 0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 8574 not shown) Histogram of bond angle deviations from ideal: 98.38 - 105.51: 139 105.51 - 112.64: 4563 112.64 - 119.78: 2755 119.78 - 126.91: 4121 126.91 - 134.05: 116 Bond angle restraints: 11694 Sorted by residual: angle pdb=" N LYS R 247 " pdb=" CA LYS R 247 " pdb=" C LYS R 247 " ideal model delta sigma weight residual 112.57 104.65 7.92 1.13e+00 7.83e-01 4.91e+01 angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 113.23 105.54 7.69 1.24e+00 6.50e-01 3.85e+01 angle pdb=" N GLN R 320 " pdb=" CA GLN R 320 " pdb=" C GLN R 320 " ideal model delta sigma weight residual 113.88 106.26 7.62 1.23e+00 6.61e-01 3.84e+01 angle pdb=" C GLN R 320 " pdb=" CA GLN R 320 " pdb=" CB GLN R 320 " ideal model delta sigma weight residual 109.03 117.62 -8.59 1.62e+00 3.81e-01 2.81e+01 angle pdb=" N GLU R 319 " pdb=" CA GLU R 319 " pdb=" C GLU R 319 " ideal model delta sigma weight residual 113.17 106.59 6.58 1.26e+00 6.30e-01 2.73e+01 ... (remaining 11689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 4913 30.36 - 60.72: 98 60.72 - 91.07: 5 91.07 - 121.43: 0 121.43 - 151.79: 1 Dihedral angle restraints: 5017 sinusoidal: 1775 harmonic: 3242 Sorted by residual: dihedral pdb=" C16 7LD R 501 " pdb=" C17 7LD R 501 " pdb=" N3 7LD R 501 " pdb=" C18 7LD R 501 " ideal model delta sinusoidal sigma weight residual 91.75 -116.46 -151.79 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA GLU R 118 " pdb=" C GLU R 118 " pdb=" N ALA R 119 " pdb=" CA ALA R 119 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LYS B 73 " pdb=" C LYS B 73 " pdb=" N PHE B 74 " pdb=" CA PHE B 74 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1187 0.065 - 0.131: 172 0.131 - 0.196: 10 0.196 - 0.261: 3 0.261 - 0.326: 3 Chirality restraints: 1375 Sorted by residual: chirality pdb=" C14 7LD R 501 " pdb=" C10 7LD R 501 " pdb=" C13 7LD R 501 " pdb=" C16 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB VAL R 325 " pdb=" CA VAL R 325 " pdb=" CG1 VAL R 325 " pdb=" CG2 VAL R 325 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C11 7LD R 501 " pdb=" C15 7LD R 501 " pdb=" C9 7LD R 501 " pdb=" N2 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1372 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 86 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C GLN R 86 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN R 86 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR R 87 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 325 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C VAL R 325 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL R 325 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 326 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 323 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C SER R 323 " -0.035 2.00e-02 2.50e+03 pdb=" O SER R 323 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS R 324 " 0.012 2.00e-02 2.50e+03 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 479 2.74 - 3.28: 7877 3.28 - 3.82: 13016 3.82 - 4.36: 15514 4.36 - 4.90: 27794 Nonbonded interactions: 64680 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.196 2.440 nonbonded pdb=" O ILE R 205 " pdb=" OG1 THR R 206 " model vdw 2.303 2.440 nonbonded pdb=" NE2 GLN C 75 " pdb=" O SER C 98 " model vdw 2.362 2.520 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.363 2.440 nonbonded pdb=" NH1 ARG E 190 " pdb=" OD2 ASP E 211 " model vdw 2.374 2.520 ... (remaining 64675 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: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 10.000 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.340 Find NCS groups from input model: 0.230 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:12.340 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 0.122 8579 Z= 0.293 Angle : 0.670 8.591 11694 Z= 0.403 Chirality : 0.048 0.326 1375 Planarity : 0.004 0.046 1469 Dihedral : 12.519 151.787 2909 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.15 (0.26), residues: 1101 helix: 0.48 (0.29), residues: 377 sheet: 1.31 (0.33), residues: 275 loop : -0.96 (0.27), residues: 449 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.041 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 1.0675 time to fit residues: 186.7341 Evaluate side-chains 148 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.1980 chunk 82 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN C 293 ASN R 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8579 Z= 0.218 Angle : 0.532 7.969 11694 Z= 0.277 Chirality : 0.043 0.150 1375 Planarity : 0.004 0.047 1469 Dihedral : 6.075 147.131 1195 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.36 (0.26), residues: 1101 helix: 0.77 (0.29), residues: 372 sheet: 1.34 (0.33), residues: 275 loop : -0.89 (0.27), residues: 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 0.949 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 163 average time/residue: 1.1097 time to fit residues: 193.5126 Evaluate side-chains 169 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 1 residues processed: 10 average time/residue: 0.1194 time to fit residues: 3.1920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 107 optimal weight: 0.0370 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 131 ASN C 293 ASN R 86 GLN R 162 GLN R 318 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 8579 Z= 0.261 Angle : 0.551 7.812 11694 Z= 0.288 Chirality : 0.044 0.163 1375 Planarity : 0.004 0.048 1469 Dihedral : 5.841 130.470 1195 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.43 (0.26), residues: 1101 helix: 0.91 (0.29), residues: 371 sheet: 1.34 (0.32), residues: 282 loop : -0.93 (0.27), residues: 448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.966 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 159 average time/residue: 1.0621 time to fit residues: 180.7731 Evaluate side-chains 168 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 1 residues processed: 9 average time/residue: 0.1224 time to fit residues: 2.8952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 131 ASN C 293 ASN R 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8579 Z= 0.231 Angle : 0.532 6.240 11694 Z= 0.279 Chirality : 0.043 0.164 1375 Planarity : 0.004 0.047 1469 Dihedral : 5.534 115.594 1195 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1101 helix: 1.03 (0.29), residues: 372 sheet: 1.37 (0.32), residues: 282 loop : -0.90 (0.27), residues: 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 0.946 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 167 average time/residue: 1.1888 time to fit residues: 211.7205 Evaluate side-chains 164 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 3 residues processed: 7 average time/residue: 0.1580 time to fit residues: 2.8770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 131 ASN R 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 8579 Z= 0.287 Angle : 0.565 6.903 11694 Z= 0.296 Chirality : 0.044 0.137 1375 Planarity : 0.004 0.048 1469 Dihedral : 5.308 97.038 1195 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.38 (0.26), residues: 1101 helix: 0.95 (0.29), residues: 374 sheet: 1.27 (0.32), residues: 276 loop : -0.99 (0.27), residues: 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 0.981 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 165 average time/residue: 1.1107 time to fit residues: 196.3169 Evaluate side-chains 164 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.1858 time to fit residues: 2.7034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 82 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN C 16 ASN R 86 GLN R 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 8579 Z= 0.282 Angle : 0.566 6.719 11694 Z= 0.295 Chirality : 0.044 0.208 1375 Planarity : 0.004 0.048 1469 Dihedral : 5.041 81.135 1195 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.44 (0.26), residues: 1101 helix: 0.91 (0.29), residues: 375 sheet: 1.37 (0.32), residues: 282 loop : -0.95 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 0.961 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 165 average time/residue: 1.1092 time to fit residues: 196.3976 Evaluate side-chains 171 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 7 residues processed: 10 average time/residue: 0.4962 time to fit residues: 6.9639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 88 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN C 16 ASN R 86 GLN R 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8579 Z= 0.221 Angle : 0.541 6.106 11694 Z= 0.284 Chirality : 0.042 0.141 1375 Planarity : 0.004 0.049 1469 Dihedral : 4.691 63.981 1195 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.55 (0.26), residues: 1101 helix: 1.06 (0.30), residues: 372 sheet: 1.36 (0.32), residues: 281 loop : -0.88 (0.27), residues: 448 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.054 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 165 average time/residue: 1.0486 time to fit residues: 185.6561 Evaluate side-chains 164 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.1729 time to fit residues: 2.5867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.0970 chunk 31 optimal weight: 0.0670 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.0270 chunk 100 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 overall best weight: 0.1574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 131 ASN C 16 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN R 86 GLN R 90 ASN R 162 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8579 Z= 0.131 Angle : 0.497 8.027 11694 Z= 0.261 Chirality : 0.041 0.188 1375 Planarity : 0.004 0.049 1469 Dihedral : 4.198 43.964 1195 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.73 (0.26), residues: 1101 helix: 1.22 (0.29), residues: 381 sheet: 1.44 (0.32), residues: 278 loop : -0.79 (0.28), residues: 442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 1.036 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 167 average time/residue: 1.0967 time to fit residues: 196.1895 Evaluate side-chains 165 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1022 time to fit residues: 1.7107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 63 optimal weight: 0.9990 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN R 90 ASN R 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8579 Z= 0.143 Angle : 0.530 14.967 11694 Z= 0.268 Chirality : 0.041 0.141 1375 Planarity : 0.004 0.056 1469 Dihedral : 4.055 36.520 1195 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.80 (0.26), residues: 1101 helix: 1.43 (0.29), residues: 372 sheet: 1.26 (0.32), residues: 288 loop : -0.75 (0.28), residues: 441 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 0.972 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 164 average time/residue: 1.1448 time to fit residues: 201.2885 Evaluate side-chains 161 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.8018 time to fit residues: 3.1063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 0.2980 chunk 86 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN C 293 ASN E 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8579 Z= 0.234 Angle : 0.572 9.454 11694 Z= 0.293 Chirality : 0.043 0.227 1375 Planarity : 0.004 0.059 1469 Dihedral : 4.247 38.112 1195 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.59 (0.26), residues: 1101 helix: 1.25 (0.30), residues: 373 sheet: 1.23 (0.32), residues: 275 loop : -0.86 (0.27), residues: 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 0.970 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 163 average time/residue: 1.0962 time to fit residues: 191.4568 Evaluate side-chains 162 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 2 average time/residue: 0.1681 time to fit residues: 1.8475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 36 optimal weight: 0.3980 chunk 88 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 131 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104119 restraints weight = 12122.137| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.63 r_work: 0.3201 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8579 Z= 0.160 Angle : 0.524 8.423 11694 Z= 0.272 Chirality : 0.041 0.141 1375 Planarity : 0.004 0.059 1469 Dihedral : 4.071 38.602 1195 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.79 (0.26), residues: 1101 helix: 1.46 (0.29), residues: 372 sheet: 1.34 (0.32), residues: 281 loop : -0.82 (0.28), residues: 448 =============================================================================== Job complete usr+sys time: 3671.68 seconds wall clock time: 65 minutes 27.04 seconds (3927.04 seconds total)