Starting phenix.real_space_refine on Thu Mar 21 10:17:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1x_15092/03_2024/8a1x_15092_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1x_15092/03_2024/8a1x_15092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1x_15092/03_2024/8a1x_15092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1x_15092/03_2024/8a1x_15092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1x_15092/03_2024/8a1x_15092_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1x_15092/03_2024/8a1x_15092_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 6 5.49 5 S 90 5.16 5 C 9621 2.51 5 N 2414 2.21 5 O 2720 1.98 5 H 14655 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 60": "OD1" <-> "OD2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 223": "OD1" <-> "OD2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "F PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 219": "OE1" <-> "OE2" Residue "F PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 398": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29510 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6879 Classifications: {'peptide': 446} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 422} Chain: "B" Number of atoms: 6086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 6086 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Chain: "C" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3774 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "D" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3154 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "E" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3041 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "F" Number of atoms: 6246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6246 Classifications: {'peptide': 407} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 382} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'3PE': 1, 'FMN': 1, 'LMT': 2, 'RBF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 18 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18403 SG CYS D 112 65.875 82.945 59.148 1.00 59.70 S ATOM 20295 SG CYS E 26 63.347 83.271 61.745 1.00 71.64 S ATOM 17070 SG CYS D 29 65.762 83.991 65.280 1.00 73.51 S ATOM 21800 SG CYS E 120 69.101 85.136 64.226 1.00 76.26 S ATOM 23964 SG CYS F 70 52.567 68.460 38.977 1.00 74.33 S ATOM 24013 SG CYS F 76 50.482 65.790 37.319 1.00 72.64 S ATOM 24047 SG CYS F 79 55.306 62.683 38.007 1.00 68.99 S ATOM 24531 SG CYS F 111 56.531 65.890 39.571 1.00 54.96 S Time building chain proxies: 13.38, per 1000 atoms: 0.45 Number of scatterers: 29510 At special positions: 0 Unit cell: (110.94, 135.871, 130.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 90 16.00 P 6 15.00 O 2720 8.00 N 2414 7.00 C 9621 6.00 H 14655 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.77 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1001 " pdb="FE1 FES E1001 " - pdb=" SG CYS E 26 " pdb="FE2 FES E1001 " - pdb=" SG CYS D 29 " pdb="FE1 FES E1001 " - pdb=" SG CYS D 112 " pdb="FE2 FES E1001 " - pdb=" SG CYS E 120 " pdb=" FES F1502 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " Number of angles added : 12 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 12 sheets defined 47.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.919A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'B' and resid 21 through 34 removed outlier: 4.595A pdb=" N ALA B 25 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 34 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 65 through 86 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 118 through 151 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 277 through 290 Processing helix chain 'B' and resid 295 through 315 Processing helix chain 'B' and resid 321 through 324 Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 354 through 374 Processing helix chain 'B' and resid 382 through 409 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'C' and resid 8 through 32 removed outlier: 3.660A pdb=" N SER C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 52 removed outlier: 3.540A pdb=" N GLU C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 93 through 98 removed outlier: 3.535A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.787A pdb=" N TRP C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'D' and resid 9 through 16 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 38 through 61 Processing helix chain 'D' and resid 71 through 92 removed outlier: 3.640A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 79 " --> pdb=" O GLN D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 104 through 109 removed outlier: 4.910A pdb=" N ILE D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 127 through 157 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.715A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 25 through 28 No H-bonds generated for 'chain 'E' and resid 25 through 28' Processing helix chain 'E' and resid 35 through 62 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 76 through 101 removed outlier: 5.030A pdb=" N PHE E 80 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE E 81 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 101 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 110 through 116 Proline residue: E 114 - end of helix No H-bonds generated for 'chain 'E' and resid 110 through 116' Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'E' and resid 136 through 166 removed outlier: 4.797A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.771A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 29 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 92 through 95 No H-bonds generated for 'chain 'F' and resid 92 through 95' Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 125 through 128 No H-bonds generated for 'chain 'F' and resid 125 through 128' Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 190 through 195 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 244 through 251 Processing helix chain 'F' and resid 282 through 296 Proline residue: F 287 - end of helix removed outlier: 4.144A pdb=" N PHE F 293 " --> pdb=" O SER F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'F' and resid 344 through 346 No H-bonds generated for 'chain 'F' and resid 344 through 346' Processing helix chain 'F' and resid 355 through 362 Processing helix chain 'F' and resid 370 through 372 No H-bonds generated for 'chain 'F' and resid 370 through 372' Processing helix chain 'F' and resid 381 through 394 Processing sheet with id= A, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.888A pdb=" N LEU A 274 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.707A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL A 76 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.325A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 237 through 240 removed outlier: 6.832A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR A 190 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.197A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.005A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.264A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 164 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU C 156 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 162 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= G, first strand: chain 'C' and resid 204 through 206 Processing sheet with id= H, first strand: chain 'F' and resid 47 through 49 removed outlier: 6.954A pdb=" N MET F 119 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 80 through 82 Processing sheet with id= J, first strand: chain 'F' and resid 208 through 213 removed outlier: 4.354A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 175 through 178 Processing sheet with id= L, first strand: chain 'F' and resid 401 through 403 removed outlier: 6.595A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1740 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: 10.80 Time building geometry restraints manager: 24.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 14642 1.11 - 1.38: 5850 1.38 - 1.66: 9203 1.66 - 1.93: 151 1.93 - 2.21: 8 Bond restraints: 29854 Sorted by residual: bond pdb=" O3P FAD F1501 " pdb=" P FAD F1501 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C4 RBF B 502 " pdb=" C4A RBF B 502 " ideal model delta sigma weight residual 1.481 1.405 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" O5' FAD F1501 " pdb=" P FAD F1501 " ideal model delta sigma weight residual 1.637 1.575 0.062 2.00e-02 2.50e+03 9.66e+00 bond pdb=" O5B FAD F1501 " pdb=" PA FAD F1501 " ideal model delta sigma weight residual 1.634 1.572 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" CB PRO F 92 " pdb=" CG PRO F 92 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.76e+00 ... (remaining 29849 not shown) Histogram of bond angle deviations from ideal: 75.06 - 86.85: 7 86.85 - 98.64: 1 98.64 - 110.43: 29988 110.43 - 122.22: 19635 122.22 - 134.00: 4333 Bond angle restraints: 53964 Sorted by residual: angle pdb=" HG2 PRO F 92 " pdb=" CG PRO F 92 " pdb=" HG3 PRO F 92 " ideal model delta sigma weight residual 110.00 76.54 33.46 3.00e+00 1.11e-01 1.24e+02 angle pdb=" CD PRO F 92 " pdb=" CG PRO F 92 " pdb=" HG2 PRO F 92 " ideal model delta sigma weight residual 110.00 79.87 30.13 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CB PRO F 92 " pdb=" CG PRO F 92 " pdb=" HG3 PRO F 92 " ideal model delta sigma weight residual 109.00 78.90 30.10 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CD PRO F 92 " pdb=" CG PRO F 92 " pdb=" HG3 PRO F 92 " ideal model delta sigma weight residual 110.00 133.74 -23.74 3.00e+00 1.11e-01 6.26e+01 angle pdb=" CB PRO F 92 " pdb=" CG PRO F 92 " pdb=" HG2 PRO F 92 " ideal model delta sigma weight residual 109.00 131.01 -22.01 3.00e+00 1.11e-01 5.38e+01 ... (remaining 53959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 13642 35.83 - 71.66: 515 71.66 - 107.48: 27 107.48 - 143.31: 6 143.31 - 179.14: 2 Dihedral angle restraints: 14192 sinusoidal: 7797 harmonic: 6395 Sorted by residual: dihedral pdb=" C10 FMN C1000 " pdb=" C1' FMN C1000 " pdb=" N10 FMN C1000 " pdb=" C2' FMN C1000 " ideal model delta sinusoidal sigma weight residual -102.41 76.73 -179.14 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN B 501 " pdb=" C1' FMN B 501 " pdb=" N10 FMN B 501 " pdb=" C2' FMN B 501 " ideal model delta sinusoidal sigma weight residual 257.59 84.64 172.96 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C4' FMN B 501 " pdb=" C5' FMN B 501 " pdb=" O5' FMN B 501 " pdb=" P FMN B 501 " ideal model delta sinusoidal sigma weight residual 187.70 110.52 77.18 1 2.00e+01 2.50e-03 1.87e+01 ... (remaining 14189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1877 0.044 - 0.089: 306 0.089 - 0.133: 131 0.133 - 0.178: 6 0.178 - 0.222: 10 Chirality restraints: 2330 Sorted by residual: chirality pdb=" C4' LMT B 504 " pdb=" C3' LMT B 504 " pdb=" C5' LMT B 504 " pdb=" O1B LMT B 504 " both_signs ideal model delta sigma weight residual False -2.55 -2.78 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C4' LMT B 503 " pdb=" C3' LMT B 503 " pdb=" C5' LMT B 503 " pdb=" O1B LMT B 503 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C5' LMT B 503 " pdb=" C4' LMT B 503 " pdb=" C6' LMT B 503 " pdb=" O5' LMT B 503 " both_signs ideal model delta sigma weight residual False -2.51 -2.29 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2327 not shown) Planarity restraints: 4372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 113 " 0.062 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO E 114 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 74 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C ASP E 74 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP E 74 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU E 75 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 70 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 71 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.021 5.00e-02 4.00e+02 ... (remaining 4369 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 816 2.13 - 2.75: 54414 2.75 - 3.37: 88218 3.37 - 3.98: 113970 3.98 - 4.60: 178581 Nonbonded interactions: 435999 Sorted by model distance: nonbonded pdb=" H ALA F 215 " pdb=" O MET F 225 " model vdw 1.513 1.850 nonbonded pdb=" OE1 GLU C 197 " pdb=" H GLU C 197 " model vdw 1.540 1.850 nonbonded pdb=" OD1 ASP A 414 " pdb=" H GLU A 415 " model vdw 1.571 1.850 nonbonded pdb=" O PRO E 114 " pdb=" HG1 THR E 117 " model vdw 1.582 1.850 nonbonded pdb=" OE1 GLU C 56 " pdb=" H GLU C 56 " model vdw 1.602 1.850 ... (remaining 435994 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: 0.470 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.440 Extract box with map and model: 3.330 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 100.970 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 15199 Z= 0.263 Angle : 0.589 18.355 20607 Z= 0.279 Chirality : 0.042 0.222 2330 Planarity : 0.003 0.091 2569 Dihedral : 17.099 179.139 5662 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.06 % Allowed : 15.48 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 1881 helix: 1.81 (0.18), residues: 863 sheet: 0.09 (0.40), residues: 169 loop : 0.52 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 103 HIS 0.005 0.001 HIS F 356 PHE 0.017 0.001 PHE F 162 TYR 0.015 0.001 TYR B 360 ARG 0.002 0.000 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 SER cc_start: 0.8560 (t) cc_final: 0.8349 (t) REVERT: B 406 LYS cc_start: 0.8002 (mttp) cc_final: 0.7722 (mtmt) REVERT: C 110 GLN cc_start: 0.7328 (mt0) cc_final: 0.7112 (mt0) outliers start: 1 outliers final: 1 residues processed: 221 average time/residue: 0.6164 time to fit residues: 198.0491 Evaluate side-chains 211 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 267 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN C 68 ASN D 68 ASN F 175 HIS F 362 ASN F 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 15199 Z= 0.358 Angle : 0.555 17.120 20607 Z= 0.282 Chirality : 0.044 0.329 2330 Planarity : 0.004 0.042 2569 Dihedral : 11.423 179.106 2346 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.10 % Allowed : 15.61 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1881 helix: 1.36 (0.18), residues: 865 sheet: -0.26 (0.38), residues: 195 loop : 0.35 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 PHE 0.020 0.001 PHE E 28 TYR 0.017 0.001 TYR B 360 ARG 0.004 0.001 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 214 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 ARG cc_start: 0.6034 (ttm-80) cc_final: 0.5833 (ttm170) outliers start: 17 outliers final: 12 residues processed: 227 average time/residue: 0.5955 time to fit residues: 199.4953 Evaluate side-chains 221 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 169 optimal weight: 0.0770 chunk 182 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 15199 Z= 0.350 Angle : 0.548 16.752 20607 Z= 0.279 Chirality : 0.043 0.339 2330 Planarity : 0.004 0.063 2569 Dihedral : 10.475 179.856 2344 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.42 % Allowed : 16.58 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.19), residues: 1881 helix: 1.10 (0.18), residues: 864 sheet: -0.39 (0.38), residues: 194 loop : 0.19 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.005 0.001 HIS B 328 PHE 0.018 0.001 PHE E 28 TYR 0.017 0.002 TYR B 360 ARG 0.006 0.001 ARG F 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7643 (mt-10) outliers start: 22 outliers final: 16 residues processed: 233 average time/residue: 0.6210 time to fit residues: 215.0393 Evaluate side-chains 223 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 179 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN D 68 ASN F 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 15199 Z= 0.224 Angle : 0.495 16.368 20607 Z= 0.250 Chirality : 0.041 0.423 2330 Planarity : 0.004 0.046 2569 Dihedral : 9.700 179.154 2344 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.55 % Allowed : 16.90 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.92 (0.20), residues: 1881 helix: 1.29 (0.18), residues: 868 sheet: -0.11 (0.39), residues: 183 loop : 0.20 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.005 0.001 HIS F 356 PHE 0.013 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.005 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7581 (mt-10) outliers start: 24 outliers final: 18 residues processed: 225 average time/residue: 0.6044 time to fit residues: 199.2509 Evaluate side-chains 224 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 205 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 161 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 HIS F 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 15199 Z= 0.249 Angle : 0.500 16.228 20607 Z= 0.254 Chirality : 0.042 0.427 2330 Planarity : 0.004 0.047 2569 Dihedral : 9.410 178.401 2344 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.42 % Allowed : 17.16 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.92 (0.19), residues: 1881 helix: 1.30 (0.18), residues: 868 sheet: -0.15 (0.38), residues: 183 loop : 0.19 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.006 0.001 HIS F 175 PHE 0.015 0.001 PHE F 162 TYR 0.016 0.001 TYR B 360 ARG 0.005 0.000 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 209 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: D 115 MET cc_start: 0.7414 (mmm) cc_final: 0.6999 (mmm) outliers start: 22 outliers final: 19 residues processed: 224 average time/residue: 0.6403 time to fit residues: 214.7279 Evaluate side-chains 223 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 83 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN C 188 GLN D 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 15199 Z= 0.303 Angle : 0.519 16.148 20607 Z= 0.265 Chirality : 0.042 0.376 2330 Planarity : 0.004 0.048 2569 Dihedral : 9.381 176.564 2344 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.75 % Allowed : 16.71 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.77 (0.19), residues: 1881 helix: 1.20 (0.18), residues: 868 sheet: -0.41 (0.36), residues: 201 loop : 0.15 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 PHE 0.017 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.004 0.000 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 THR cc_start: 0.8567 (p) cc_final: 0.8346 (t) REVERT: E 131 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7719 (mt0) outliers start: 27 outliers final: 22 residues processed: 223 average time/residue: 0.5796 time to fit residues: 191.7947 Evaluate side-chains 228 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN D 137 ASN F 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 15199 Z= 0.382 Angle : 0.557 16.092 20607 Z= 0.288 Chirality : 0.044 0.316 2330 Planarity : 0.005 0.049 2569 Dihedral : 9.628 174.473 2344 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.40 % Allowed : 16.32 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 1881 helix: 0.96 (0.18), residues: 869 sheet: -0.51 (0.36), residues: 200 loop : -0.03 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.006 0.001 HIS B 328 PHE 0.020 0.002 PHE E 28 TYR 0.017 0.002 TYR B 360 ARG 0.005 0.001 ARG F 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 217 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7060 (tpp-160) REVERT: B 43 ARG cc_start: 0.7869 (ptp90) cc_final: 0.7359 (ptp-110) REVERT: C 114 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8336 (mmtm) REVERT: C 252 ARG cc_start: 0.6300 (ttm-80) cc_final: 0.5941 (ttm170) REVERT: D 100 GLN cc_start: 0.7764 (mt0) cc_final: 0.7497 (mt0) REVERT: E 131 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: F 31 PRO cc_start: 0.4956 (Cg_endo) cc_final: 0.4410 (Cg_exo) REVERT: F 102 GLU cc_start: 0.6583 (mm-30) cc_final: 0.6309 (mm-30) outliers start: 37 outliers final: 28 residues processed: 242 average time/residue: 0.6123 time to fit residues: 218.1844 Evaluate side-chains 237 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 207 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 62 GLN C 198 ASN D 68 ASN F 295 GLN F 343 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 15199 Z= 0.238 Angle : 0.508 16.076 20607 Z= 0.259 Chirality : 0.041 0.306 2330 Planarity : 0.004 0.049 2569 Dihedral : 9.420 174.778 2344 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.01 % Allowed : 16.97 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.63 (0.19), residues: 1881 helix: 1.08 (0.18), residues: 868 sheet: -0.27 (0.37), residues: 189 loop : 0.00 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.006 0.001 HIS F 175 PHE 0.014 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.005 0.000 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ARG cc_start: 0.7805 (ptp90) cc_final: 0.7258 (ptp-110) REVERT: C 114 LYS cc_start: 0.8531 (mmtm) cc_final: 0.8325 (mmtm) REVERT: C 252 ARG cc_start: 0.6239 (ttm-80) cc_final: 0.5913 (ttm170) REVERT: D 100 GLN cc_start: 0.7757 (mt0) cc_final: 0.7501 (mt0) REVERT: E 131 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: F 31 PRO cc_start: 0.4738 (Cg_endo) cc_final: 0.4192 (Cg_exo) REVERT: F 102 GLU cc_start: 0.6561 (mm-30) cc_final: 0.6314 (mm-30) outliers start: 31 outliers final: 24 residues processed: 233 average time/residue: 0.6365 time to fit residues: 219.0541 Evaluate side-chains 236 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 211 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 30.0000 chunk 171 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 15199 Z= 0.451 Angle : 0.583 16.026 20607 Z= 0.303 Chirality : 0.045 0.315 2330 Planarity : 0.005 0.050 2569 Dihedral : 9.659 172.587 2344 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.88 % Allowed : 17.29 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.29 (0.19), residues: 1881 helix: 0.84 (0.18), residues: 866 sheet: -0.65 (0.38), residues: 183 loop : -0.17 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 103 HIS 0.006 0.001 HIS B 328 PHE 0.019 0.002 PHE E 28 TYR 0.018 0.002 TYR B 360 ARG 0.005 0.001 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 206 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 THR cc_start: 0.8553 (p) cc_final: 0.8333 (t) REVERT: A 349 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8319 (mtm-85) REVERT: B 43 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7365 (ptp-110) REVERT: C 252 ARG cc_start: 0.6330 (ttm-80) cc_final: 0.6011 (ttm170) REVERT: D 86 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8242 (t) REVERT: D 100 GLN cc_start: 0.7844 (mt0) cc_final: 0.7558 (mt0) REVERT: E 131 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: F 31 PRO cc_start: 0.4847 (Cg_endo) cc_final: 0.4293 (Cg_exo) REVERT: F 102 GLU cc_start: 0.6546 (mm-30) cc_final: 0.6306 (mm-30) outliers start: 29 outliers final: 25 residues processed: 225 average time/residue: 0.6230 time to fit residues: 204.2097 Evaluate side-chains 230 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 15199 Z= 0.253 Angle : 0.512 16.066 20607 Z= 0.262 Chirality : 0.041 0.300 2330 Planarity : 0.004 0.050 2569 Dihedral : 9.417 173.375 2344 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.81 % Allowed : 17.36 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.19), residues: 1881 helix: 1.05 (0.18), residues: 868 sheet: -0.65 (0.38), residues: 183 loop : -0.02 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.005 0.001 HIS F 356 PHE 0.017 0.001 PHE B 34 TYR 0.017 0.001 TYR B 360 ARG 0.006 0.000 ARG F 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8262 (mtm-85) REVERT: C 252 ARG cc_start: 0.6238 (ttm-80) cc_final: 0.5960 (ttm170) REVERT: D 100 GLN cc_start: 0.7834 (mt0) cc_final: 0.7548 (mt0) REVERT: E 131 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: F 31 PRO cc_start: 0.4884 (Cg_endo) cc_final: 0.4337 (Cg_exo) REVERT: F 102 GLU cc_start: 0.6521 (mm-30) cc_final: 0.6281 (mm-30) outliers start: 28 outliers final: 24 residues processed: 230 average time/residue: 0.6295 time to fit residues: 211.7474 Evaluate side-chains 228 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 198 ASN D 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.167644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116350 restraints weight = 49756.358| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.71 r_work: 0.2978 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 15199 Z= 0.322 Angle : 0.533 16.029 20607 Z= 0.274 Chirality : 0.042 0.304 2330 Planarity : 0.004 0.049 2569 Dihedral : 9.449 172.348 2344 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.01 % Allowed : 17.29 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1881 helix: 0.99 (0.18), residues: 868 sheet: -0.67 (0.38), residues: 183 loop : -0.08 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.005 0.001 HIS B 328 PHE 0.016 0.001 PHE E 28 TYR 0.017 0.001 TYR B 360 ARG 0.006 0.000 ARG F 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6291.78 seconds wall clock time: 111 minutes 53.28 seconds (6713.28 seconds total)