Starting phenix.real_space_refine on Thu Mar 21 10:31:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1t_15088/03_2024/8a1t_15088_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1t_15088/03_2024/8a1t_15088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1t_15088/03_2024/8a1t_15088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1t_15088/03_2024/8a1t_15088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1t_15088/03_2024/8a1t_15088_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1t_15088/03_2024/8a1t_15088_trim_updated.pdb" } resolution = 3.37 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= 0.007 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: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 4 7.16 5 P 7 5.49 5 S 90 5.16 5 Na 1 4.78 5 C 9646 2.51 5 N 2408 2.21 5 O 2724 1.98 5 H 14626 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 98": "OD1" <-> "OD2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 366": "OD1" <-> "OD2" 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: 29507 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6880 Classifications: {'peptide': 446} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 422} Chain: "B" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6011 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} 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: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3147 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "E" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3078 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "F" Number of atoms: 6234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6234 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 24, 'TRANS': 380} Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 213 Unusual residues: {' K': 1, ' NA': 1, '3PE': 2, 'FMN': 1, 'LMT': 2, 'RBF': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'3PE': 1, 'FES': 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 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 18322 SG CYS D 112 66.864 83.803 58.614 1.00 80.66 S ATOM 20214 SG CYS E 26 64.411 83.907 61.435 1.00 74.26 S ATOM 16996 SG CYS D 29 67.273 85.465 64.840 1.00 62.78 S ATOM 21719 SG CYS E 120 70.352 85.885 62.729 1.00 64.82 S ATOM 23920 SG CYS F 70 53.305 69.159 38.939 1.00213.23 S ATOM 23969 SG CYS F 76 51.317 66.358 37.391 1.00210.35 S ATOM 24004 SG CYS F 79 56.224 63.469 37.898 1.00199.79 S ATOM 24488 SG CYS F 111 57.448 66.701 39.384 1.00205.71 S Time building chain proxies: 12.94, per 1000 atoms: 0.44 Number of scatterers: 29507 At special positions: 0 Unit cell: (113.433, 137.117, 130.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 4 26.01 K 1 19.00 S 90 16.00 P 7 15.00 Na 1 11.00 O 2724 8.00 N 2408 7.00 C 9646 6.00 H 14626 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: 23.22 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 302 " pdb="FE1 FES D 302 " - pdb=" SG CYS E 26 " pdb="FE2 FES D 302 " - pdb=" SG CYS E 120 " pdb="FE2 FES D 302 " - pdb=" SG CYS D 29 " pdb="FE1 FES D 302 " - pdb=" SG CYS D 112 " pdb=" FES F1502 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " Number of angles added : 12 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 14 sheets defined 47.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' 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 107 through 112 removed outlier: 4.308A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) 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 184 removed outlier: 3.813A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) 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 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 402 through 407 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 415 through 423 removed outlier: 4.589A pdb=" N LEU A 420 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 65 through 86 Processing helix chain 'B' and resid 90 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 159 through 168 removed outlier: 3.565A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) 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 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' 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 removed outlier: 3.531A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) 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 removed outlier: 3.583A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) 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 removed outlier: 3.629A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 34 through 53 removed outlier: 3.818A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (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 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.846A 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 Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 104 through 109 removed outlier: 5.090A pdb=" N ILE D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' 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 removed outlier: 3.585A pdb=" N LEU D 182 " --> pdb=" O GLY D 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 179 through 182' Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.894A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 201 " --> pdb=" O ALA D 197 " (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 17 through 21 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 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 80 through 101 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: 3.605A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.635A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.400A 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 96 removed outlier: 3.777A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 96' 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 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 186 through 195 removed outlier: 4.329A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) 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 246 through 251 Processing helix chain 'F' and resid 282 through 296 Proline residue: F 287 - end of helix 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 355 through 362 removed outlier: 4.535A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 394 Processing helix chain 'F' and resid 398 through 400 No H-bonds generated for 'chain 'F' and resid 398 through 400' Processing sheet with id= A, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.477A pdb=" N LEU A 274 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 5.977A 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 31 removed outlier: 3.726A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.830A 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: 7.110A 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: 6.808A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.349A 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: 3.511A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.165A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.315A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (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 35 through 37 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 134 through 136 Processing sheet with id= K, first strand: chain 'F' and resid 147 through 153 Processing sheet with id= L, first strand: chain 'F' and resid 167 through 172 Processing sheet with id= M, first strand: chain 'F' and resid 175 through 178 Processing sheet with id= N, first strand: chain 'F' and resid 401 through 403 removed outlier: 6.299A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1797 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: 10.97 Time building geometry restraints manager: 24.18 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: 14611 1.11 - 1.38: 5845 1.38 - 1.66: 9232 1.66 - 1.93: 151 1.93 - 2.20: 8 Bond restraints: 29847 Sorted by residual: bond pdb=" O3P FAD F1501 " pdb=" P FAD F1501 " ideal model delta sigma weight residual 1.660 1.583 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C4 RBF B 502 " pdb=" C4A RBF B 502 " ideal model delta sigma weight residual 1.481 1.407 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O5' FAD F1501 " pdb=" P FAD F1501 " ideal model delta sigma weight residual 1.637 1.577 0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" O5B FAD F1501 " pdb=" PA FAD F1501 " ideal model delta sigma weight residual 1.634 1.574 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" O3P FAD F1501 " pdb=" PA FAD F1501 " ideal model delta sigma weight residual 1.633 1.584 0.049 2.00e-02 2.50e+03 5.92e+00 ... (remaining 29842 not shown) Histogram of bond angle deviations from ideal: 75.02 - 86.82: 4 86.82 - 98.62: 0 98.62 - 110.42: 29950 110.42 - 122.22: 19711 122.22 - 134.02: 4247 Bond angle restraints: 53912 Sorted by residual: angle pdb=" C2 LMT B 506 " pdb=" C3 LMT B 506 " pdb=" C4 LMT B 506 " ideal model delta sigma weight residual 117.09 107.49 9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C2 LMT E 201 " pdb=" C3 LMT E 201 " pdb=" C4 LMT E 201 " ideal model delta sigma weight residual 117.09 107.69 9.40 3.00e+00 1.11e-01 9.82e+00 angle pdb=" C2 LMT B 503 " pdb=" C3 LMT B 503 " pdb=" C4 LMT B 503 " ideal model delta sigma weight residual 117.09 107.77 9.32 3.00e+00 1.11e-01 9.64e+00 angle pdb=" N VAL E 31 " pdb=" CA VAL E 31 " pdb=" C VAL E 31 " ideal model delta sigma weight residual 111.91 109.27 2.64 8.90e-01 1.26e+00 8.77e+00 angle pdb=" C10 LMT B 506 " pdb=" C9 LMT B 506 " pdb=" C8 LMT B 506 " ideal model delta sigma weight residual 116.03 107.53 8.50 3.00e+00 1.11e-01 8.03e+00 ... (remaining 53907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 13657 35.93 - 71.85: 524 71.85 - 107.78: 30 107.78 - 143.70: 7 143.70 - 179.63: 2 Dihedral angle restraints: 14220 sinusoidal: 7835 harmonic: 6385 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 257.59 77.97 179.63 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 90.88 166.72 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' FMN B 501 " pdb=" O5' FMN B 501 " pdb=" P FMN B 501 " pdb=" O1P FMN B 501 " ideal model delta sinusoidal sigma weight residual 75.26 -151.44 -133.31 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 14217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1907 0.046 - 0.093: 295 0.093 - 0.139: 117 0.139 - 0.185: 2 0.185 - 0.231: 9 Chirality restraints: 2330 Sorted by residual: 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 -2.79 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C4' LMT E 201 " pdb=" C3' LMT E 201 " pdb=" C5' LMT E 201 " pdb=" O1B LMT E 201 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.16e+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 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2327 not shown) Planarity restraints: 4366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 134 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 135 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 213 " 0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO A 214 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 375 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 376 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " 0.015 5.00e-02 4.00e+02 ... (remaining 4363 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.30: 6106 2.30 - 3.01: 82530 3.01 - 3.72: 112725 3.72 - 4.43: 173347 4.43 - 5.14: 268340 Nonbonded interactions: 643048 Sorted by model distance: nonbonded pdb=" O CYS F 373 " pdb="HD22 ASN F 400 " model vdw 1.584 1.850 nonbonded pdb="HH21 ARG B 372 " pdb=" OE2 GLU B 380 " model vdw 1.585 1.850 nonbonded pdb=" OE2 GLU B 144 " pdb=" HZ1 LYS B 191 " model vdw 1.588 1.850 nonbonded pdb=" O TRP C 238 " pdb=" H PHE C 244 " model vdw 1.616 1.850 nonbonded pdb=" O LEU E 105 " pdb=" H LEU E 109 " model vdw 1.621 1.850 ... (remaining 643043 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.400 Extract box with map and model: 3.460 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 107.880 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 0.077 15221 Z= 0.235 Angle : 0.524 9.599 20628 Z= 0.239 Chirality : 0.041 0.231 2330 Planarity : 0.003 0.029 2567 Dihedral : 17.341 179.627 5700 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.20), residues: 1877 helix: 1.89 (0.18), residues: 879 sheet: -0.38 (0.37), residues: 198 loop : 0.51 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.002 0.001 HIS F 356 PHE 0.010 0.001 PHE E 28 TYR 0.008 0.001 TYR F 167 ARG 0.002 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.126 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 VAL cc_start: 0.9018 (t) cc_final: 0.8738 (m) REVERT: A 403 ASP cc_start: 0.7652 (m-30) cc_final: 0.7368 (m-30) REVERT: A 431 TYR cc_start: 0.8889 (m-80) cc_final: 0.8652 (m-80) REVERT: B 112 MET cc_start: 0.8053 (mmp) cc_final: 0.7444 (mmp) REVERT: B 154 GLU cc_start: 0.6927 (tt0) cc_final: 0.6617 (mt-10) REVERT: C 252 ARG cc_start: 0.6506 (ttm110) cc_final: 0.6172 (ttm-80) REVERT: D 87 ASP cc_start: 0.7900 (t70) cc_final: 0.7518 (t0) REVERT: F 54 LYS cc_start: 0.4630 (mmtm) cc_final: 0.3968 (mttt) REVERT: F 133 TRP cc_start: 0.5539 (m-10) cc_final: 0.5246 (m-10) REVERT: F 276 MET cc_start: 0.5820 (mtt) cc_final: 0.5422 (mtt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.5453 time to fit residues: 174.9055 Evaluate side-chains 176 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 0.0030 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 HIS F 227 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15221 Z= 0.219 Angle : 0.495 6.940 20628 Z= 0.256 Chirality : 0.041 0.248 2330 Planarity : 0.003 0.030 2567 Dihedral : 12.826 173.445 2390 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.91 % Allowed : 14.14 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1877 helix: 1.68 (0.18), residues: 881 sheet: -0.36 (0.39), residues: 179 loop : 0.40 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.003 0.001 HIS B 85 PHE 0.013 0.001 PHE F 128 TYR 0.023 0.001 TYR F 217 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 2.415 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: symmetry clash REVERT: A 403 ASP cc_start: 0.7568 (m-30) cc_final: 0.7186 (m-30) REVERT: B 69 PHE cc_start: 0.8716 (m-10) cc_final: 0.8342 (m-80) REVERT: B 112 MET cc_start: 0.7980 (mmp) cc_final: 0.7231 (mmp) REVERT: C 252 ARG cc_start: 0.6668 (ttm110) cc_final: 0.6327 (ttm-80) REVERT: D 87 ASP cc_start: 0.7985 (t70) cc_final: 0.7574 (t0) REVERT: D 146 MET cc_start: 0.8785 (mmp) cc_final: 0.8469 (mmp) REVERT: E 197 GLN cc_start: 0.3860 (pm20) cc_final: 0.3570 (pm20) REVERT: F 54 LYS cc_start: 0.4653 (mmtm) cc_final: 0.3989 (mttt) REVERT: F 217 TYR cc_start: 0.4840 (p90) cc_final: 0.4521 (p90) REVERT: F 264 PHE cc_start: 0.4163 (m-80) cc_final: 0.3919 (m-80) outliers start: 14 outliers final: 11 residues processed: 186 average time/residue: 0.5441 time to fit residues: 156.2684 Evaluate side-chains 178 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 383 MET 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: 6.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 150 optimal weight: 0.0870 chunk 167 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 overall best weight: 4.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15221 Z= 0.332 Angle : 0.545 7.920 20628 Z= 0.280 Chirality : 0.043 0.389 2330 Planarity : 0.004 0.052 2567 Dihedral : 11.664 174.639 2390 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.10 % Allowed : 15.56 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1877 helix: 1.24 (0.17), residues: 881 sheet: -0.58 (0.38), residues: 179 loop : 0.15 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.016 0.001 HIS C 199 PHE 0.015 0.001 PHE E 28 TYR 0.016 0.002 TYR B 360 ARG 0.004 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 2.168 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: symmetry clash REVERT: A 342 LYS cc_start: 0.7697 (tttm) cc_final: 0.6915 (ttpt) REVERT: A 403 ASP cc_start: 0.7644 (m-30) cc_final: 0.7219 (m-30) REVERT: B 107 MET cc_start: 0.8318 (mtp) cc_final: 0.8106 (mtp) REVERT: B 112 MET cc_start: 0.7962 (mmp) cc_final: 0.7120 (mmp) REVERT: B 144 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8160 (tp30) REVERT: D 87 ASP cc_start: 0.8033 (t70) cc_final: 0.7618 (t0) REVERT: F 54 LYS cc_start: 0.4728 (mmtm) cc_final: 0.4063 (mttt) REVERT: F 217 TYR cc_start: 0.5093 (p90) cc_final: 0.4679 (p90) outliers start: 17 outliers final: 13 residues processed: 184 average time/residue: 0.5704 time to fit residues: 163.6894 Evaluate side-chains 174 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 169 optimal weight: 0.0770 chunk 179 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 HIS F 175 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15221 Z= 0.208 Angle : 0.488 9.211 20628 Z= 0.248 Chirality : 0.041 0.397 2330 Planarity : 0.004 0.032 2567 Dihedral : 11.025 171.000 2390 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.23 % Allowed : 15.95 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.19), residues: 1877 helix: 1.32 (0.18), residues: 877 sheet: -0.55 (0.39), residues: 173 loop : 0.15 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.016 0.001 HIS C 199 PHE 0.013 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.002 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 2.417 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 134 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6404 (tpp-160) REVERT: A 342 LYS cc_start: 0.7654 (tttm) cc_final: 0.6874 (ttpt) REVERT: A 403 ASP cc_start: 0.7626 (m-30) cc_final: 0.7176 (m-30) REVERT: B 112 MET cc_start: 0.8015 (mmp) cc_final: 0.7166 (mmp) REVERT: B 144 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8160 (tp30) REVERT: D 87 ASP cc_start: 0.8038 (t70) cc_final: 0.7614 (t0) REVERT: D 141 TYR cc_start: 0.8537 (t80) cc_final: 0.8261 (t80) REVERT: F 50 GLN cc_start: 0.3675 (mm110) cc_final: 0.3295 (tt0) REVERT: F 54 LYS cc_start: 0.4668 (mmtm) cc_final: 0.4011 (mttt) REVERT: F 217 TYR cc_start: 0.5059 (p90) cc_final: 0.4653 (p90) REVERT: F 378 CYS cc_start: 0.5833 (OUTLIER) cc_final: 0.5625 (m) outliers start: 19 outliers final: 14 residues processed: 176 average time/residue: 0.5275 time to fit residues: 145.9285 Evaluate side-chains 176 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15221 Z= 0.352 Angle : 0.547 9.439 20628 Z= 0.280 Chirality : 0.043 0.371 2330 Planarity : 0.004 0.047 2567 Dihedral : 11.177 172.172 2390 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.62 % Allowed : 16.28 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 1877 helix: 1.05 (0.17), residues: 878 sheet: -0.70 (0.38), residues: 175 loop : -0.05 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 103 HIS 0.006 0.001 HIS F 175 PHE 0.016 0.002 PHE E 28 TYR 0.017 0.002 TYR B 360 ARG 0.004 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 2.326 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: A 134 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6238 (tpp-160) REVERT: A 342 LYS cc_start: 0.7725 (tttm) cc_final: 0.6948 (ttpt) REVERT: A 403 ASP cc_start: 0.7730 (m-30) cc_final: 0.7241 (m-30) REVERT: B 112 MET cc_start: 0.8031 (mmp) cc_final: 0.7122 (mmp) REVERT: B 144 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7985 (tp30) REVERT: D 87 ASP cc_start: 0.8081 (t70) cc_final: 0.7656 (t0) REVERT: D 141 TYR cc_start: 0.8537 (t80) cc_final: 0.8234 (t80) REVERT: F 50 GLN cc_start: 0.3687 (mm110) cc_final: 0.3314 (tt0) REVERT: F 54 LYS cc_start: 0.4646 (mmtm) cc_final: 0.3977 (mttt) REVERT: F 217 TYR cc_start: 0.4999 (p90) cc_final: 0.4636 (p90) REVERT: F 295 GLN cc_start: 0.5956 (mp10) cc_final: 0.5583 (mp10) outliers start: 25 outliers final: 19 residues processed: 182 average time/residue: 0.5823 time to fit residues: 166.1266 Evaluate side-chains 182 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 406 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15221 Z= 0.307 Angle : 0.530 9.986 20628 Z= 0.271 Chirality : 0.042 0.318 2330 Planarity : 0.004 0.037 2567 Dihedral : 11.021 170.887 2390 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.69 % Allowed : 16.80 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.19), residues: 1877 helix: 1.05 (0.17), residues: 872 sheet: -0.82 (0.37), residues: 177 loop : -0.09 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.004 0.001 HIS C 199 PHE 0.015 0.001 PHE E 28 TYR 0.017 0.002 TYR B 360 ARG 0.004 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 2.776 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: A 134 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6366 (tpp-160) REVERT: A 342 LYS cc_start: 0.7777 (tttm) cc_final: 0.6983 (ttpt) REVERT: A 403 ASP cc_start: 0.7744 (m-30) cc_final: 0.7238 (m-30) REVERT: B 54 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8699 (mttp) REVERT: B 112 MET cc_start: 0.7927 (mmp) cc_final: 0.6993 (mmp) REVERT: B 144 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7960 (tp30) REVERT: D 39 GLU cc_start: 0.7986 (pt0) cc_final: 0.7785 (pt0) REVERT: D 87 ASP cc_start: 0.8093 (t70) cc_final: 0.7665 (t0) REVERT: D 115 MET cc_start: 0.7442 (mtm) cc_final: 0.6941 (mtm) REVERT: D 141 TYR cc_start: 0.8541 (t80) cc_final: 0.8248 (t80) REVERT: F 50 GLN cc_start: 0.3711 (mm110) cc_final: 0.3351 (tt0) REVERT: F 54 LYS cc_start: 0.4642 (mmtm) cc_final: 0.3975 (mttt) REVERT: F 119 MET cc_start: 0.3664 (ptp) cc_final: 0.3065 (ptp) REVERT: F 217 TYR cc_start: 0.4990 (p90) cc_final: 0.4640 (p90) outliers start: 26 outliers final: 23 residues processed: 185 average time/residue: 0.5386 time to fit residues: 153.1187 Evaluate side-chains 186 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 406 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15221 Z= 0.369 Angle : 0.567 6.221 20628 Z= 0.292 Chirality : 0.043 0.157 2330 Planarity : 0.004 0.043 2567 Dihedral : 10.950 169.414 2390 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.33 % Allowed : 16.86 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1877 helix: 0.85 (0.17), residues: 872 sheet: -0.90 (0.37), residues: 173 loop : -0.25 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 103 HIS 0.005 0.001 HIS B 85 PHE 0.016 0.002 PHE E 28 TYR 0.018 0.002 TYR B 360 ARG 0.004 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 2.234 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: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6209 (tpp-160) REVERT: A 342 LYS cc_start: 0.7856 (tttm) cc_final: 0.7056 (ttpt) REVERT: A 403 ASP cc_start: 0.7799 (m-30) cc_final: 0.7259 (m-30) REVERT: B 54 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8758 (mttp) REVERT: B 144 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7981 (tp30) REVERT: D 39 GLU cc_start: 0.8000 (pt0) cc_final: 0.7789 (pt0) REVERT: D 87 ASP cc_start: 0.8164 (t70) cc_final: 0.7798 (t0) REVERT: D 141 TYR cc_start: 0.8584 (t80) cc_final: 0.8318 (t80) REVERT: E 107 ASN cc_start: 0.6023 (OUTLIER) cc_final: 0.5598 (m110) REVERT: E 132 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7342 (mtt-85) REVERT: F 54 LYS cc_start: 0.4645 (mmtm) cc_final: 0.4048 (mttt) REVERT: F 119 MET cc_start: 0.3456 (ptp) cc_final: 0.2882 (ptp) outliers start: 36 outliers final: 29 residues processed: 195 average time/residue: 0.5588 time to fit residues: 166.3847 Evaluate side-chains 198 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 406 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN C 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15221 Z= 0.210 Angle : 0.495 6.241 20628 Z= 0.253 Chirality : 0.040 0.138 2330 Planarity : 0.004 0.035 2567 Dihedral : 10.441 167.075 2390 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.08 % Allowed : 17.25 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 1877 helix: 1.05 (0.18), residues: 879 sheet: -0.79 (0.38), residues: 169 loop : -0.15 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.002 0.001 HIS F 97 PHE 0.014 0.001 PHE E 28 TYR 0.017 0.001 TYR B 360 ARG 0.003 0.000 ARG F 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 2.102 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6339 (tpp-160) REVERT: A 342 LYS cc_start: 0.7847 (tttm) cc_final: 0.7059 (ttpt) REVERT: A 403 ASP cc_start: 0.7767 (m-30) cc_final: 0.7220 (m-30) REVERT: B 54 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8731 (mttp) REVERT: B 144 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7899 (tp30) REVERT: D 141 TYR cc_start: 0.8544 (t80) cc_final: 0.8251 (t80) REVERT: E 22 PHE cc_start: 0.6249 (m-80) cc_final: 0.5712 (m-10) REVERT: E 132 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7320 (mtt-85) REVERT: F 54 LYS cc_start: 0.4539 (mmtm) cc_final: 0.3877 (mttt) REVERT: F 119 MET cc_start: 0.3476 (ptp) cc_final: 0.2888 (ptp) outliers start: 32 outliers final: 27 residues processed: 196 average time/residue: 0.5858 time to fit residues: 174.0621 Evaluate side-chains 195 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 406 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 15221 Z= 0.470 Angle : 0.607 6.158 20628 Z= 0.315 Chirality : 0.045 0.166 2330 Planarity : 0.005 0.045 2567 Dihedral : 10.952 169.502 2390 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.20 % Allowed : 17.19 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 1877 helix: 0.71 (0.17), residues: 869 sheet: -0.96 (0.37), residues: 173 loop : -0.43 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 103 HIS 0.028 0.002 HIS C 199 PHE 0.019 0.002 PHE C 235 TYR 0.018 0.002 TYR B 360 ARG 0.005 0.001 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 2.228 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7885 (tttm) cc_final: 0.7089 (ttpt) REVERT: A 403 ASP cc_start: 0.7841 (m-30) cc_final: 0.7425 (m-30) REVERT: B 54 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8779 (mttp) REVERT: B 144 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7699 (tp30) REVERT: E 22 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6175 (m-10) REVERT: E 132 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7366 (mtt-85) REVERT: F 54 LYS cc_start: 0.4556 (mmtm) cc_final: 0.3920 (mttt) REVERT: F 119 MET cc_start: 0.3529 (ptp) cc_final: 0.2965 (ptp) outliers start: 34 outliers final: 29 residues processed: 190 average time/residue: 0.5569 time to fit residues: 160.9430 Evaluate side-chains 193 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 406 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15221 Z= 0.191 Angle : 0.493 6.464 20628 Z= 0.251 Chirality : 0.040 0.149 2330 Planarity : 0.004 0.041 2567 Dihedral : 10.338 167.668 2390 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.75 % Allowed : 17.51 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 1877 helix: 1.02 (0.18), residues: 880 sheet: -0.82 (0.38), residues: 169 loop : -0.21 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 PHE 0.015 0.001 PHE C 235 TYR 0.017 0.001 TYR B 360 ARG 0.003 0.000 ARG A 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 2.213 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7814 (tttm) cc_final: 0.7037 (ttpt) REVERT: B 54 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8726 (mttp) REVERT: B 144 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7779 (tp30) REVERT: D 115 MET cc_start: 0.7379 (mtm) cc_final: 0.6834 (mtm) REVERT: D 141 TYR cc_start: 0.8663 (t80) cc_final: 0.8359 (t80) REVERT: E 22 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.6097 (m-10) REVERT: E 132 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7338 (mtt-85) REVERT: F 54 LYS cc_start: 0.4606 (mmtm) cc_final: 0.3984 (mttt) REVERT: F 119 MET cc_start: 0.3549 (ptp) cc_final: 0.2952 (ptp) REVERT: F 304 LYS cc_start: 0.8030 (tttt) cc_final: 0.7828 (tttp) outliers start: 27 outliers final: 23 residues processed: 189 average time/residue: 0.5927 time to fit residues: 170.1192 Evaluate side-chains 190 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 406 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.147911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101714 restraints weight = 63173.247| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.72 r_work: 0.3047 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15221 Z= 0.288 Angle : 0.526 6.525 20628 Z= 0.269 Chirality : 0.041 0.145 2330 Planarity : 0.004 0.036 2567 Dihedral : 10.434 170.643 2390 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.27 % Allowed : 17.06 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 1877 helix: 0.96 (0.18), residues: 880 sheet: -0.83 (0.38), residues: 169 loop : -0.25 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.003 0.001 HIS B 85 PHE 0.016 0.001 PHE E 28 TYR 0.018 0.002 TYR B 360 ARG 0.003 0.000 ARG F 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5886.32 seconds wall clock time: 105 minutes 10.15 seconds (6310.15 seconds total)