Starting phenix.real_space_refine on Fri Mar 15 14:45:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/03_2024/8ew3_28641_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/03_2024/8ew3_28641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65159 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/03_2024/8ew3_28641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/03_2024/8ew3_28641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/03_2024/8ew3_28641_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/03_2024/8ew3_28641_updated.pdb" } resolution = 2.65159 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= 0.001 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 S 68 5.16 5 C 7746 2.51 5 N 1949 2.21 5 O 2135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 11902 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3182 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "C" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1894 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain: "D" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1545 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 9, 'TRANS': 192} Chain: "E" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1512 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 244 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'FMN': 1, 'RBF': 1, 'UQ1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 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: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9290 SG CYS D 112 66.314 41.140 63.217 1.00 95.11 S ATOM 10247 SG CYS E 26 64.807 44.084 64.882 1.00 82.26 S ATOM 8651 SG CYS D 29 62.941 41.588 68.946 1.00104.84 S ATOM 10969 SG CYS E 120 64.555 38.368 67.743 1.00 78.16 S Time building chain proxies: 6.54, per 1000 atoms: 0.55 Number of scatterers: 11902 At special positions: 0 Unit cell: (99.324, 108.936, 132.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 68 16.00 P 2 15.00 O 2135 8.00 N 1949 7.00 C 7746 6.00 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: 4.49 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " Number of angles added : 6 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 8 sheets defined 53.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 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 115 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.531A 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 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 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.678A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 383' 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 416 through 423 removed outlier: 4.842A 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 4 through 14 removed outlier: 4.634A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N HIS B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 removed outlier: 4.730A pdb=" N ALA B 25 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR B 32 " --> pdb=" O ALA B 29 " (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 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 169 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 248 removed outlier: 8.658A pdb=" N ALA B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N GLY B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 277 through 289 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: 3.581A 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: 3.624A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.526A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 3.503A 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 removed outlier: 3.510A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) 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: 3.758A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 4.196A 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 252 Processing helix chain 'D' and resid 9 through 16 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.545A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N THR D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 61 Processing helix chain 'D' and resid 71 through 93 Processing helix chain 'D' and resid 95 through 108 removed outlier: 6.330A pdb=" N VAL D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 108 " --> pdb=" O PHE D 104 " (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 Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.780A 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 2 through 12 Processing helix chain 'E' and resid 25 through 33 removed outlier: 3.518A pdb=" N ALA E 30 " --> pdb=" O CYS E 26 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER E 32 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) 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: 4.633A pdb=" N PHE E 80 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 81 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE E 83 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 90 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 98 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP E 99 " --> pdb=" O MET E 96 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG E 100 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E 101 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 116 removed outlier: 4.657A pdb=" N ILE E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 136 through 166 removed outlier: 3.817A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 192 removed outlier: 3.513A pdb=" N ILE E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.754A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.791A 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: 7.088A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 132 through 134 removed outlier: 6.793A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR A 190 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 306 through 308 removed outlier: 5.606A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N SER A 17 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N ARG A 276 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 12.654A pdb=" N VAL A 19 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 14.300A pdb=" N VAL A 278 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 14.013A pdb=" N SER A 21 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 71 through 77 removed outlier: 14.213A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.378A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= H, first strand: chain 'C' and resid 204 through 206 557 hydrogen bonds defined for protein. 1566 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: 3.14 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 5004 1.42 - 1.61: 7042 1.61 - 1.81: 120 1.81 - 2.01: 0 2.01 - 2.20: 4 Bond restraints: 12170 Sorted by residual: bond pdb=" C2 UQ1 B 602 " pdb=" C3 UQ1 B 602 " ideal model delta sigma weight residual 1.339 1.421 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C4 RBF B 601 " pdb=" C4A RBF B 601 " ideal model delta sigma weight residual 1.481 1.405 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C4A FMN B 600 " pdb=" N5 FMN B 600 " ideal model delta sigma weight residual 1.380 1.306 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4A FMN C 301 " pdb=" N5 FMN C 301 " ideal model delta sigma weight residual 1.380 1.307 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " ideal model delta sigma weight residual 1.485 1.412 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 12165 not shown) Histogram of bond angle deviations from ideal: 75.60 - 87.28: 2 87.28 - 98.96: 0 98.96 - 110.64: 3974 110.64 - 122.32: 11099 122.32 - 134.01: 1442 Bond angle restraints: 16517 Sorted by residual: angle pdb=" C ILE C 115 " pdb=" N GLN C 116 " pdb=" CA GLN C 116 " ideal model delta sigma weight residual 121.54 126.49 -4.95 1.91e+00 2.74e-01 6.73e+00 angle pdb=" C3 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 122.52 130.03 -7.51 3.00e+00 1.11e-01 6.26e+00 angle pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 117.10 110.63 6.47 3.00e+00 1.11e-01 4.65e+00 angle pdb=" N VAL A 287 " pdb=" CA VAL A 287 " pdb=" CB VAL A 287 " ideal model delta sigma weight residual 111.81 107.29 4.52 2.24e+00 1.99e-01 4.07e+00 angle pdb=" CA TRP B 103 " pdb=" CB TRP B 103 " pdb=" CG TRP B 103 " ideal model delta sigma weight residual 113.60 116.95 -3.35 1.90e+00 2.77e-01 3.11e+00 ... (remaining 16512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 7073 35.58 - 71.16: 29 71.16 - 106.75: 4 106.75 - 142.33: 1 142.33 - 177.91: 3 Dihedral angle restraints: 7110 sinusoidal: 2753 harmonic: 4357 Sorted by residual: dihedral pdb=" C10 FMN C 301 " pdb=" C1' FMN C 301 " pdb=" N10 FMN C 301 " pdb=" C2' FMN C 301 " ideal model delta sinusoidal sigma weight residual 257.59 79.68 177.91 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' FMN C 301 " pdb=" O5' FMN C 301 " pdb=" P FMN C 301 " pdb=" O1P FMN C 301 " ideal model delta sinusoidal sigma weight residual 75.26 -115.18 -169.57 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C10 FMN B 600 " pdb=" C1' FMN B 600 " pdb=" N10 FMN B 600 " pdb=" C2' FMN B 600 " ideal model delta sinusoidal sigma weight residual 257.59 89.23 168.37 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 7107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1330 0.036 - 0.072: 427 0.072 - 0.108: 117 0.108 - 0.144: 24 0.144 - 0.180: 1 Chirality restraints: 1899 Sorted by residual: chirality pdb=" C4' RBF B 601 " pdb=" C3' RBF B 601 " pdb=" C5' RBF B 601 " pdb=" O4' RBF B 601 " both_signs ideal model delta sigma weight residual False -2.27 -2.45 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA VAL A 139 " pdb=" N VAL A 139 " pdb=" C VAL A 139 " pdb=" CB VAL A 139 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL A 90 " pdb=" N VAL A 90 " pdb=" C VAL A 90 " pdb=" CB VAL A 90 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1896 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 602 " 0.081 2.00e-02 2.50e+03 1.21e-01 4.42e+02 pdb=" C2 UQ1 B 602 " -0.017 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 602 " -0.030 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 602 " 0.093 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 602 " -0.005 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 602 " -0.032 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.157 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 602 " -0.085 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 602 " 0.202 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 602 " -0.073 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 602 " -0.190 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 602 " 0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 B 602 " 0.005 2.00e-02 2.50e+03 2.18e-02 5.92e+00 pdb=" C11 UQ1 B 602 " -0.019 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.026 2.00e-02 2.50e+03 pdb=" C8 UQ1 B 602 " 0.036 2.00e-02 2.50e+03 pdb=" C9 UQ1 B 602 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.012 2.00e-02 2.50e+03 7.40e-03 2.60e+00 pdb=" C10 FMN C 301 " 0.006 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " 0.006 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " -0.005 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " -0.006 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " -0.009 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.005 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.019 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " 0.002 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2791 2.79 - 3.32: 11331 3.32 - 3.84: 20144 3.84 - 4.37: 24935 4.37 - 4.90: 41667 Nonbonded interactions: 100868 Sorted by model distance: nonbonded pdb=" O GLU C 99 " pdb=" OG SER C 103 " model vdw 2.260 2.440 nonbonded pdb=" O ALA B 377 " pdb=" O2' FMN C 301 " model vdw 2.293 2.440 nonbonded pdb=" O GLU B 28 " pdb=" OG1 THR B 32 " model vdw 2.295 2.440 nonbonded pdb=" NH1 ARG C 118 " pdb=" O MET C 242 " model vdw 2.327 2.520 nonbonded pdb=" NH1 ARG B 199 " pdb=" O TYR E 166 " model vdw 2.335 2.520 ... (remaining 100863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.420 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 35.010 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 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 : 0.003 0.082 12170 Z= 0.214 Angle : 0.446 7.509 16517 Z= 0.217 Chirality : 0.039 0.180 1899 Planarity : 0.004 0.121 2060 Dihedral : 10.100 177.911 4326 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.16 % Allowed : 1.35 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.12 (0.21), residues: 1528 helix: 1.44 (0.18), residues: 772 sheet: 0.54 (0.58), residues: 76 loop : 0.05 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.013 0.001 PHE D 104 TYR 0.006 0.001 TYR A 429 ARG 0.003 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9473 (mtm) cc_final: 0.9250 (mtm) REVERT: D 87 ASP cc_start: 0.8625 (t70) cc_final: 0.8317 (t0) REVERT: D 95 TYR cc_start: 0.9140 (t80) cc_final: 0.8807 (t80) REVERT: D 202 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7187 (mmmt) REVERT: E 82 THR cc_start: 0.9251 (m) cc_final: 0.9026 (m) REVERT: F 28 LYS cc_start: 0.5812 (mmmt) cc_final: 0.4756 (tttm) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 1.5298 time to fit residues: 278.2985 Evaluate side-chains 116 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 0.3980 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN E 119 ASN E 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 12170 Z= 0.372 Angle : 0.562 8.358 16517 Z= 0.294 Chirality : 0.043 0.135 1899 Planarity : 0.004 0.059 2060 Dihedral : 9.251 177.833 1661 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.35 % Allowed : 6.85 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.42 (0.22), residues: 1528 helix: 1.76 (0.19), residues: 787 sheet: -0.13 (0.52), residues: 90 loop : 0.20 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS A 225 PHE 0.026 0.002 PHE E 22 TYR 0.014 0.001 TYR D 141 ARG 0.008 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: D 202 LYS cc_start: 0.7573 (mmtt) cc_final: 0.7284 (mptm) REVERT: E 17 MET cc_start: 0.8553 (mmm) cc_final: 0.8254 (mtt) REVERT: F 16 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7854 (mm) REVERT: F 28 LYS cc_start: 0.5634 (mmmt) cc_final: 0.4741 (tttm) outliers start: 17 outliers final: 3 residues processed: 123 average time/residue: 1.4750 time to fit residues: 194.9254 Evaluate side-chains 118 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 0.0040 chunk 38 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 110 optimal weight: 0.0370 overall best weight: 0.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12170 Z= 0.132 Angle : 0.460 8.974 16517 Z= 0.241 Chirality : 0.040 0.129 1899 Planarity : 0.004 0.032 2060 Dihedral : 8.797 177.545 1661 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.19 % Allowed : 8.28 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.55 (0.22), residues: 1528 helix: 1.88 (0.19), residues: 787 sheet: 0.30 (0.56), residues: 76 loop : 0.18 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.004 0.001 HIS B 12 PHE 0.014 0.001 PHE D 50 TYR 0.017 0.001 TYR E 106 ARG 0.006 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.8000 (mtm180) REVERT: D 87 ASP cc_start: 0.8737 (t0) cc_final: 0.8532 (t0) REVERT: D 115 MET cc_start: 0.8419 (tpt) cc_final: 0.8064 (tpp) REVERT: D 202 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6848 (mptm) REVERT: E 17 MET cc_start: 0.8556 (mmm) cc_final: 0.8287 (mtt) REVERT: E 151 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8190 (tpp) REVERT: F 6 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7831 (t80) REVERT: F 16 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7904 (tm) REVERT: F 28 LYS cc_start: 0.5665 (mmmt) cc_final: 0.4809 (tttm) outliers start: 15 outliers final: 4 residues processed: 123 average time/residue: 1.4624 time to fit residues: 193.6682 Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12170 Z= 0.241 Angle : 0.498 8.239 16517 Z= 0.256 Chirality : 0.041 0.129 1899 Planarity : 0.004 0.032 2060 Dihedral : 8.600 175.983 1661 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.67 % Allowed : 8.68 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.22), residues: 1528 helix: 1.89 (0.19), residues: 787 sheet: 0.23 (0.57), residues: 76 loop : 0.13 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.003 0.001 HIS B 13 PHE 0.015 0.001 PHE D 104 TYR 0.016 0.001 TYR E 106 ARG 0.004 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.8152 (mtm180) REVERT: C 110 GLN cc_start: 0.7977 (mt0) cc_final: 0.7771 (mt0) REVERT: D 202 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7297 (mptm) REVERT: E 17 MET cc_start: 0.8521 (mmm) cc_final: 0.8250 (mtt) REVERT: E 151 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8075 (tpp) REVERT: F 6 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.8025 (t80) REVERT: F 16 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8022 (tm) REVERT: F 28 LYS cc_start: 0.5751 (mmmt) cc_final: 0.4849 (tttm) outliers start: 21 outliers final: 5 residues processed: 125 average time/residue: 1.4964 time to fit residues: 201.0372 Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 12170 Z= 0.476 Angle : 0.607 8.726 16517 Z= 0.311 Chirality : 0.045 0.147 1899 Planarity : 0.004 0.038 2060 Dihedral : 8.766 172.734 1661 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.75 % Allowed : 9.24 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.25 (0.21), residues: 1528 helix: 1.68 (0.19), residues: 784 sheet: -0.31 (0.54), residues: 88 loop : 0.05 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 103 HIS 0.005 0.001 HIS B 330 PHE 0.019 0.002 PHE E 28 TYR 0.017 0.002 TYR D 141 ARG 0.004 0.001 ARG E 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8634 (mt-10) REVERT: D 99 LYS cc_start: 0.9355 (mtpp) cc_final: 0.9148 (mtpp) REVERT: D 202 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7489 (mptt) REVERT: E 17 MET cc_start: 0.8541 (mmm) cc_final: 0.8282 (mtt) REVERT: F 6 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8072 (t80) REVERT: F 16 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8185 (tm) REVERT: F 28 LYS cc_start: 0.5971 (mmmt) cc_final: 0.5216 (tttm) outliers start: 22 outliers final: 10 residues processed: 121 average time/residue: 1.5569 time to fit residues: 201.8224 Evaluate side-chains 124 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.7980 chunk 132 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12170 Z= 0.150 Angle : 0.483 9.719 16517 Z= 0.250 Chirality : 0.040 0.130 1899 Planarity : 0.004 0.034 2060 Dihedral : 8.534 174.222 1661 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.19 % Allowed : 10.03 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.22), residues: 1528 helix: 1.92 (0.19), residues: 781 sheet: 0.36 (0.60), residues: 74 loop : 0.04 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS B 13 PHE 0.014 0.001 PHE E 22 TYR 0.016 0.001 TYR E 106 ARG 0.007 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8574 (mt-10) REVERT: D 99 LYS cc_start: 0.9342 (mtpp) cc_final: 0.9020 (mtpp) REVERT: D 202 LYS cc_start: 0.7489 (mmtt) cc_final: 0.6925 (mptt) REVERT: E 17 MET cc_start: 0.8476 (mmm) cc_final: 0.8253 (mtt) REVERT: F 6 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.8012 (t80) REVERT: F 16 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8188 (tm) REVERT: F 28 LYS cc_start: 0.5951 (mmmt) cc_final: 0.5269 (tttm) outliers start: 15 outliers final: 6 residues processed: 123 average time/residue: 1.5299 time to fit residues: 202.1806 Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12170 Z= 0.215 Angle : 0.503 10.334 16517 Z= 0.259 Chirality : 0.041 0.135 1899 Planarity : 0.004 0.033 2060 Dihedral : 8.498 174.584 1661 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.19 % Allowed : 10.83 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.22), residues: 1528 helix: 1.91 (0.19), residues: 788 sheet: 0.25 (0.59), residues: 76 loop : 0.09 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 13 PHE 0.014 0.001 PHE D 104 TYR 0.026 0.001 TYR E 106 ARG 0.008 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8569 (mt-10) REVERT: D 115 MET cc_start: 0.8283 (tpt) cc_final: 0.8076 (mmm) REVERT: D 202 LYS cc_start: 0.7513 (mmtt) cc_final: 0.7232 (mttp) REVERT: E 17 MET cc_start: 0.8487 (mmm) cc_final: 0.8257 (mtt) REVERT: F 6 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.8015 (t80) REVERT: F 16 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8228 (tm) REVERT: F 28 LYS cc_start: 0.6022 (mmmt) cc_final: 0.5347 (tttm) outliers start: 15 outliers final: 7 residues processed: 115 average time/residue: 1.5469 time to fit residues: 190.6797 Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12170 Z= 0.357 Angle : 0.565 10.885 16517 Z= 0.290 Chirality : 0.043 0.141 1899 Planarity : 0.004 0.038 2060 Dihedral : 8.532 174.199 1661 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.51 % Allowed : 10.67 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.34 (0.22), residues: 1528 helix: 1.76 (0.19), residues: 789 sheet: -0.20 (0.56), residues: 86 loop : 0.05 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.004 0.001 HIS B 46 PHE 0.042 0.002 PHE E 22 TYR 0.018 0.001 TYR E 106 ARG 0.009 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8602 (mt-10) REVERT: D 202 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7190 (mptt) REVERT: F 6 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.8069 (t80) REVERT: F 16 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8210 (tm) REVERT: F 28 LYS cc_start: 0.6027 (mmmt) cc_final: 0.5271 (tttm) outliers start: 19 outliers final: 7 residues processed: 119 average time/residue: 1.4918 time to fit residues: 190.4686 Evaluate side-chains 120 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12170 Z= 0.213 Angle : 0.512 11.252 16517 Z= 0.263 Chirality : 0.041 0.134 1899 Planarity : 0.004 0.034 2060 Dihedral : 8.393 175.216 1661 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.96 % Allowed : 11.23 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.45 (0.22), residues: 1528 helix: 1.88 (0.19), residues: 788 sheet: -0.19 (0.56), residues: 86 loop : 0.06 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.002 0.001 HIS B 13 PHE 0.048 0.001 PHE E 22 TYR 0.028 0.001 TYR E 106 ARG 0.008 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8582 (mt-10) REVERT: D 202 LYS cc_start: 0.7510 (mmtt) cc_final: 0.7261 (mttp) REVERT: F 6 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.8034 (t80) REVERT: F 16 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8266 (tm) REVERT: F 28 LYS cc_start: 0.5591 (mmmt) cc_final: 0.4902 (tttm) outliers start: 12 outliers final: 7 residues processed: 116 average time/residue: 1.5504 time to fit residues: 193.1707 Evaluate side-chains 120 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 151 optimal weight: 0.0020 chunk 139 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 0.0020 chunk 128 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12170 Z= 0.148 Angle : 0.504 12.625 16517 Z= 0.257 Chirality : 0.040 0.132 1899 Planarity : 0.004 0.034 2060 Dihedral : 8.215 176.389 1661 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.80 % Allowed : 11.62 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.22), residues: 1528 helix: 1.94 (0.19), residues: 789 sheet: 0.35 (0.61), residues: 74 loop : 0.03 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.002 0.000 HIS B 13 PHE 0.041 0.001 PHE E 22 TYR 0.020 0.001 TYR E 106 ARG 0.008 0.000 ARG B 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8552 (mt-10) REVERT: D 202 LYS cc_start: 0.7420 (mmtt) cc_final: 0.7176 (mttp) REVERT: E 15 GLU cc_start: 0.7842 (mm-30) cc_final: 0.6969 (tm-30) REVERT: E 25 MET cc_start: 0.8918 (mmm) cc_final: 0.8710 (mmp) REVERT: F 6 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.8023 (t80) REVERT: F 10 MET cc_start: 0.8357 (tpt) cc_final: 0.8138 (tpp) REVERT: F 28 LYS cc_start: 0.5502 (mmmt) cc_final: 0.4911 (tttm) outliers start: 10 outliers final: 4 residues processed: 117 average time/residue: 1.5343 time to fit residues: 192.5440 Evaluate side-chains 116 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 13 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.048079 restraints weight = 31179.847| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.44 r_work: 0.2633 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12170 Z= 0.205 Angle : 0.525 12.487 16517 Z= 0.264 Chirality : 0.040 0.132 1899 Planarity : 0.004 0.032 2060 Dihedral : 8.181 176.677 1661 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.80 % Allowed : 11.70 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.52 (0.22), residues: 1528 helix: 1.95 (0.19), residues: 788 sheet: -0.22 (0.56), residues: 86 loop : 0.10 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.002 0.001 HIS B 13 PHE 0.040 0.001 PHE E 22 TYR 0.029 0.001 TYR E 106 ARG 0.007 0.000 ARG B 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4090.46 seconds wall clock time: 73 minutes 12.82 seconds (4392.82 seconds total)