Starting phenix.real_space_refine on Fri Jun 5 10:46:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tan_55752/06_2026/9tan_55752.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tan_55752/06_2026/9tan_55752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tan_55752/06_2026/9tan_55752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tan_55752/06_2026/9tan_55752.map" model { file = "/net/cci-nas-00/data/ceres_data/9tan_55752/06_2026/9tan_55752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tan_55752/06_2026/9tan_55752.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Fe 32 7.16 5 P 1 5.49 5 S 150 5.16 5 C 12206 2.51 5 N 3402 2.21 5 O 3883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19678 Number of models: 1 Model: "" Number of chains: 17 Chain: "B" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1684 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 1 Chain: "C" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4760 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 551} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "G" Number of atoms: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "I" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1185 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 135} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' CA': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' CA': 2, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' CA': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "G" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "I" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 962 SG CYS B 129 59.761 74.615 103.880 1.00 4.37 S ATOM 459 SG CYS B 64 60.464 80.467 105.467 1.00 10.47 S ATOM 453 SG CYS B 63 65.524 77.388 105.618 1.00 11.26 S ATOM 1179 SG CYS B 158 62.226 77.687 100.239 1.00 9.86 S ATOM 7091 SG CYS E 92 80.254 65.612 32.309 1.00 34.56 S ATOM 7125 SG CYS E 97 82.732 67.650 29.821 1.00 19.20 S ATOM 7429 SG CYS E 137 85.865 60.899 30.484 1.00 16.25 S ATOM 10385 SG CYS F 354 77.041 54.552 53.407 1.00 4.02 S ATOM 10405 SG CYS F 357 78.048 58.265 50.033 1.00 5.67 S ATOM 10726 SG CYS F 398 79.008 52.086 48.146 1.00 3.17 S ATOM 10361 SG CYS F 351 73.327 53.633 48.096 1.00 3.43 S ATOM 11920 SG CYS G 114 63.853 60.930 69.188 1.00 0.67 S ATOM 11860 SG CYS G 105 64.651 67.163 70.496 1.00 0.88 S ATOM 11880 SG CYS G 108 59.492 64.666 67.650 1.00 3.47 S ATOM 12274 SG CYS G 156 65.183 54.340 60.869 1.00 1.50 S ATOM 12255 SG CYS G 153 63.662 59.281 57.584 1.00 2.66 S ATOM 12303 SG CYS G 159 60.473 54.149 57.078 1.00 1.01 S ATOM 12651 SG CYS G 203 60.279 56.925 62.424 1.00 1.55 S ATOM 12876 SG CYS G 230 43.224 44.628 71.972 1.00 6.28 S ATOM 13161 SG CYS G 265 44.280 44.673 66.040 1.00 3.27 S ATOM 12924 SG CYS G 237 47.460 40.936 70.287 1.00 1.82 S ATOM 12900 SG CYS G 233 41.789 39.906 68.750 1.00 3.56 S ATOM 11321 SG CYS G 36 70.760 49.402 60.122 1.00 1.17 S ATOM 11397 SG CYS G 47 72.459 53.153 62.061 1.00 1.13 S ATOM 11423 SG CYS G 50 76.325 47.996 64.619 1.00 4.40 S ATOM 11572 SG CYS G 69 74.316 45.877 61.776 1.00 5.95 S ATOM 18673 SG CYS I 102 63.151 75.839 91.769 1.00 2.52 S ATOM 18648 SG CYS I 99 57.686 78.734 92.614 1.00 4.25 S ATOM 18691 SG CYS I 105 60.107 77.940 87.028 1.00 2.78 S ATOM 18406 SG CYS I 70 58.430 72.998 90.339 1.00 1.54 S ATOM 18720 SG CYS I 109 60.365 78.198 78.410 1.00 2.32 S ATOM 18383 SG CYS I 66 57.027 74.468 82.311 1.00 0.87 S ATOM 18343 SG CYS I 60 53.964 76.887 77.702 1.00 4.32 S ATOM 18361 SG CYS I 63 58.670 72.674 76.754 1.00 0.84 S Time building chain proxies: 4.48, per 1000 atoms: 0.23 Number of scatterers: 19678 At special positions: 0 Unit cell: (117.15, 113.85, 153.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 4 19.99 S 150 16.00 P 1 15.00 O 3883 8.00 N 3402 7.00 C 12206 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 822.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb=" SF4 F 501 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb=" SF4 I 201 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 23 sheets defined 42.7% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 35 through 53 removed outlier: 3.955A pdb=" N ASN B 43 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.613A pdb=" N LYS B 147 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 148 " --> pdb=" O VAL B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.585A pdb=" N TYR B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 210 removed outlier: 4.666A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 34 removed outlier: 3.524A pdb=" N GLY C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 Processing helix chain 'C' and resid 133 through 146 removed outlier: 4.320A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.513A pdb=" N GLY C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 removed outlier: 3.507A pdb=" N THR C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 268 through 274' Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.661A pdb=" N GLU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 300 through 330 Processing helix chain 'C' and resid 335 through 355 removed outlier: 3.916A pdb=" N THR C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 398 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 401 through 409 Processing helix chain 'C' and resid 415 through 423 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 437 through 442 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 462 through 487 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 511 through 524 Processing helix chain 'C' and resid 563 through 577 removed outlier: 4.048A pdb=" N ALA C 567 " --> pdb=" O THR C 563 " (cutoff:3.500A) Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 591 Processing helix chain 'C' and resid 594 through 600 Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 31 through 34 Processing helix chain 'E' and resid 35 through 48 Processing helix chain 'E' and resid 51 through 63 removed outlier: 3.731A pdb=" N ILE E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 94 through 101 Processing helix chain 'E' and resid 101 through 114 removed outlier: 4.039A pdb=" N ILE E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 removed outlier: 3.793A pdb=" N GLY E 140 " --> pdb=" O CYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 164 removed outlier: 3.756A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 17 removed outlier: 4.280A pdb=" N ARG F 16 " --> pdb=" O LEU F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 31 Processing helix chain 'F' and resid 35 through 45 Processing helix chain 'F' and resid 46 through 58 removed outlier: 3.647A pdb=" N GLY F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.530A pdb=" N LEU F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.756A pdb=" N LEU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 153 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 182 through 191 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 219 through 232 removed outlier: 3.688A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 232 through 238 removed outlier: 3.560A pdb=" N TYR F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 276 removed outlier: 3.547A pdb=" N ILE F 273 " --> pdb=" O THR F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.129A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 316 Processing helix chain 'F' and resid 334 through 349 Processing helix chain 'F' and resid 354 through 373 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 379 through 391 Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.523A pdb=" N GLU F 406 " --> pdb=" O PRO F 402 " (cutoff:3.500A) Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 415 through 421 removed outlier: 3.695A pdb=" N PHE F 419 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 83 through 99 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 150 through 153 Processing helix chain 'G' and resid 157 through 164 Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.822A pdb=" N VAL G 181 " --> pdb=" O HIS G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.337A pdb=" N ARG G 216 " --> pdb=" O THR G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 265 through 271 Processing helix chain 'G' and resid 272 through 277 removed outlier: 3.556A pdb=" N LEU G 277 " --> pdb=" O TYR G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 310 removed outlier: 3.633A pdb=" N ALA G 300 " --> pdb=" O ASN G 296 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN G 310 " --> pdb=" O ASP G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 335 Processing helix chain 'G' and resid 344 through 360 Processing helix chain 'G' and resid 369 through 374 Processing helix chain 'G' and resid 383 through 388 Processing helix chain 'G' and resid 388 through 400 Processing helix chain 'G' and resid 400 through 410 removed outlier: 3.950A pdb=" N ARG G 404 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 425 Processing helix chain 'G' and resid 452 through 468 Processing helix chain 'G' and resid 478 through 494 removed outlier: 3.541A pdb=" N LYS G 484 " --> pdb=" O GLU G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 525 removed outlier: 3.935A pdb=" N ILE G 512 " --> pdb=" O SER G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 547 Processing helix chain 'G' and resid 550 through 561 Processing helix chain 'G' and resid 578 through 589 Processing helix chain 'G' and resid 600 through 605 removed outlier: 3.504A pdb=" N GLU G 604 " --> pdb=" O ALA G 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 618 removed outlier: 3.585A pdb=" N SER G 618 " --> pdb=" O PHE G 615 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 664 Processing helix chain 'G' and resid 670 through 682 Processing helix chain 'G' and resid 683 through 691 removed outlier: 4.738A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE G 688 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 771 Processing helix chain 'G' and resid 824 through 829 removed outlier: 3.868A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) Processing helix chain 'G' and resid 832 through 837 removed outlier: 4.174A pdb=" N ARG G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 845 through 853 Processing helix chain 'G' and resid 894 through 898 removed outlier: 3.548A pdb=" N ALA G 898 " --> pdb=" O PRO G 895 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 70 removed outlier: 3.623A pdb=" N VAL I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 126 through 129 Processing helix chain 'I' and resid 133 through 138 Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 60 removed outlier: 6.393A pdb=" N MET B 96 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N MET B 126 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL B 98 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL B 123 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE B 155 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 125 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.152A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER C 97 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY C 79 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE C 99 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU C 77 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N HIS C 101 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.631A pdb=" N VAL C 124 " --> pdb=" O ASP C 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 217 through 219 removed outlier: 3.501A pdb=" N ARG C 232 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 241 through 242 removed outlier: 3.665A pdb=" N SER C 579 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AA8, first strand: chain 'C' and resid 531 through 538 removed outlier: 3.503A pdb=" N ARG C 558 " --> pdb=" O THR C 549 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 126 through 131 Processing sheet with id=AB1, first strand: chain 'F' and resid 168 through 173 Processing sheet with id=AB2, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.574A pdb=" N PHE F 252 " --> pdb=" O GLY F 260 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA F 326 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLY F 251 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA F 328 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER F 253 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ASP F 330 " --> pdb=" O SER F 253 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET F 327 " --> pdb=" O TRP F 290 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP F 290 " --> pdb=" O MET F 327 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL F 329 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 11 through 14 removed outlier: 3.693A pdb=" N THR G 77 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 146 through 148 Processing sheet with id=AB5, first strand: chain 'G' and resid 173 through 175 Processing sheet with id=AB6, first strand: chain 'G' and resid 224 through 225 Processing sheet with id=AB7, first strand: chain 'G' and resid 224 through 225 removed outlier: 3.514A pdb=" N ARG G 250 " --> pdb=" O GLY G 242 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 292 through 294 removed outlier: 6.540A pdb=" N VAL G 592 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU G 610 " --> pdb=" O VAL G 592 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL G 594 " --> pdb=" O LEU G 610 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N TYR G 340 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY G 316 " --> pdb=" O TYR G 340 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 447 through 450 removed outlier: 3.813A pdb=" N TRP G 447 " --> pdb=" O LEU G 431 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR G 532 " --> pdb=" O PRO G 498 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE G 500 " --> pdb=" O THR G 532 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE G 534 " --> pdb=" O ILE G 500 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER G 502 " --> pdb=" O ILE G 534 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 620 through 623 Processing sheet with id=AC2, first strand: chain 'G' and resid 704 through 705 removed outlier: 6.500A pdb=" N LEU G 704 " --> pdb=" O THR G 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 870 through 871 removed outlier: 3.733A pdb=" N LYS G 906 " --> pdb=" O SER G 861 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N SER G 863 " --> pdb=" O ASP G 904 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP G 904 " --> pdb=" O SER G 863 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE G 842 " --> pdb=" O GLU G 874 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=AC5, first strand: chain 'I' and resid 75 through 81 removed outlier: 6.845A pdb=" N SER I 76 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE I 92 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN I 78 " --> pdb=" O GLU I 90 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2040 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: 4.19 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 8261 1.41 - 1.63: 11321 1.63 - 1.85: 188 1.85 - 2.07: 0 2.07 - 2.30: 92 Bond restraints: 19862 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.376 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.604 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C ASN G 218 " pdb=" N ARG G 219 " ideal model delta sigma weight residual 1.330 1.375 -0.045 1.38e-02 5.25e+03 1.05e+01 bond pdb=" S2 SF4 G1002 " pdb="FE1 SF4 G1002 " ideal model delta sigma weight residual 2.280 2.187 0.093 3.00e-02 1.11e+03 9.62e+00 ... (remaining 19857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 26201 1.49 - 2.99: 639 2.99 - 4.48: 104 4.48 - 5.97: 24 5.97 - 7.46: 5 Bond angle restraints: 26973 Sorted by residual: angle pdb=" CA ASN G 253 " pdb=" CB ASN G 253 " pdb=" CG ASN G 253 " ideal model delta sigma weight residual 112.60 116.24 -3.64 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA ASP I 84 " pdb=" CB ASP I 84 " pdb=" CG ASP I 84 " ideal model delta sigma weight residual 112.60 116.10 -3.50 1.00e+00 1.00e+00 1.22e+01 angle pdb=" N ALA G 389 " pdb=" CA ALA G 389 " pdb=" C ALA G 389 " ideal model delta sigma weight residual 111.33 115.45 -4.12 1.21e+00 6.83e-01 1.16e+01 angle pdb=" CA THR I 82 " pdb=" C THR I 82 " pdb=" O THR I 82 " ideal model delta sigma weight residual 121.89 118.00 3.89 1.17e+00 7.31e-01 1.11e+01 angle pdb=" C ALA C 196 " pdb=" N LEU C 197 " pdb=" CA LEU C 197 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 ... (remaining 26968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10149 17.85 - 35.69: 1197 35.69 - 53.54: 381 53.54 - 71.39: 93 71.39 - 89.24: 39 Dihedral angle restraints: 11859 sinusoidal: 4837 harmonic: 7022 Sorted by residual: dihedral pdb=" CA PHE G 821 " pdb=" C PHE G 821 " pdb=" N GLY G 822 " pdb=" CA GLY G 822 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ASN G 238 " pdb=" CB ASN G 238 " pdb=" CG ASN G 238 " pdb=" OD1 ASN G 238 " ideal model delta sinusoidal sigma weight residual -90.00 -163.55 73.55 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP C 273 " pdb=" CB ASP C 273 " pdb=" CG ASP C 273 " pdb=" OD1 ASP C 273 " ideal model delta sinusoidal sigma weight residual -30.00 -86.11 56.11 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 11856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.227: 2868 4.227 - 8.453: 0 8.453 - 12.680: 0 12.680 - 16.906: 0 16.906 - 21.133: 28 Chirality restraints: 2896 Sorted by residual: chirality pdb="FE4 SF4 G1001 " pdb=" S1 SF4 G1001 " pdb=" S2 SF4 G1001 " pdb=" S3 SF4 G1001 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 10.45 -21.00 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.43 -20.99 2.00e-01 2.50e+01 1.10e+04 ... (remaining 2893 not shown) Planarity restraints: 3531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP I 87 " -0.011 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C TRP I 87 " 0.041 2.00e-02 2.50e+03 pdb=" O TRP I 87 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR I 88 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 119 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO B 120 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 569 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C LEU G 569 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU G 569 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU G 570 " 0.010 2.00e-02 2.50e+03 ... (remaining 3528 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1556 2.74 - 3.28: 19146 3.28 - 3.82: 35654 3.82 - 4.36: 45586 4.36 - 4.90: 74144 Nonbonded interactions: 176086 Sorted by model distance: nonbonded pdb=" OH TYR G 255 " pdb=" O GLY G 776 " model vdw 2.197 3.040 nonbonded pdb=" O HOH G1216 " pdb=" O HOH G1219 " model vdw 2.202 3.040 nonbonded pdb=" OG SER F 68 " pdb=" O HOH F 601 " model vdw 2.230 3.040 nonbonded pdb=" O HOH G1198 " pdb=" O HOH G1225 " model vdw 2.230 3.040 nonbonded pdb=" CG ARG F 320 " pdb=" O HOH F 602 " model vdw 2.230 3.440 ... (remaining 176081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 22.750 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.016 0.721 19898 Z= 0.438 Angle : 0.893 30.374 27066 Z= 0.334 Chirality : 2.032 21.133 2896 Planarity : 0.004 0.056 3531 Dihedral : 17.905 89.237 7363 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 3.34 % Allowed : 21.91 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2435 helix: 0.79 (0.18), residues: 890 sheet: 0.22 (0.32), residues: 290 loop : -0.18 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 64 TYR 0.011 0.001 TYR G 711 PHE 0.027 0.001 PHE E 126 TRP 0.011 0.001 TRP G 653 HIS 0.004 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.23 (19862) covalent geometry : angle 0.55819 / 0.33 (26973) hydrogen bonds : bond 0.17176 / 11.14 ( 742) hydrogen bonds : angle 7.11595 / 4.98 ( 2040) metal coordination : bond 0.35506 / 20.79 ( 36) metal coordination : angle 11.91327 / 7.51 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 257 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 333 MET cc_start: 0.7609 (ptt) cc_final: 0.7261 (ptm) REVERT: F 252 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: G 298 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: G 718 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7177 (mtt-85) outliers start: 68 outliers final: 23 residues processed: 306 average time/residue: 0.7958 time to fit residues: 268.3811 Evaluate side-chains 240 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 571 ASN Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 659 SER Chi-restraints excluded: chain G residue 718 ARG Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 896 VAL Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 0.0570 chunk 98 optimal weight: 0.0370 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN C 359 HIS E 78 GLN F 90 ASN F 237 GLN F 341 ASN F 437 GLN G 54 GLN G 422 ASN G 571 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.075984 restraints weight = 19782.387| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.61 r_work: 0.2877 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.245 19898 Z= 0.524 Angle : 3.422 50.689 27066 Z= 1.973 Chirality : 0.623 6.462 2896 Planarity : 0.004 0.058 3531 Dihedral : 5.629 79.576 2756 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 3.09 % Allowed : 22.64 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2435 helix: 0.97 (0.18), residues: 896 sheet: 0.25 (0.32), residues: 282 loop : -0.10 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 90 TYR 0.011 0.001 TYR E 76 PHE 0.022 0.001 PHE C 340 TRP 0.011 0.001 TRP C 386 HIS 0.014 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01546 / 0.52 (19862) covalent geometry : angle 2.97421 / 1.97 (26973) hydrogen bonds : bond 0.04282 / 2.80 ( 742) hydrogen bonds : angle 5.69156 / 3.98 ( 2040) metal coordination : bond 0.03881 / 1.72 ( 36) metal coordination : angle 29.01593 / 18.73 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 228 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: C 237 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6356 (pp) REVERT: C 276 GLU cc_start: 0.8550 (tt0) cc_final: 0.8042 (tt0) REVERT: C 333 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6884 (ptm) REVERT: C 597 ASP cc_start: 0.8809 (t70) cc_final: 0.8597 (t0) REVERT: F 252 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: F 253 SER cc_start: 0.9020 (t) cc_final: 0.8559 (p) REVERT: G 57 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8165 (p0) REVERT: G 187 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8161 (pp20) REVERT: G 215 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8326 (tm-30) REVERT: G 298 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7890 (mp0) outliers start: 63 outliers final: 17 residues processed: 276 average time/residue: 0.7679 time to fit residues: 235.1712 Evaluate side-chains 235 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 478 GLU Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 804 ARG Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 126 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 chunk 240 optimal weight: 0.6980 chunk 238 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN C 317 ASN E 119 GLN F 409 GLN G 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.076215 restraints weight = 19884.522| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.61 r_work: 0.2882 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.243 19898 Z= 0.524 Angle : 3.418 50.626 27066 Z= 1.971 Chirality : 0.622 6.407 2896 Planarity : 0.004 0.060 3531 Dihedral : 4.565 57.006 2725 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 3.14 % Allowed : 22.30 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.17), residues: 2435 helix: 1.09 (0.18), residues: 897 sheet: 0.10 (0.31), residues: 276 loop : -0.11 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 475 TYR 0.011 0.001 TYR E 76 PHE 0.021 0.001 PHE C 340 TRP 0.010 0.001 TRP G 653 HIS 0.011 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01555 / 0.52 (19862) covalent geometry : angle 2.97041 / 1.97 (26973) hydrogen bonds : bond 0.03658 / 2.39 ( 742) hydrogen bonds : angle 5.36081 / 3.74 ( 2040) metal coordination : bond 0.02966 / 1.36 ( 36) metal coordination : angle 28.99924 / 18.70 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 229 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.5749 (tpt) REVERT: B 185 TRP cc_start: 0.3839 (OUTLIER) cc_final: 0.2653 (t60) REVERT: C 109 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7543 (mmp80) REVERT: C 154 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7472 (p0) REVERT: C 165 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8060 (mtpp) REVERT: C 237 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6549 (pp) REVERT: C 276 GLU cc_start: 0.8586 (tt0) cc_final: 0.8045 (tt0) REVERT: C 333 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6911 (ptm) REVERT: C 396 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7894 (tppp) REVERT: C 507 ARG cc_start: 0.8493 (mtt90) cc_final: 0.8284 (ttm-80) REVERT: F 55 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8415 (ttpm) REVERT: F 182 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: F 252 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: F 253 SER cc_start: 0.9035 (t) cc_final: 0.8566 (p) REVERT: G 215 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8384 (tm-30) REVERT: G 298 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: I 84 ASP cc_start: 0.8617 (p0) cc_final: 0.8274 (p0) REVERT: I 119 ASP cc_start: 0.8712 (t0) cc_final: 0.8369 (t0) outliers start: 64 outliers final: 19 residues processed: 277 average time/residue: 0.7625 time to fit residues: 235.0629 Evaluate side-chains 241 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 804 ARG Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 216 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN E 119 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075409 restraints weight = 19919.192| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.61 r_work: 0.2872 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.241 19898 Z= 0.525 Angle : 3.418 50.614 27066 Z= 1.971 Chirality : 0.623 6.399 2896 Planarity : 0.004 0.061 3531 Dihedral : 4.474 57.911 2721 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 3.59 % Allowed : 22.15 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2435 helix: 1.06 (0.18), residues: 904 sheet: 0.01 (0.31), residues: 282 loop : -0.10 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 90 TYR 0.030 0.001 TYR B 65 PHE 0.021 0.001 PHE C 340 TRP 0.009 0.001 TRP G 653 HIS 0.009 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01554 / 0.52 (19862) covalent geometry : angle 2.97116 / 1.97 (26973) hydrogen bonds : bond 0.03590 / 2.34 ( 742) hydrogen bonds : angle 5.24191 / 3.66 ( 2040) metal coordination : bond 0.02755 / 1.25 ( 36) metal coordination : angle 28.97498 / 18.68 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 223 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 109 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7499 (mmp80) REVERT: C 154 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7494 (p0) REVERT: C 165 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8062 (mtpp) REVERT: C 208 ARG cc_start: 0.7712 (tpp-160) cc_final: 0.7367 (tpp-160) REVERT: C 276 GLU cc_start: 0.8605 (tt0) cc_final: 0.8106 (tt0) REVERT: C 333 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6950 (ptm) REVERT: C 396 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7891 (tppp) REVERT: C 507 ARG cc_start: 0.8500 (mtt90) cc_final: 0.8176 (ttm-80) REVERT: F 55 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8406 (ttpm) REVERT: F 182 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: F 252 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: F 320 ARG cc_start: 0.8312 (ttm170) cc_final: 0.8032 (ttm170) REVERT: G 215 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8380 (tm-30) REVERT: G 298 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: I 84 ASP cc_start: 0.8649 (p0) cc_final: 0.8253 (p0) REVERT: I 119 ASP cc_start: 0.8801 (t0) cc_final: 0.8474 (t0) outliers start: 73 outliers final: 30 residues processed: 275 average time/residue: 0.7747 time to fit residues: 236.8345 Evaluate side-chains 253 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain G residue 478 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 804 ARG Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN E 119 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.096843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.074124 restraints weight = 19760.309| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.59 r_work: 0.2843 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.241 19898 Z= 0.532 Angle : 3.420 50.634 27066 Z= 1.973 Chirality : 0.624 6.411 2896 Planarity : 0.004 0.060 3531 Dihedral : 4.592 59.406 2721 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 3.44 % Allowed : 22.64 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2435 helix: 1.02 (0.18), residues: 910 sheet: -0.05 (0.30), residues: 296 loop : -0.11 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 90 TYR 0.039 0.001 TYR B 65 PHE 0.021 0.001 PHE E 126 TRP 0.010 0.001 TRP B 185 HIS 0.008 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01563 / 0.53 (19862) covalent geometry : angle 2.97440 / 1.97 (26973) hydrogen bonds : bond 0.03813 / 2.48 ( 742) hydrogen bonds : angle 5.23034 / 3.65 ( 2040) metal coordination : bond 0.02937 / 1.35 ( 36) metal coordination : angle 28.95330 / 18.67 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 217 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.5719 (tpt) REVERT: B 185 TRP cc_start: 0.3972 (OUTLIER) cc_final: 0.3339 (t-100) REVERT: C 109 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7499 (mmp80) REVERT: C 154 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7438 (p0) REVERT: C 165 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8079 (mtpp) REVERT: C 276 GLU cc_start: 0.8663 (tt0) cc_final: 0.8151 (tt0) REVERT: C 333 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6892 (ptm) REVERT: C 344 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7666 (tm130) REVERT: C 396 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7935 (tppp) REVERT: C 475 ARG cc_start: 0.8705 (ttm-80) cc_final: 0.8467 (ttm-80) REVERT: F 55 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8401 (ttpm) REVERT: F 182 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: F 252 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: G 215 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8482 (tm-30) REVERT: G 298 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: I 84 ASP cc_start: 0.8643 (p0) cc_final: 0.8267 (p0) REVERT: I 119 ASP cc_start: 0.8838 (t0) cc_final: 0.8516 (t0) outliers start: 70 outliers final: 28 residues processed: 270 average time/residue: 0.7714 time to fit residues: 230.7576 Evaluate side-chains 252 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 804 ARG Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 158 optimal weight: 1.9990 chunk 237 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN E 119 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN G 808 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.076401 restraints weight = 20827.805| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.67 r_work: 0.2872 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.241 19898 Z= 0.525 Angle : 3.419 50.630 27066 Z= 1.972 Chirality : 0.623 6.400 2896 Planarity : 0.004 0.065 3531 Dihedral : 4.557 58.275 2721 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 3.54 % Allowed : 22.84 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2435 helix: 1.07 (0.18), residues: 909 sheet: 0.11 (0.31), residues: 281 loop : -0.14 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 90 TYR 0.013 0.001 TYR B 193 PHE 0.023 0.001 PHE E 126 TRP 0.010 0.001 TRP G 653 HIS 0.007 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01554 / 0.52 (19862) covalent geometry : angle 2.97224 / 1.97 (26973) hydrogen bonds : bond 0.03554 / 2.31 ( 742) hydrogen bonds : angle 5.16532 / 3.60 ( 2040) metal coordination : bond 0.02654 / 1.22 ( 36) metal coordination : angle 28.97764 / 18.68 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 216 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.5708 (tpt) REVERT: B 119 GLU cc_start: 0.4989 (OUTLIER) cc_final: 0.4574 (tp30) REVERT: B 185 TRP cc_start: 0.3896 (OUTLIER) cc_final: 0.3305 (t-100) REVERT: C 154 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7535 (p0) REVERT: C 165 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8093 (mtpp) REVERT: C 276 GLU cc_start: 0.8687 (tt0) cc_final: 0.8185 (tt0) REVERT: C 333 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6907 (ptm) REVERT: C 396 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7919 (tppp) REVERT: C 475 ARG cc_start: 0.8736 (ttm-80) cc_final: 0.8491 (ttm-80) REVERT: F 55 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8376 (ttpm) REVERT: F 182 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: F 252 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: G 215 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8486 (tm-30) REVERT: G 298 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: G 336 GLU cc_start: 0.7825 (pm20) cc_final: 0.7567 (mp0) REVERT: G 804 ARG cc_start: 0.8783 (ptm160) cc_final: 0.8387 (ptm160) REVERT: I 84 ASP cc_start: 0.8636 (p0) cc_final: 0.8269 (p0) REVERT: I 119 ASP cc_start: 0.8872 (t0) cc_final: 0.8507 (t0) outliers start: 72 outliers final: 33 residues processed: 269 average time/residue: 0.7608 time to fit residues: 228.2643 Evaluate side-chains 253 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain G residue 478 GLU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 185 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN E 119 GLN F 237 GLN G 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.075957 restraints weight = 21008.080| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.68 r_work: 0.2861 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.241 19898 Z= 0.528 Angle : 3.420 50.633 27066 Z= 1.973 Chirality : 0.623 6.406 2896 Planarity : 0.004 0.063 3531 Dihedral : 4.590 58.934 2721 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.26 % Rotamer: Outliers : 3.09 % Allowed : 23.28 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.17), residues: 2435 helix: 1.08 (0.18), residues: 909 sheet: 0.12 (0.31), residues: 281 loop : -0.14 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 90 TYR 0.035 0.001 TYR B 65 PHE 0.023 0.001 PHE E 126 TRP 0.009 0.001 TRP G 653 HIS 0.007 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01559 / 0.53 (19862) covalent geometry : angle 2.97385 / 1.97 (26973) hydrogen bonds : bond 0.03617 / 2.35 ( 742) hydrogen bonds : angle 5.15593 / 3.60 ( 2040) metal coordination : bond 0.02771 / 1.28 ( 36) metal coordination : angle 28.96167 / 18.66 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 211 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.5702 (tpt) REVERT: B 185 TRP cc_start: 0.3985 (OUTLIER) cc_final: 0.3369 (t-100) REVERT: B 199 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8327 (p) REVERT: C 109 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7489 (mmp80) REVERT: C 154 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7517 (p0) REVERT: C 165 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8099 (mtpp) REVERT: C 276 GLU cc_start: 0.8710 (tt0) cc_final: 0.8208 (tt0) REVERT: C 333 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6932 (ptm) REVERT: C 356 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.9030 (t80) REVERT: C 396 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7928 (tppp) REVERT: F 55 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8389 (ttpm) REVERT: F 182 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: F 252 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: F 302 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8407 (tp30) REVERT: G 215 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8493 (tm-30) REVERT: G 298 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: G 336 GLU cc_start: 0.7832 (pm20) cc_final: 0.7222 (mp0) REVERT: G 469 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8539 (m-40) REVERT: G 804 ARG cc_start: 0.8789 (ptm160) cc_final: 0.8420 (ptm160) REVERT: G 808 GLN cc_start: 0.8000 (pt0) cc_final: 0.7540 (pt0) REVERT: G 851 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8077 (tptp) REVERT: I 84 ASP cc_start: 0.8638 (p0) cc_final: 0.8274 (p0) REVERT: I 119 ASP cc_start: 0.8880 (t0) cc_final: 0.8520 (t0) outliers start: 63 outliers final: 33 residues processed: 254 average time/residue: 0.7182 time to fit residues: 203.9025 Evaluate side-chains 258 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain G residue 469 ASN Chi-restraints excluded: chain G residue 478 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 53 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 91 optimal weight: 0.0060 chunk 119 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN E 119 GLN F 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.074073 restraints weight = 20763.828| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.66 r_work: 0.2845 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.240 19898 Z= 0.548 Angle : 3.425 50.667 27066 Z= 1.976 Chirality : 0.625 6.453 2896 Planarity : 0.005 0.062 3531 Dihedral : 4.674 58.322 2720 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.18 % Rotamer: Outliers : 3.09 % Allowed : 23.58 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2435 helix: 0.95 (0.17), residues: 910 sheet: -0.02 (0.30), residues: 293 loop : -0.15 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 62 TYR 0.041 0.002 TYR B 65 PHE 0.024 0.002 PHE E 126 TRP 0.008 0.001 TRP G 653 HIS 0.007 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01589 / 0.55 (19862) covalent geometry : angle 2.98138 / 1.97 (26973) hydrogen bonds : bond 0.04113 / 2.67 ( 742) hydrogen bonds : angle 5.26286 / 3.67 ( 2040) metal coordination : bond 0.03305 / 1.54 ( 36) metal coordination : angle 28.92675 / 18.63 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.5747 (tpt) REVERT: B 119 GLU cc_start: 0.5197 (OUTLIER) cc_final: 0.4602 (tp30) REVERT: B 185 TRP cc_start: 0.3901 (OUTLIER) cc_final: 0.3329 (t-100) REVERT: B 219 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8456 (mm-30) REVERT: C 109 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7461 (mmp80) REVERT: C 154 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7479 (p0) REVERT: C 165 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8095 (mtpp) REVERT: C 276 GLU cc_start: 0.8750 (tt0) cc_final: 0.8222 (tt0) REVERT: C 333 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6956 (ptm) REVERT: C 396 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7981 (tppp) REVERT: C 475 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.8495 (ttm-80) REVERT: F 55 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8342 (ttpm) REVERT: F 182 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: F 252 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: G 62 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7645 (ptm-80) REVERT: G 215 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8481 (tm-30) REVERT: G 298 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: G 469 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8544 (m-40) REVERT: G 480 GLU cc_start: 0.8308 (pm20) cc_final: 0.7939 (pm20) REVERT: G 808 GLN cc_start: 0.8170 (pt0) cc_final: 0.7666 (pt0) REVERT: G 874 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: I 84 ASP cc_start: 0.8632 (p0) cc_final: 0.8279 (p0) REVERT: I 119 ASP cc_start: 0.8868 (t0) cc_final: 0.8570 (t0) outliers start: 63 outliers final: 31 residues processed: 255 average time/residue: 0.7428 time to fit residues: 210.5511 Evaluate side-chains 250 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain G residue 469 ASN Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 804 ARG Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 46 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN E 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.074974 restraints weight = 20883.846| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.67 r_work: 0.2864 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.241 19898 Z= 0.531 Angle : 3.423 50.634 27066 Z= 1.974 Chirality : 0.624 6.430 2896 Planarity : 0.004 0.062 3531 Dihedral : 4.627 59.741 2720 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.78 % Favored : 96.14 % Rotamer: Outliers : 2.85 % Allowed : 23.67 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2435 helix: 1.00 (0.18), residues: 907 sheet: 0.10 (0.30), residues: 281 loop : -0.18 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 62 TYR 0.045 0.001 TYR B 65 PHE 0.025 0.001 PHE E 126 TRP 0.010 0.001 TRP G 653 HIS 0.006 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01562 / 0.53 (19862) covalent geometry : angle 2.97712 / 1.97 (26973) hydrogen bonds : bond 0.03797 / 2.47 ( 742) hydrogen bonds : angle 5.21683 / 3.63 ( 2040) metal coordination : bond 0.02944 / 1.36 ( 36) metal coordination : angle 28.95632 / 18.65 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.5713 (tpt) REVERT: B 119 GLU cc_start: 0.5074 (OUTLIER) cc_final: 0.4574 (tp30) REVERT: B 185 TRP cc_start: 0.3893 (OUTLIER) cc_final: 0.3321 (t-100) REVERT: B 199 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8264 (p) REVERT: C 109 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7508 (mmp80) REVERT: C 154 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7478 (p0) REVERT: C 165 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8072 (mtpp) REVERT: C 276 GLU cc_start: 0.8735 (tt0) cc_final: 0.8202 (tt0) REVERT: C 333 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6965 (ptm) REVERT: C 356 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8994 (t80) REVERT: C 396 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7968 (tppp) REVERT: C 475 ARG cc_start: 0.8735 (ttm-80) cc_final: 0.8465 (ttm-80) REVERT: F 55 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8373 (ttpm) REVERT: F 152 GLU cc_start: 0.8863 (tp30) cc_final: 0.8621 (tp30) REVERT: F 182 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: F 252 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: G 215 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8482 (tm-30) REVERT: G 298 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: G 469 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8547 (m-40) REVERT: G 684 GLU cc_start: 0.8567 (mp0) cc_final: 0.8294 (mp0) REVERT: I 84 ASP cc_start: 0.8618 (p0) cc_final: 0.8258 (p0) REVERT: I 119 ASP cc_start: 0.8865 (t0) cc_final: 0.8499 (t0) outliers start: 58 outliers final: 30 residues processed: 252 average time/residue: 0.7202 time to fit residues: 202.8253 Evaluate side-chains 256 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain G residue 469 ASN Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 3 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 191 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 158 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN E 119 GLN F 237 GLN G 808 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.098918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.076331 restraints weight = 20973.698| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.68 r_work: 0.2873 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.243 19898 Z= 0.523 Angle : 3.421 50.627 27066 Z= 1.973 Chirality : 0.622 6.424 2896 Planarity : 0.004 0.064 3531 Dihedral : 4.526 57.953 2720 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 2.55 % Allowed : 24.17 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2435 helix: 1.08 (0.18), residues: 908 sheet: 0.14 (0.30), residues: 281 loop : -0.15 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 62 TYR 0.045 0.001 TYR B 65 PHE 0.024 0.001 PHE E 126 TRP 0.011 0.001 TRP G 653 HIS 0.006 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01553 / 0.52 (19862) covalent geometry : angle 2.97384 / 1.97 (26973) hydrogen bonds : bond 0.03480 / 2.26 ( 742) hydrogen bonds : angle 5.14556 / 3.58 ( 2040) metal coordination : bond 0.02582 / 1.19 ( 36) metal coordination : angle 29.00486 / 18.68 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.5709 (tpt) REVERT: B 119 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.4547 (tp30) REVERT: B 185 TRP cc_start: 0.3928 (OUTLIER) cc_final: 0.3326 (t-100) REVERT: B 199 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 219 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8405 (mm-30) REVERT: C 109 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7515 (mmp80) REVERT: C 154 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7511 (p0) REVERT: C 165 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8101 (mtpp) REVERT: C 333 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7026 (ptm) REVERT: C 356 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.9026 (t80) REVERT: C 396 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7924 (tppp) REVERT: F 55 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8384 (ttpm) REVERT: F 182 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: F 252 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: F 302 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8396 (tp30) REVERT: G 215 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8566 (tm-30) REVERT: G 298 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: G 469 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8543 (m-40) REVERT: I 84 ASP cc_start: 0.8607 (p0) cc_final: 0.8235 (p0) REVERT: I 119 ASP cc_start: 0.8893 (t0) cc_final: 0.8513 (t0) outliers start: 52 outliers final: 30 residues processed: 249 average time/residue: 0.7494 time to fit residues: 208.0981 Evaluate side-chains 256 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain G residue 469 ASN Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 204 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN F 237 GLN G 808 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.074513 restraints weight = 20947.407| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.67 r_work: 0.2855 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.240 19898 Z= 0.539 Angle : 3.425 50.645 27066 Z= 1.975 Chirality : 0.625 6.449 2896 Planarity : 0.005 0.065 3531 Dihedral : 4.652 59.707 2720 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.18 % Rotamer: Outliers : 2.65 % Allowed : 24.26 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2435 helix: 0.99 (0.17), residues: 907 sheet: 0.13 (0.30), residues: 281 loop : -0.18 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 62 TYR 0.015 0.001 TYR F 178 PHE 0.025 0.001 PHE E 126 TRP 0.010 0.001 TRP G 653 HIS 0.007 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01575 / 0.54 (19862) covalent geometry : angle 2.98030 / 1.97 (26973) hydrogen bonds : bond 0.03904 / 2.53 ( 742) hydrogen bonds : angle 5.21217 / 3.63 ( 2040) metal coordination : bond 0.03108 / 1.43 ( 36) metal coordination : angle 28.93457 / 18.63 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8043.55 seconds wall clock time: 137 minutes 55.35 seconds (8275.35 seconds total)