Starting phenix.real_space_refine on Sat Mar 16 10:34:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/03_2024/8g3f_29694_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/03_2024/8g3f_29694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/03_2024/8g3f_29694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/03_2024/8g3f_29694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/03_2024/8g3f_29694_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3f_29694/03_2024/8g3f_29694_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 62 5.16 5 C 9385 2.51 5 N 2374 2.21 5 O 2619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14442 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'6OU': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.88, per 1000 atoms: 0.55 Number of scatterers: 14442 At special positions: 0 Unit cell: (95.048, 113.36, 198.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 2 15.00 O 2619 8.00 N 2374 7.00 C 9385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.50 Conformation dependent library (CDL) restraints added in 2.6 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 11 sheets defined 54.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 20 through 39 Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.836A pdb=" N ASN A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 93 removed outlier: 3.621A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.957A pdb=" N PHE A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.560A pdb=" N LYS A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 3.815A pdb=" N GLN A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 221 removed outlier: 4.371A pdb=" N GLY A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.812A pdb=" N ALA A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.614A pdb=" N SER A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 293 through 324 removed outlier: 3.653A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 removed outlier: 3.902A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.720A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.601A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 516 through 555 removed outlier: 4.418A pdb=" N GLN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 567 removed outlier: 3.544A pdb=" N LYS A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 603 removed outlier: 3.774A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 3.514A pdb=" N GLN A 602 " --> pdb=" O TYR A 598 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 607 No H-bonds generated for 'chain 'A' and resid 605 through 607' Processing helix chain 'A' and resid 615 through 632 removed outlier: 4.625A pdb=" N PHE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 removed outlier: 3.804A pdb=" N LYS A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 102 through 105 No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 118 through 131 removed outlier: 3.745A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.779A pdb=" N GLN B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 192 Processing helix chain 'B' and resid 204 through 209 removed outlier: 4.091A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.526A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 131 Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.928A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'D' and resid 2 through 28 removed outlier: 6.072A pdb=" N SER D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TRP D 12 " --> pdb=" O GLU D 8 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 14 " --> pdb=" O ARG D 10 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 60 Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.612A pdb=" N GLU D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 138 removed outlier: 4.381A pdb=" N VAL D 90 " --> pdb=" O PHE D 86 " (cutoff:3.500A) Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 143 through 170 removed outlier: 3.950A pdb=" N SER D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'D' and resid 218 through 234 Processing helix chain 'D' and resid 265 through 270 Proline residue: D 269 - end of helix Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 291 through 299 Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.708A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 12 through 29 Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 39 through 60 removed outlier: 4.090A pdb=" N ARG E 58 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS E 59 " --> pdb=" O PHE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 70 removed outlier: 4.075A pdb=" N LYS E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 137 removed outlier: 3.937A pdb=" N MET E 89 " --> pdb=" O PRO E 85 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 144 through 169 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 193 Processing helix chain 'E' and resid 195 through 201 Processing helix chain 'E' and resid 219 through 234 Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 282 through 286 removed outlier: 3.748A pdb=" N ALA E 286 " --> pdb=" O HIS E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 299 Processing helix chain 'E' and resid 325 through 332 removed outlier: 3.914A pdb=" N HIS E 330 " --> pdb=" O GLN E 327 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 3.893A pdb=" N ALA A 457 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 404 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 4 through 7 Processing sheet with id= C, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= D, first strand: chain 'B' and resid 212 through 215 removed outlier: 6.754A pdb=" N ILE B 197 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE B 38 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET B 199 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 200 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.024A pdb=" N GLU C 5 " --> pdb=" O HIS C 65 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS C 65 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 37 through 39 Processing sheet with id= G, first strand: chain 'C' and resid 164 through 167 removed outlier: 6.596A pdb=" N THR C 196 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ALA C 167 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE C 198 " --> pdb=" O ALA C 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 179 through 182 Processing sheet with id= I, first strand: chain 'D' and resid 205 through 209 removed outlier: 5.656A pdb=" N ILE D 241 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN D 208 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE D 243 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 179 through 181 removed outlier: 3.725A pdb=" N GLU E 179 " --> pdb=" O SER E 216 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 216 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 205 through 209 removed outlier: 7.294A pdb=" N ILE E 241 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLN E 208 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE E 243 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 320 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS E 305 " --> pdb=" O THR E 321 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 2019 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: 4.01 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2343 1.32 - 1.44: 3765 1.44 - 1.57: 8465 1.57 - 1.69: 22 1.69 - 1.82: 114 Bond restraints: 14709 Sorted by residual: bond pdb=" C10 OLA E 401 " pdb=" C9 OLA E 401 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C16 6OU A 702 " pdb=" O18 6OU A 702 " ideal model delta sigma weight residual 1.327 1.464 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.462 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C31 6OU A 703 " pdb=" O30 6OU A 703 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C14 6OU A 702 " pdb=" C15 6OU A 702 " ideal model delta sigma weight residual 1.521 1.609 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 14704 not shown) Histogram of bond angle deviations from ideal: 98.04 - 108.91: 626 108.91 - 119.78: 12207 119.78 - 130.64: 6887 130.64 - 141.51: 56 141.51 - 152.37: 2 Bond angle restraints: 19778 Sorted by residual: angle pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " pdb=" C42 6OU A 703 " ideal model delta sigma weight residual 127.56 152.37 -24.81 3.00e+00 1.11e-01 6.84e+01 angle pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " pdb=" C42 6OU A 702 " ideal model delta sigma weight residual 127.56 152.10 -24.54 3.00e+00 1.11e-01 6.69e+01 angle pdb=" O22 6OU A 702 " pdb=" P23 6OU A 702 " pdb=" O26 6OU A 702 " ideal model delta sigma weight residual 93.95 110.79 -16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C39 6OU A 702 " pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " ideal model delta sigma weight residual 127.60 111.61 15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O22 6OU A 703 " pdb=" P23 6OU A 703 " pdb=" O26 6OU A 703 " ideal model delta sigma weight residual 93.95 109.65 -15.70 3.00e+00 1.11e-01 2.74e+01 ... (remaining 19773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 8665 35.61 - 71.21: 215 71.21 - 106.82: 16 106.82 - 142.42: 1 142.42 - 178.03: 4 Dihedral angle restraints: 8901 sinusoidal: 3689 harmonic: 5212 Sorted by residual: dihedral pdb=" CA ILE A 282 " pdb=" C ILE A 282 " pdb=" N MET A 283 " pdb=" CA MET A 283 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ARG D 139 " pdb=" C ARG D 139 " pdb=" N MET D 140 " pdb=" CA MET D 140 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" C21 6OU A 703 " pdb=" O22 6OU A 703 " ideal model delta sinusoidal sigma weight residual -59.00 119.03 -178.03 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1731 0.048 - 0.097: 402 0.097 - 0.145: 97 0.145 - 0.193: 13 0.193 - 0.241: 3 Chirality restraints: 2246 Sorted by residual: chirality pdb=" C20 6OU A 702 " pdb=" C19 6OU A 702 " pdb=" C21 6OU A 702 " pdb=" O30 6OU A 702 " both_signs ideal model delta sigma weight residual False 2.35 2.59 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA PHE A 174 " pdb=" N PHE A 174 " pdb=" C PHE A 174 " pdb=" CB PHE A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE E 156 " pdb=" N ILE E 156 " pdb=" C ILE E 156 " pdb=" CB ILE E 156 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2243 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " -0.197 2.00e-02 2.50e+03 1.52e-01 2.32e+02 pdb=" C11 OLA E 401 " 0.088 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " -0.088 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 173 " 0.021 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C THR A 173 " -0.068 2.00e-02 2.50e+03 pdb=" O THR A 173 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE A 174 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 30 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO E 31 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 31 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 31 " 0.030 5.00e-02 4.00e+02 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 268 2.70 - 3.25: 14190 3.25 - 3.80: 22027 3.80 - 4.35: 27093 4.35 - 4.90: 44906 Nonbonded interactions: 108484 Sorted by model distance: nonbonded pdb=" OD1 ASP C 168 " pdb=" N GLU C 169 " model vdw 2.148 2.520 nonbonded pdb=" O PHE A 251 " pdb=" OG SER A 255 " model vdw 2.227 2.440 nonbonded pdb=" OG SER A 421 " pdb=" O TYR A 437 " model vdw 2.241 2.440 nonbonded pdb=" ND2 ASN C 7 " pdb=" OD1 ASP C 27 " model vdw 2.250 2.520 nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.259 2.440 ... (remaining 108479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 334) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.030 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 39.230 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 14709 Z= 0.309 Angle : 0.791 24.814 19778 Z= 0.404 Chirality : 0.044 0.241 2246 Planarity : 0.005 0.152 2468 Dihedral : 16.236 178.030 5527 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.90 % Allowed : 0.83 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1779 helix: 1.42 (0.17), residues: 998 sheet: -0.51 (0.43), residues: 159 loop : -1.81 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 153 HIS 0.008 0.001 HIS C 86 PHE 0.019 0.001 PHE A 124 TYR 0.022 0.001 TYR C 222 ARG 0.007 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 231 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 THR cc_start: 0.7393 (m) cc_final: 0.7084 (p) REVERT: C 215 PHE cc_start: 0.7535 (m-80) cc_final: 0.7254 (m-80) REVERT: D 157 HIS cc_start: 0.5035 (t-90) cc_final: 0.4750 (t-90) REVERT: E 18 PHE cc_start: 0.6522 (m-80) cc_final: 0.6121 (t80) REVERT: E 23 MET cc_start: 0.7482 (tpp) cc_final: 0.7075 (tpp) REVERT: E 110 LEU cc_start: 0.8446 (tp) cc_final: 0.8176 (tt) REVERT: E 158 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7265 (tt) outliers start: 14 outliers final: 2 residues processed: 237 average time/residue: 0.2625 time to fit residues: 90.6996 Evaluate side-chains 187 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 0.0770 chunk 160 optimal weight: 8.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 GLN E 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14709 Z= 0.179 Angle : 0.585 10.365 19778 Z= 0.296 Chirality : 0.041 0.168 2246 Planarity : 0.004 0.067 2468 Dihedral : 11.619 166.212 2023 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.66 % Allowed : 9.15 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1779 helix: 1.64 (0.17), residues: 982 sheet: -0.69 (0.42), residues: 170 loop : -1.64 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 220 HIS 0.012 0.001 HIS C 160 PHE 0.014 0.001 PHE A 529 TYR 0.026 0.002 TYR E 151 ARG 0.012 0.001 ARG E 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 201 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7601 (mmmt) cc_final: 0.7388 (mmtp) REVERT: E 18 PHE cc_start: 0.6513 (m-80) cc_final: 0.6181 (t80) REVERT: E 157 HIS cc_start: 0.5000 (t70) cc_final: 0.4573 (t70) outliers start: 26 outliers final: 17 residues processed: 215 average time/residue: 0.2706 time to fit residues: 84.1208 Evaluate side-chains 192 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 227 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 0.0020 chunk 173 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14709 Z= 0.365 Angle : 0.694 11.434 19778 Z= 0.354 Chirality : 0.045 0.186 2246 Planarity : 0.004 0.052 2468 Dihedral : 11.484 157.269 2019 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.69 % Allowed : 13.76 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1779 helix: 1.12 (0.17), residues: 983 sheet: -0.62 (0.42), residues: 165 loop : -1.72 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 197 HIS 0.011 0.001 HIS E 157 PHE 0.026 0.002 PHE A 529 TYR 0.026 0.002 TYR A 561 ARG 0.009 0.001 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 188 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ILE cc_start: 0.8044 (pt) cc_final: 0.7841 (pt) REVERT: E 18 PHE cc_start: 0.6655 (m-80) cc_final: 0.6245 (t80) outliers start: 42 outliers final: 28 residues processed: 217 average time/residue: 0.2536 time to fit residues: 81.2655 Evaluate side-chains 193 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 76 optimal weight: 0.2980 chunk 108 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14709 Z= 0.384 Angle : 0.716 13.178 19778 Z= 0.362 Chirality : 0.045 0.178 2246 Planarity : 0.004 0.058 2468 Dihedral : 11.357 153.557 2019 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.07 % Allowed : 17.40 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1779 helix: 0.90 (0.17), residues: 986 sheet: -0.80 (0.41), residues: 166 loop : -1.81 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 220 HIS 0.009 0.001 HIS C 160 PHE 0.023 0.002 PHE A 529 TYR 0.022 0.002 TYR E 151 ARG 0.006 0.001 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 180 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 ASP cc_start: 0.7752 (t0) cc_final: 0.7483 (t0) REVERT: B 106 ILE cc_start: 0.8076 (pt) cc_final: 0.7850 (pt) REVERT: E 18 PHE cc_start: 0.6672 (m-80) cc_final: 0.6272 (t80) REVERT: E 140 MET cc_start: 0.3804 (ppp) cc_final: 0.3281 (ppp) outliers start: 48 outliers final: 37 residues processed: 210 average time/residue: 0.2668 time to fit residues: 83.6287 Evaluate side-chains 207 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 118 optimal weight: 0.0010 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 153 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14709 Z= 0.175 Angle : 0.609 10.841 19778 Z= 0.301 Chirality : 0.041 0.195 2246 Planarity : 0.003 0.060 2468 Dihedral : 10.729 153.095 2018 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.37 % Allowed : 20.22 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1779 helix: 1.42 (0.17), residues: 985 sheet: -0.56 (0.42), residues: 162 loop : -1.74 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 220 HIS 0.008 0.001 HIS C 160 PHE 0.013 0.001 PHE A 529 TYR 0.038 0.001 TYR D 151 ARG 0.011 0.001 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7284 (mp) REVERT: A 556 ASP cc_start: 0.7753 (t0) cc_final: 0.7465 (t0) REVERT: E 18 PHE cc_start: 0.6590 (m-80) cc_final: 0.6219 (t80) outliers start: 37 outliers final: 29 residues processed: 200 average time/residue: 0.2664 time to fit residues: 78.3531 Evaluate side-chains 194 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 153 TRP Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 142 optimal weight: 0.0970 chunk 79 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS D 157 HIS ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14709 Z= 0.178 Angle : 0.608 12.606 19778 Z= 0.299 Chirality : 0.041 0.201 2246 Planarity : 0.003 0.062 2468 Dihedral : 10.378 146.176 2018 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.94 % Allowed : 20.79 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1779 helix: 1.56 (0.18), residues: 973 sheet: -0.50 (0.41), residues: 171 loop : -1.67 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D 197 HIS 0.009 0.001 HIS C 160 PHE 0.016 0.001 PHE A 529 TYR 0.028 0.001 TYR D 151 ARG 0.008 0.001 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 319 LYS cc_start: 0.7836 (mmmt) cc_final: 0.7589 (mmtp) REVERT: A 534 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7245 (mp) REVERT: A 556 ASP cc_start: 0.7747 (t0) cc_final: 0.7477 (t0) REVERT: C 74 MET cc_start: -0.1110 (tmm) cc_final: -0.1419 (tmm) REVERT: E 18 PHE cc_start: 0.6584 (m-80) cc_final: 0.6198 (t80) outliers start: 46 outliers final: 30 residues processed: 202 average time/residue: 0.2525 time to fit residues: 75.3760 Evaluate side-chains 195 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 153 TRP Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 20.0000 chunk 19 optimal weight: 0.5980 chunk 97 optimal weight: 0.0970 chunk 125 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14709 Z= 0.157 Angle : 0.618 12.749 19778 Z= 0.302 Chirality : 0.042 0.274 2246 Planarity : 0.003 0.064 2468 Dihedral : 10.023 137.632 2018 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.24 % Allowed : 21.69 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1779 helix: 1.67 (0.18), residues: 977 sheet: -0.41 (0.41), residues: 171 loop : -1.60 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 197 HIS 0.016 0.001 HIS C 160 PHE 0.018 0.001 PHE E 223 TYR 0.025 0.001 TYR D 151 ARG 0.009 0.000 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6408 (ppp) cc_final: 0.5816 (ppp) REVERT: A 200 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6918 (t80) REVERT: A 319 LYS cc_start: 0.7678 (mmmt) cc_final: 0.7410 (mmtp) REVERT: A 534 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7250 (mp) REVERT: A 556 ASP cc_start: 0.7726 (t0) cc_final: 0.7449 (t0) REVERT: C 50 LEU cc_start: 0.3836 (OUTLIER) cc_final: 0.3470 (mm) REVERT: E 18 PHE cc_start: 0.6582 (m-80) cc_final: 0.6230 (t80) outliers start: 35 outliers final: 27 residues processed: 199 average time/residue: 0.2684 time to fit residues: 78.4550 Evaluate side-chains 196 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 153 TRP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 134 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS E 157 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14709 Z= 0.217 Angle : 0.653 12.394 19778 Z= 0.318 Chirality : 0.042 0.269 2246 Planarity : 0.003 0.067 2468 Dihedral : 10.031 135.229 2018 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.13 % Allowed : 20.60 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1779 helix: 1.54 (0.18), residues: 973 sheet: -0.41 (0.42), residues: 168 loop : -1.62 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 197 HIS 0.008 0.001 HIS C 160 PHE 0.020 0.001 PHE A 529 TYR 0.027 0.001 TYR D 151 ARG 0.010 0.001 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 168 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6433 (ppp) cc_final: 0.5950 (ppp) REVERT: A 200 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6917 (t80) REVERT: A 319 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7449 (mmtp) REVERT: A 534 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7277 (mp) REVERT: A 556 ASP cc_start: 0.7745 (t0) cc_final: 0.7464 (t0) REVERT: E 18 PHE cc_start: 0.6634 (m-80) cc_final: 0.6255 (t80) outliers start: 49 outliers final: 39 residues processed: 197 average time/residue: 0.2642 time to fit residues: 77.1679 Evaluate side-chains 206 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 153 TRP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 168 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14709 Z= 0.243 Angle : 0.669 12.423 19778 Z= 0.327 Chirality : 0.043 0.262 2246 Planarity : 0.003 0.070 2468 Dihedral : 10.063 134.169 2018 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.88 % Allowed : 20.99 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1779 helix: 1.48 (0.17), residues: 972 sheet: -0.43 (0.42), residues: 168 loop : -1.61 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 197 HIS 0.011 0.001 HIS C 160 PHE 0.019 0.001 PHE A 529 TYR 0.026 0.001 TYR D 151 ARG 0.009 0.001 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6512 (ppp) cc_final: 0.6071 (ppp) REVERT: A 200 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6933 (t80) REVERT: A 319 LYS cc_start: 0.7758 (mmmt) cc_final: 0.7498 (mmtp) REVERT: A 534 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7329 (mp) REVERT: A 556 ASP cc_start: 0.7772 (t0) cc_final: 0.7512 (t0) REVERT: E 18 PHE cc_start: 0.6624 (m-80) cc_final: 0.6213 (t80) outliers start: 45 outliers final: 42 residues processed: 193 average time/residue: 0.2552 time to fit residues: 73.2768 Evaluate side-chains 203 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 159 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 153 TRP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14709 Z= 0.202 Angle : 0.678 13.261 19778 Z= 0.328 Chirality : 0.042 0.254 2246 Planarity : 0.003 0.071 2468 Dihedral : 9.913 132.627 2018 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.82 % Allowed : 21.43 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1779 helix: 1.57 (0.18), residues: 968 sheet: -0.51 (0.43), residues: 159 loop : -1.59 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 197 HIS 0.007 0.001 HIS C 160 PHE 0.016 0.001 PHE A 529 TYR 0.027 0.001 TYR D 151 ARG 0.010 0.001 ARG D 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6406 (ppp) cc_final: 0.6053 (ppp) REVERT: A 147 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.6996 (p-80) REVERT: A 200 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6927 (t80) REVERT: A 319 LYS cc_start: 0.7699 (mmmt) cc_final: 0.7444 (mmtp) REVERT: A 534 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7313 (mp) REVERT: A 556 ASP cc_start: 0.7768 (t0) cc_final: 0.7512 (t0) REVERT: E 18 PHE cc_start: 0.6596 (m-80) cc_final: 0.6217 (t80) REVERT: E 140 MET cc_start: 0.2725 (ppp) cc_final: 0.1746 (pmm) outliers start: 44 outliers final: 39 residues processed: 195 average time/residue: 0.2592 time to fit residues: 74.9440 Evaluate side-chains 206 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 144 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.203784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.161329 restraints weight = 23279.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.157955 restraints weight = 36073.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.152546 restraints weight = 28453.853| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14709 Z= 0.188 Angle : 0.674 13.257 19778 Z= 0.323 Chirality : 0.042 0.253 2246 Planarity : 0.003 0.070 2468 Dihedral : 9.731 131.645 2018 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.75 % Allowed : 21.31 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1779 helix: 1.63 (0.18), residues: 965 sheet: -0.43 (0.43), residues: 159 loop : -1.53 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 122 HIS 0.009 0.001 HIS C 160 PHE 0.017 0.001 PHE B 35 TYR 0.022 0.001 TYR D 151 ARG 0.010 0.001 ARG D 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2767.78 seconds wall clock time: 51 minutes 4.97 seconds (3064.97 seconds total)