Starting phenix.real_space_refine on Fri Jul 3 03:50:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d8x_30614/07_2026/7d8x_30614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d8x_30614/07_2026/7d8x_30614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d8x_30614/07_2026/7d8x_30614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d8x_30614/07_2026/7d8x_30614.map" model { file = "/net/cci-nas-00/data/ceres_data/7d8x_30614/07_2026/7d8x_30614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d8x_30614/07_2026/7d8x_30614.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7d8x_30614/07_2026/7d8x_30614.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d8x_30614/07_2026/7d8x_30614.cif" } resolution = 2.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 40 5.16 5 C 7182 2.51 5 N 1713 2.21 5 O 1989 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10928 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2436 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'FTO': 1, 'GZR': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 2.16, per 1000 atoms: 0.20 Number of scatterers: 10928 At special positions: 0 Unit cell: (109.332, 95.26, 133.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 3 15.00 F 1 9.00 O 1989 8.00 N 1713 7.00 C 7182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 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 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 367.7 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2470 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 58.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 80 through 87 removed outlier: 4.336A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.524A pdb=" N MET A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.986A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 4.039A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.503A pdb=" N TYR A 173 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 174' Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.780A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.589A pdb=" N THR A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.913A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.597A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.688A pdb=" N VAL A 511 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.622A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.621A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.561A pdb=" N ASP A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.794A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 632 through 637' Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.639A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.506A pdb=" N PHE A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 156 removed outlier: 4.537A pdb=" N ILE B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 175 removed outlier: 3.594A pdb=" N ILE B 162 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.683A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.659A pdb=" N THR B 274 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 404 through 429 Processing helix chain 'B' and resid 434 through 452 removed outlier: 4.514A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.052A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 14 through 25 removed outlier: 3.552A pdb=" N ALA C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 60 removed outlier: 3.721A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 100 removed outlier: 3.734A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 3.533A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.557A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.819A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.506A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 21 Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.671A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 82 removed outlier: 3.597A pdb=" N TRP D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.595A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR A 94 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA A 122 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 96 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N SER A 124 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 98 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 9.072A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.612A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.567A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 560 hydrogen bonds defined for protein. 1623 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: 1.99 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1639 1.31 - 1.43: 3168 1.43 - 1.56: 6327 1.56 - 1.69: 15 1.69 - 1.81: 61 Bond restraints: 11210 Sorted by residual: bond pdb=" C07 GZR B 502 " pdb=" N04 GZR B 502 " ideal model delta sigma weight residual 1.471 1.644 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C20 GZR B 502 " pdb=" C26 GZR B 502 " ideal model delta sigma weight residual 1.387 1.552 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C13 GZR B 502 " pdb=" C18 GZR B 502 " ideal model delta sigma weight residual 1.397 1.560 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C21 GZR B 502 " pdb=" C25 GZR B 502 " ideal model delta sigma weight residual 1.380 1.542 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" C07 GZR B 502 " pdb=" C08 GZR B 502 " ideal model delta sigma weight residual 1.533 1.374 0.159 2.00e-02 2.50e+03 6.36e+01 ... (remaining 11205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 14986 3.32 - 6.64: 250 6.64 - 9.97: 41 9.97 - 13.29: 3 13.29 - 16.61: 1 Bond angle restraints: 15281 Sorted by residual: angle pdb=" C THR A 209 " pdb=" N PHE A 210 " pdb=" CA PHE A 210 " ideal model delta sigma weight residual 120.09 126.19 -6.10 1.25e+00 6.40e-01 2.38e+01 angle pdb=" N TRP A 289 " pdb=" CA TRP A 289 " pdb=" C TRP A 289 " ideal model delta sigma weight residual 110.97 116.29 -5.32 1.09e+00 8.42e-01 2.38e+01 angle pdb=" CA LEU B 286 " pdb=" CB LEU B 286 " pdb=" CG LEU B 286 " ideal model delta sigma weight residual 116.30 132.91 -16.61 3.50e+00 8.16e-02 2.25e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 116.25 -5.55 1.22e+00 6.72e-01 2.07e+01 angle pdb=" N ASN C 207 " pdb=" CA ASN C 207 " pdb=" C ASN C 207 " ideal model delta sigma weight residual 109.81 118.95 -9.14 2.21e+00 2.05e-01 1.71e+01 ... (remaining 15276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.45: 6171 24.45 - 48.90: 157 48.90 - 73.34: 16 73.34 - 97.79: 3 97.79 - 122.24: 1 Dihedral angle restraints: 6348 sinusoidal: 2515 harmonic: 3833 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -176.23 90.23 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta harmonic sigma weight residual -180.00 -142.44 -37.56 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA LEU C 206 " pdb=" C LEU C 206 " pdb=" N ASN C 207 " pdb=" CA ASN C 207 " ideal model delta harmonic sigma weight residual -180.00 -149.84 -30.16 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 6345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1649 0.102 - 0.204: 148 0.204 - 0.307: 14 0.307 - 0.409: 3 0.409 - 0.511: 1 Chirality restraints: 1815 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.15 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1812 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 GZR B 502 " -0.036 2.00e-02 2.50e+03 2.56e-01 8.22e+02 pdb=" C11 GZR B 502 " -0.097 2.00e-02 2.50e+03 pdb=" C12 GZR B 502 " -0.085 2.00e-02 2.50e+03 pdb=" C15 GZR B 502 " 0.488 2.00e-02 2.50e+03 pdb=" C16 GZR B 502 " -0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " 0.032 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP C 227 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO A 560 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.047 5.00e-02 4.00e+02 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1585 2.76 - 3.29: 9996 3.29 - 3.83: 18080 3.83 - 4.36: 21734 4.36 - 4.90: 37271 Nonbonded interactions: 88666 Sorted by model distance: nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.270 3.040 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.299 3.040 nonbonded pdb=" O PRO B 436 " pdb=" OG1 THR B 440 " model vdw 2.307 3.040 nonbonded pdb=" O LEU C 20 " pdb=" OG1 THR C 24 " model vdw 2.310 3.040 ... (remaining 88661 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 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.150 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 : 0.010 0.173 11235 Z= 0.466 Angle : 1.156 16.608 15352 Z= 0.584 Chirality : 0.063 0.511 1815 Planarity : 0.010 0.256 1840 Dihedral : 11.056 122.241 3866 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.18 % Allowed : 2.04 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % 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: -3.36 (0.19), residues: 1303 helix: -1.91 (0.15), residues: 698 sheet: -1.53 (0.44), residues: 123 loop : -2.70 (0.23), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG A 285 TYR 0.036 0.004 TYR A 565 PHE 0.052 0.004 PHE C 132 TRP 0.054 0.005 TRP C 227 HIS 0.025 0.004 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.01016 / 0.47 (11210) covalent geometry : angle 1.12549 / 0.58 (15281) SS BOND : bond 0.00838 / 0.42 ( 4) SS BOND : angle 2.16524 / 1.05 ( 8) hydrogen bonds : bond 0.18706 / 12.55 ( 560) hydrogen bonds : angle 6.83997 / 4.73 ( 1623) link_BETA1-3 : bond 0.00093 / 0.05 ( 1) link_BETA1-3 : angle 1.05217 / 0.77 ( 3) link_BETA1-4 : bond 0.00564 / 0.28 ( 7) link_BETA1-4 : angle 2.75622 / 1.74 ( 21) link_BETA1-6 : bond 0.00284 / 0.15 ( 1) link_BETA1-6 : angle 1.91090 / 1.16 ( 3) link_NAG-ASN : bond 0.00971 / 0.53 ( 12) link_NAG-ASN : angle 5.10737 / 3.41 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 LYS cc_start: 0.7981 (tptt) cc_final: 0.7688 (ttpt) REVERT: B 84 MET cc_start: 0.8559 (mtt) cc_final: 0.8228 (mtt) REVERT: B 139 MET cc_start: 0.7606 (tpp) cc_final: 0.7313 (tpt) REVERT: B 157 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7177 (mtt-85) REVERT: B 269 ARG cc_start: 0.7420 (ttt-90) cc_final: 0.7205 (ttt180) REVERT: C 66 ARG cc_start: 0.6682 (ttt90) cc_final: 0.6435 (ttt180) REVERT: C 98 ASP cc_start: 0.8199 (t70) cc_final: 0.7965 (t0) REVERT: D 39 ARG cc_start: 0.6869 (ttm-80) cc_final: 0.6614 (ttm170) REVERT: D 40 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7769 (mm-30) outliers start: 2 outliers final: 1 residues processed: 209 average time/residue: 0.5886 time to fit residues: 131.4899 Evaluate side-chains 115 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 163 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN A 163 GLN A 243 ASN A 313 GLN A 355 GLN A 358 ASN A 454 GLN A 531 ASN A 553 HIS A 606 GLN B 214 HIS B 454 GLN D 8 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.094056 restraints weight = 15246.972| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.87 r_work: 0.3014 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11235 Z= 0.134 Angle : 0.691 13.967 15352 Z= 0.338 Chirality : 0.044 0.265 1815 Planarity : 0.005 0.042 1840 Dihedral : 8.451 105.049 1559 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.31 % Allowed : 7.90 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.99 (0.22), residues: 1303 helix: 0.39 (0.19), residues: 700 sheet: -0.90 (0.46), residues: 119 loop : -2.14 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 114 TYR 0.016 0.001 TYR A 337 PHE 0.034 0.002 PHE A 302 TRP 0.019 0.001 TRP C 227 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (11210) covalent geometry : angle 0.66714 / 0.33 (15281) SS BOND : bond 0.00398 / 0.20 ( 4) SS BOND : angle 1.44309 / 0.77 ( 8) hydrogen bonds : bond 0.05345 / 3.65 ( 560) hydrogen bonds : angle 4.53612 / 3.09 ( 1623) link_BETA1-3 : bond 0.00655 / 0.34 ( 1) link_BETA1-3 : angle 1.75351 / 1.44 ( 3) link_BETA1-4 : bond 0.00499 / 0.25 ( 7) link_BETA1-4 : angle 1.47634 / 0.95 ( 21) link_BETA1-6 : bond 0.01133 / 0.60 ( 1) link_BETA1-6 : angle 1.47129 / 1.18 ( 3) link_NAG-ASN : bond 0.00556 / 0.30 ( 12) link_NAG-ASN : angle 3.51374 / 2.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9290 (mmm) cc_final: 0.8903 (tpp) REVERT: A 364 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: A 388 GLU cc_start: 0.8032 (tp30) cc_final: 0.7218 (mp0) REVERT: A 391 ARG cc_start: 0.8325 (ttm110) cc_final: 0.8088 (ttp80) REVERT: A 619 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7709 (ptt-90) REVERT: A 644 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: A 666 LYS cc_start: 0.7986 (tptt) cc_final: 0.7519 (ttpt) REVERT: A 681 ILE cc_start: 0.8595 (mt) cc_final: 0.8378 (mm) REVERT: B 84 MET cc_start: 0.8952 (mtt) cc_final: 0.8706 (mtt) REVERT: B 139 MET cc_start: 0.7771 (tpp) cc_final: 0.7421 (tpt) REVERT: B 157 ARG cc_start: 0.7793 (mtt90) cc_final: 0.6908 (mtt-85) REVERT: B 269 ARG cc_start: 0.7353 (ttt-90) cc_final: 0.7123 (ttt180) REVERT: C 66 ARG cc_start: 0.6742 (ttt90) cc_final: 0.6510 (ttt180) REVERT: C 98 ASP cc_start: 0.8403 (t70) cc_final: 0.8175 (t0) REVERT: C 184 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7769 (mtm180) REVERT: C 224 MET cc_start: 0.9090 (tpp) cc_final: 0.8878 (mmm) REVERT: C 241 ARG cc_start: 0.8091 (tmm160) cc_final: 0.7023 (mmp-170) REVERT: D 39 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6612 (ttm170) REVERT: D 40 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7810 (mm-30) REVERT: D 44 VAL cc_start: 0.6852 (t) cc_final: 0.6505 (m) outliers start: 26 outliers final: 9 residues processed: 152 average time/residue: 0.6163 time to fit residues: 100.5416 Evaluate side-chains 128 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 111 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS A 197 GLN A 385 GLN B 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.089500 restraints weight = 15369.354| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.87 r_work: 0.2943 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11235 Z= 0.187 Angle : 0.711 14.678 15352 Z= 0.343 Chirality : 0.046 0.233 1815 Planarity : 0.005 0.048 1840 Dihedral : 8.162 86.607 1557 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.73 % Allowed : 8.53 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.12 (0.23), residues: 1303 helix: 1.16 (0.19), residues: 717 sheet: -0.66 (0.47), residues: 126 loop : -1.93 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 114 TYR 0.018 0.002 TYR A 337 PHE 0.035 0.002 PHE A 302 TRP 0.018 0.002 TRP C 209 HIS 0.008 0.002 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (11210) covalent geometry : angle 0.69191 / 0.34 (15281) SS BOND : bond 0.00367 / 0.19 ( 4) SS BOND : angle 1.01258 / 0.56 ( 8) hydrogen bonds : bond 0.05322 / 3.61 ( 560) hydrogen bonds : angle 4.23750 / 2.90 ( 1623) link_BETA1-3 : bond 0.00299 / 0.16 ( 1) link_BETA1-3 : angle 1.48892 / 1.20 ( 3) link_BETA1-4 : bond 0.00339 / 0.16 ( 7) link_BETA1-4 : angle 1.65897 / 1.09 ( 21) link_BETA1-6 : bond 0.01044 / 0.55 ( 1) link_BETA1-6 : angle 1.57836 / 1.25 ( 3) link_NAG-ASN : bond 0.00501 / 0.25 ( 12) link_NAG-ASN : angle 3.14890 / 2.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9206 (mmm) cc_final: 0.8798 (tpp) REVERT: A 253 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8615 (t70) REVERT: A 364 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: A 388 GLU cc_start: 0.8120 (tp30) cc_final: 0.7155 (mp0) REVERT: A 391 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8046 (ttm110) REVERT: A 500 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8600 (tt0) REVERT: A 561 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8399 (t) REVERT: A 619 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8089 (ptt-90) REVERT: A 644 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: A 666 LYS cc_start: 0.8074 (tptt) cc_final: 0.7516 (ttpp) REVERT: A 681 ILE cc_start: 0.8596 (mt) cc_final: 0.8388 (mm) REVERT: B 84 MET cc_start: 0.8940 (mtt) cc_final: 0.8674 (mtt) REVERT: B 139 MET cc_start: 0.7773 (tpp) cc_final: 0.7443 (tpt) REVERT: B 157 ARG cc_start: 0.7696 (mtt90) cc_final: 0.6860 (mtt-85) REVERT: B 269 ARG cc_start: 0.7548 (ttt-90) cc_final: 0.7129 (ttt180) REVERT: C 66 ARG cc_start: 0.6714 (ttt90) cc_final: 0.6476 (ttt180) REVERT: C 184 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7784 (mtm180) REVERT: C 241 ARG cc_start: 0.8169 (ttm170) cc_final: 0.6895 (mmm160) REVERT: D 39 ARG cc_start: 0.7216 (ttm-80) cc_final: 0.6626 (ttm110) REVERT: D 40 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7805 (mm-30) REVERT: D 44 VAL cc_start: 0.6862 (t) cc_final: 0.6521 (m) outliers start: 42 outliers final: 17 residues processed: 145 average time/residue: 0.6035 time to fit residues: 93.9930 Evaluate side-chains 131 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.086649 restraints weight = 15217.180| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.88 r_work: 0.2898 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11235 Z= 0.240 Angle : 0.768 15.085 15352 Z= 0.371 Chirality : 0.049 0.218 1815 Planarity : 0.005 0.056 1840 Dihedral : 8.481 84.365 1557 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.46 % Allowed : 10.30 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.07 (0.23), residues: 1303 helix: 1.37 (0.19), residues: 715 sheet: -1.18 (0.43), residues: 137 loop : -1.73 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 114 TYR 0.018 0.002 TYR A 337 PHE 0.036 0.002 PHE A 302 TRP 0.017 0.002 TRP C 209 HIS 0.007 0.002 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (11210) covalent geometry : angle 0.74968 / 0.37 (15281) SS BOND : bond 0.00383 / 0.19 ( 4) SS BOND : angle 0.96113 / 0.52 ( 8) hydrogen bonds : bond 0.05714 / 3.87 ( 560) hydrogen bonds : angle 4.22887 / 2.90 ( 1623) link_BETA1-3 : bond 0.00283 / 0.15 ( 1) link_BETA1-3 : angle 1.42399 / 1.22 ( 3) link_BETA1-4 : bond 0.00376 / 0.18 ( 7) link_BETA1-4 : angle 1.78987 / 1.15 ( 21) link_BETA1-6 : bond 0.00800 / 0.42 ( 1) link_BETA1-6 : angle 1.58637 / 1.26 ( 3) link_NAG-ASN : bond 0.00500 / 0.23 ( 12) link_NAG-ASN : angle 3.26694 / 2.38 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8621 (t70) REVERT: A 351 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8397 (mmmt) REVERT: A 364 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: A 391 ARG cc_start: 0.8454 (ttm170) cc_final: 0.8108 (ttm110) REVERT: A 500 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8602 (tt0) REVERT: A 561 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8526 (t) REVERT: A 644 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: A 666 LYS cc_start: 0.8151 (tptt) cc_final: 0.7582 (ttpp) REVERT: A 681 ILE cc_start: 0.8600 (mt) cc_final: 0.8398 (mm) REVERT: B 84 MET cc_start: 0.8952 (mtt) cc_final: 0.8704 (mtt) REVERT: B 139 MET cc_start: 0.7883 (tpp) cc_final: 0.7559 (tpt) REVERT: B 157 ARG cc_start: 0.7653 (mtt90) cc_final: 0.6839 (mtt-85) REVERT: B 201 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8691 (mp) REVERT: B 269 ARG cc_start: 0.7628 (ttt-90) cc_final: 0.7032 (ttt180) REVERT: C 66 ARG cc_start: 0.6861 (ttt90) cc_final: 0.6525 (ttt-90) REVERT: C 184 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7816 (mtm180) REVERT: C 241 ARG cc_start: 0.8268 (ttm170) cc_final: 0.7019 (mmp80) REVERT: D 39 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.6651 (ttm110) REVERT: D 40 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7687 (mm-30) REVERT: D 44 VAL cc_start: 0.6919 (t) cc_final: 0.6565 (m) outliers start: 39 outliers final: 18 residues processed: 141 average time/residue: 0.5766 time to fit residues: 87.4459 Evaluate side-chains 138 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.089947 restraints weight = 15150.586| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.89 r_work: 0.2952 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11235 Z= 0.129 Angle : 0.624 14.641 15352 Z= 0.303 Chirality : 0.043 0.228 1815 Planarity : 0.004 0.038 1840 Dihedral : 7.949 86.966 1557 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.84 % Allowed : 11.46 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.24), residues: 1303 helix: 1.84 (0.20), residues: 715 sheet: -1.00 (0.44), residues: 140 loop : -1.56 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 114 TYR 0.014 0.001 TYR A 337 PHE 0.031 0.001 PHE A 302 TRP 0.010 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (11210) covalent geometry : angle 0.61019 / 0.30 (15281) SS BOND : bond 0.00214 / 0.11 ( 4) SS BOND : angle 0.58559 / 0.41 ( 8) hydrogen bonds : bond 0.04422 / 3.01 ( 560) hydrogen bonds : angle 4.00682 / 2.74 ( 1623) link_BETA1-3 : bond 0.00357 / 0.19 ( 1) link_BETA1-3 : angle 1.37305 / 1.14 ( 3) link_BETA1-4 : bond 0.00383 / 0.19 ( 7) link_BETA1-4 : angle 1.36957 / 0.88 ( 21) link_BETA1-6 : bond 0.00871 / 0.46 ( 1) link_BETA1-6 : angle 1.52383 / 1.21 ( 3) link_NAG-ASN : bond 0.00389 / 0.20 ( 12) link_NAG-ASN : angle 2.53381 / 1.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7740 (mtp-110) REVERT: A 108 MET cc_start: 0.9137 (mmm) cc_final: 0.8668 (tpp) REVERT: A 114 ARG cc_start: 0.7558 (mtp85) cc_final: 0.7110 (mtp-110) REVERT: A 364 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: A 388 GLU cc_start: 0.8157 (tp30) cc_final: 0.7216 (mp0) REVERT: A 391 ARG cc_start: 0.8402 (ttm170) cc_final: 0.8132 (ttm110) REVERT: A 561 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8362 (t) REVERT: A 644 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: A 666 LYS cc_start: 0.8046 (tptt) cc_final: 0.7506 (ttpp) REVERT: A 681 ILE cc_start: 0.8648 (mt) cc_final: 0.8415 (mm) REVERT: B 84 MET cc_start: 0.8933 (mtt) cc_final: 0.8676 (mtt) REVERT: B 139 MET cc_start: 0.7808 (tpp) cc_final: 0.7481 (tpt) REVERT: B 157 ARG cc_start: 0.7607 (mtt90) cc_final: 0.6796 (mtt-85) REVERT: B 269 ARG cc_start: 0.7491 (ttt-90) cc_final: 0.6996 (ttt180) REVERT: C 66 ARG cc_start: 0.6938 (ttt90) cc_final: 0.6641 (ttt180) REVERT: C 98 ASP cc_start: 0.8141 (t0) cc_final: 0.7816 (t0) REVERT: C 184 ARG cc_start: 0.8033 (mtp180) cc_final: 0.7748 (mtm180) REVERT: C 241 ARG cc_start: 0.8233 (ttm170) cc_final: 0.6859 (mmm160) REVERT: D 39 ARG cc_start: 0.7259 (ttm-80) cc_final: 0.6704 (ttm110) REVERT: D 40 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7683 (mm-30) REVERT: D 44 VAL cc_start: 0.6894 (t) cc_final: 0.6529 (m) outliers start: 32 outliers final: 11 residues processed: 135 average time/residue: 0.5944 time to fit residues: 86.3636 Evaluate side-chains 125 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.090668 restraints weight = 15222.027| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.89 r_work: 0.2962 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11235 Z= 0.122 Angle : 0.606 14.400 15352 Z= 0.294 Chirality : 0.042 0.233 1815 Planarity : 0.004 0.038 1840 Dihedral : 7.634 88.438 1557 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.46 % Allowed : 11.55 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.24), residues: 1303 helix: 2.10 (0.20), residues: 715 sheet: -0.89 (0.44), residues: 140 loop : -1.45 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 114 TYR 0.015 0.001 TYR A 337 PHE 0.030 0.001 PHE A 302 TRP 0.010 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11210) covalent geometry : angle 0.59309 / 0.29 (15281) SS BOND : bond 0.00211 / 0.11 ( 4) SS BOND : angle 0.55419 / 0.38 ( 8) hydrogen bonds : bond 0.04169 / 2.83 ( 560) hydrogen bonds : angle 3.91118 / 2.67 ( 1623) link_BETA1-3 : bond 0.00394 / 0.21 ( 1) link_BETA1-3 : angle 1.36309 / 1.13 ( 3) link_BETA1-4 : bond 0.00341 / 0.17 ( 7) link_BETA1-4 : angle 1.37821 / 0.90 ( 21) link_BETA1-6 : bond 0.00746 / 0.39 ( 1) link_BETA1-6 : angle 1.56856 / 1.24 ( 3) link_NAG-ASN : bond 0.00433 / 0.21 ( 12) link_NAG-ASN : angle 2.40637 / 1.70 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7761 (mtp-110) REVERT: A 108 MET cc_start: 0.9097 (mmm) cc_final: 0.8660 (tpp) REVERT: A 253 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8612 (t70) REVERT: A 364 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: A 388 GLU cc_start: 0.8151 (tp30) cc_final: 0.7224 (mp0) REVERT: A 391 ARG cc_start: 0.8421 (ttm170) cc_final: 0.8144 (ttm110) REVERT: A 561 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8441 (t) REVERT: A 644 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: A 666 LYS cc_start: 0.8001 (tptt) cc_final: 0.7440 (ttpp) REVERT: A 681 ILE cc_start: 0.8642 (mt) cc_final: 0.8419 (mm) REVERT: B 84 MET cc_start: 0.8940 (mtt) cc_final: 0.8690 (mtt) REVERT: B 139 MET cc_start: 0.7794 (tpp) cc_final: 0.7088 (mtp) REVERT: B 157 ARG cc_start: 0.7583 (mtt90) cc_final: 0.6765 (mtt-85) REVERT: B 269 ARG cc_start: 0.7493 (ttt-90) cc_final: 0.7013 (ttt180) REVERT: B 280 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: C 66 ARG cc_start: 0.7000 (ttt90) cc_final: 0.6687 (ttt180) REVERT: C 184 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7698 (mtm180) REVERT: C 241 ARG cc_start: 0.8202 (ttm170) cc_final: 0.6833 (mmm160) REVERT: D 39 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6768 (ttm110) REVERT: D 40 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7615 (mm-30) REVERT: D 44 VAL cc_start: 0.6891 (t) cc_final: 0.6564 (m) outliers start: 39 outliers final: 19 residues processed: 140 average time/residue: 0.5091 time to fit residues: 77.0344 Evaluate side-chains 133 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN ** B 204 ASN ** 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 = 0.3412 r_free = 0.3412 target = 0.113905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089186 restraints weight = 15065.711| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.84 r_work: 0.2934 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11235 Z= 0.157 Angle : 0.649 14.511 15352 Z= 0.314 Chirality : 0.044 0.227 1815 Planarity : 0.004 0.041 1840 Dihedral : 7.725 88.699 1557 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.75 % Allowed : 12.61 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.24), residues: 1303 helix: 2.05 (0.20), residues: 716 sheet: -1.02 (0.44), residues: 139 loop : -1.38 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 114 TYR 0.016 0.001 TYR A 337 PHE 0.030 0.002 PHE A 302 TRP 0.010 0.001 TRP C 209 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (11210) covalent geometry : angle 0.63528 / 0.31 (15281) SS BOND : bond 0.00254 / 0.13 ( 4) SS BOND : angle 0.65339 / 0.39 ( 8) hydrogen bonds : bond 0.04594 / 3.11 ( 560) hydrogen bonds : angle 3.94660 / 2.70 ( 1623) link_BETA1-3 : bond 0.00360 / 0.19 ( 1) link_BETA1-3 : angle 1.39099 / 1.18 ( 3) link_BETA1-4 : bond 0.00331 / 0.16 ( 7) link_BETA1-4 : angle 1.49585 / 0.97 ( 21) link_BETA1-6 : bond 0.00684 / 0.36 ( 1) link_BETA1-6 : angle 1.58491 / 1.26 ( 3) link_NAG-ASN : bond 0.00389 / 0.19 ( 12) link_NAG-ASN : angle 2.54664 / 1.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7729 (mtp-110) REVERT: A 108 MET cc_start: 0.9110 (mmm) cc_final: 0.8684 (tpp) REVERT: A 253 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8684 (t70) REVERT: A 364 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: A 388 GLU cc_start: 0.8163 (tp30) cc_final: 0.7207 (mp0) REVERT: A 391 ARG cc_start: 0.8449 (ttm170) cc_final: 0.8174 (ttm110) REVERT: A 644 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: A 666 LYS cc_start: 0.8031 (tptt) cc_final: 0.7462 (ttpp) REVERT: A 681 ILE cc_start: 0.8625 (mt) cc_final: 0.8398 (mm) REVERT: B 84 MET cc_start: 0.8918 (mtt) cc_final: 0.8673 (mtt) REVERT: B 139 MET cc_start: 0.7807 (tpp) cc_final: 0.7470 (tpt) REVERT: B 157 ARG cc_start: 0.7563 (mtt90) cc_final: 0.6788 (mtt-85) REVERT: B 269 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.6955 (ttt180) REVERT: C 66 ARG cc_start: 0.6965 (ttt90) cc_final: 0.6591 (ttt-90) REVERT: C 184 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7720 (mtm180) REVERT: C 240 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6601 (tt0) REVERT: C 241 ARG cc_start: 0.8172 (ttm170) cc_final: 0.6801 (mmm160) REVERT: D 39 ARG cc_start: 0.7260 (ttm-80) cc_final: 0.6706 (ttm110) REVERT: D 40 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7651 (mm-30) REVERT: D 44 VAL cc_start: 0.6895 (t) cc_final: 0.6527 (m) outliers start: 31 outliers final: 17 residues processed: 129 average time/residue: 0.5334 time to fit residues: 73.9860 Evaluate side-chains 131 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090255 restraints weight = 15307.947| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.87 r_work: 0.2955 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11235 Z= 0.125 Angle : 0.604 14.437 15352 Z= 0.293 Chirality : 0.042 0.230 1815 Planarity : 0.004 0.041 1840 Dihedral : 7.563 89.409 1557 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.31 % Allowed : 13.32 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.24), residues: 1303 helix: 2.19 (0.20), residues: 716 sheet: -0.94 (0.44), residues: 139 loop : -1.27 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 114 TYR 0.014 0.001 TYR A 337 PHE 0.030 0.001 PHE A 302 TRP 0.009 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (11210) covalent geometry : angle 0.59157 / 0.29 (15281) SS BOND : bond 0.00201 / 0.10 ( 4) SS BOND : angle 0.50152 / 0.34 ( 8) hydrogen bonds : bond 0.04181 / 2.83 ( 560) hydrogen bonds : angle 3.89171 / 2.65 ( 1623) link_BETA1-3 : bond 0.00371 / 0.20 ( 1) link_BETA1-3 : angle 1.40356 / 1.17 ( 3) link_BETA1-4 : bond 0.00346 / 0.17 ( 7) link_BETA1-4 : angle 1.36282 / 0.89 ( 21) link_BETA1-6 : bond 0.00750 / 0.39 ( 1) link_BETA1-6 : angle 1.53957 / 1.21 ( 3) link_NAG-ASN : bond 0.00370 / 0.18 ( 12) link_NAG-ASN : angle 2.34695 / 1.65 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7768 (mtp-110) REVERT: A 108 MET cc_start: 0.9098 (mmm) cc_final: 0.8689 (tpp) REVERT: A 253 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8650 (t70) REVERT: A 364 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: A 388 GLU cc_start: 0.8154 (tp30) cc_final: 0.7201 (mp0) REVERT: A 391 ARG cc_start: 0.8470 (ttm170) cc_final: 0.8156 (ttm110) REVERT: A 644 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: A 666 LYS cc_start: 0.7967 (tptt) cc_final: 0.7419 (ttpp) REVERT: A 681 ILE cc_start: 0.8618 (mt) cc_final: 0.8398 (mm) REVERT: B 84 MET cc_start: 0.8940 (mtt) cc_final: 0.8709 (mtt) REVERT: B 139 MET cc_start: 0.7806 (tpp) cc_final: 0.7478 (tpt) REVERT: B 157 ARG cc_start: 0.7600 (mtt90) cc_final: 0.6778 (mtt-85) REVERT: B 269 ARG cc_start: 0.7508 (ttt-90) cc_final: 0.7007 (ttt180) REVERT: C 66 ARG cc_start: 0.7072 (ttt90) cc_final: 0.6687 (ttt180) REVERT: C 184 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7644 (mtm180) REVERT: C 241 ARG cc_start: 0.8164 (ttm170) cc_final: 0.6727 (mmm160) REVERT: D 39 ARG cc_start: 0.7240 (ttm-80) cc_final: 0.6698 (ttm110) REVERT: D 40 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7568 (mm-30) REVERT: D 44 VAL cc_start: 0.6887 (t) cc_final: 0.6546 (m) outliers start: 26 outliers final: 17 residues processed: 124 average time/residue: 0.5580 time to fit residues: 74.1691 Evaluate side-chains 128 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 91 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.090757 restraints weight = 15162.212| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.86 r_work: 0.2965 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11235 Z= 0.122 Angle : 0.599 14.319 15352 Z= 0.291 Chirality : 0.042 0.234 1815 Planarity : 0.004 0.039 1840 Dihedral : 7.383 87.420 1557 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 12.97 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.24), residues: 1303 helix: 2.38 (0.19), residues: 708 sheet: -0.89 (0.44), residues: 139 loop : -1.19 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 114 TYR 0.014 0.001 TYR A 337 PHE 0.029 0.001 PHE A 302 TRP 0.009 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11210) covalent geometry : angle 0.58711 / 0.29 (15281) SS BOND : bond 0.00208 / 0.11 ( 4) SS BOND : angle 0.50116 / 0.32 ( 8) hydrogen bonds : bond 0.04056 / 2.75 ( 560) hydrogen bonds : angle 3.85935 / 2.63 ( 1623) link_BETA1-3 : bond 0.00396 / 0.21 ( 1) link_BETA1-3 : angle 1.44757 / 1.20 ( 3) link_BETA1-4 : bond 0.00329 / 0.16 ( 7) link_BETA1-4 : angle 1.34358 / 0.88 ( 21) link_BETA1-6 : bond 0.00668 / 0.35 ( 1) link_BETA1-6 : angle 1.57385 / 1.24 ( 3) link_NAG-ASN : bond 0.00351 / 0.17 ( 12) link_NAG-ASN : angle 2.28307 / 1.60 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7777 (mtp-110) REVERT: A 108 MET cc_start: 0.9086 (mmm) cc_final: 0.8689 (tpp) REVERT: A 114 ARG cc_start: 0.7576 (mtp85) cc_final: 0.7138 (mtp-110) REVERT: A 253 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8653 (t70) REVERT: A 364 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: A 388 GLU cc_start: 0.8152 (tp30) cc_final: 0.7202 (mp0) REVERT: A 391 ARG cc_start: 0.8451 (ttm170) cc_final: 0.8154 (ttm110) REVERT: A 644 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: A 666 LYS cc_start: 0.7949 (tptt) cc_final: 0.7407 (ttpp) REVERT: A 681 ILE cc_start: 0.8629 (mt) cc_final: 0.8409 (mm) REVERT: B 84 MET cc_start: 0.8933 (mtt) cc_final: 0.8702 (mtt) REVERT: B 139 MET cc_start: 0.7803 (tpp) cc_final: 0.7488 (tpt) REVERT: B 157 ARG cc_start: 0.7585 (mtt90) cc_final: 0.6772 (mtt-85) REVERT: B 269 ARG cc_start: 0.7504 (ttt-90) cc_final: 0.6978 (ttt180) REVERT: C 66 ARG cc_start: 0.7072 (ttt90) cc_final: 0.6684 (ttt180) REVERT: C 184 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7635 (mtm180) REVERT: C 241 ARG cc_start: 0.8177 (ttm170) cc_final: 0.6700 (mmm160) REVERT: D 39 ARG cc_start: 0.7235 (ttm-80) cc_final: 0.6700 (ttm110) REVERT: D 40 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7567 (mm-30) REVERT: D 44 VAL cc_start: 0.6880 (t) cc_final: 0.6539 (m) outliers start: 27 outliers final: 19 residues processed: 132 average time/residue: 0.5541 time to fit residues: 78.5260 Evaluate side-chains 133 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN ** B 204 ASN ** 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 = 0.3434 r_free = 0.3434 target = 0.115537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.090835 restraints weight = 15201.992| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.86 r_work: 0.2966 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11235 Z= 0.122 Angle : 0.597 14.288 15352 Z= 0.290 Chirality : 0.042 0.233 1815 Planarity : 0.004 0.040 1840 Dihedral : 7.332 86.829 1557 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.22 % Allowed : 13.68 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.27 (0.24), residues: 1303 helix: 2.39 (0.19), residues: 710 sheet: -0.90 (0.44), residues: 139 loop : -1.15 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 114 TYR 0.014 0.001 TYR A 337 PHE 0.029 0.001 PHE A 302 TRP 0.008 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (11210) covalent geometry : angle 0.58478 / 0.29 (15281) SS BOND : bond 0.00200 / 0.10 ( 4) SS BOND : angle 0.52685 / 0.35 ( 8) hydrogen bonds : bond 0.04061 / 2.75 ( 560) hydrogen bonds : angle 3.85617 / 2.63 ( 1623) link_BETA1-3 : bond 0.00380 / 0.20 ( 1) link_BETA1-3 : angle 1.43325 / 1.20 ( 3) link_BETA1-4 : bond 0.00333 / 0.16 ( 7) link_BETA1-4 : angle 1.34882 / 0.89 ( 21) link_BETA1-6 : bond 0.00698 / 0.37 ( 1) link_BETA1-6 : angle 1.56661 / 1.23 ( 3) link_NAG-ASN : bond 0.00355 / 0.18 ( 12) link_NAG-ASN : angle 2.26666 / 1.60 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7780 (mtp-110) REVERT: A 108 MET cc_start: 0.9084 (mmm) cc_final: 0.8701 (tpp) REVERT: A 114 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7185 (mtp-110) REVERT: A 253 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8658 (t70) REVERT: A 364 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: A 388 GLU cc_start: 0.8150 (tp30) cc_final: 0.7201 (mp0) REVERT: A 391 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8154 (ttm110) REVERT: A 644 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: A 666 LYS cc_start: 0.7944 (tptt) cc_final: 0.7400 (ttpp) REVERT: A 681 ILE cc_start: 0.8631 (mt) cc_final: 0.8412 (mm) REVERT: B 84 MET cc_start: 0.8939 (mtt) cc_final: 0.8710 (mtt) REVERT: B 139 MET cc_start: 0.7688 (tpp) cc_final: 0.7311 (tpt) REVERT: B 157 ARG cc_start: 0.7548 (mtt90) cc_final: 0.6725 (mtt-85) REVERT: B 269 ARG cc_start: 0.7509 (ttt-90) cc_final: 0.6989 (ttt180) REVERT: C 66 ARG cc_start: 0.7071 (ttt90) cc_final: 0.6683 (ttt180) REVERT: C 184 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7636 (mtm180) REVERT: C 241 ARG cc_start: 0.8163 (ttm170) cc_final: 0.6715 (mmm160) REVERT: D 39 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6695 (ttm110) REVERT: D 40 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7567 (mm-30) REVERT: D 44 VAL cc_start: 0.6865 (t) cc_final: 0.6524 (m) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.5564 time to fit residues: 74.6904 Evaluate side-chains 131 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.091148 restraints weight = 15209.568| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.87 r_work: 0.2970 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11235 Z= 0.119 Angle : 0.591 14.254 15352 Z= 0.288 Chirality : 0.042 0.232 1815 Planarity : 0.004 0.040 1840 Dihedral : 7.239 85.919 1557 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.22 % Allowed : 13.32 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.25), residues: 1303 helix: 2.48 (0.20), residues: 707 sheet: -0.86 (0.45), residues: 135 loop : -1.13 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 114 TYR 0.014 0.001 TYR A 337 PHE 0.029 0.001 PHE A 302 TRP 0.008 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (11210) covalent geometry : angle 0.57928 / 0.29 (15281) SS BOND : bond 0.00201 / 0.10 ( 4) SS BOND : angle 0.51815 / 0.36 ( 8) hydrogen bonds : bond 0.03986 / 2.70 ( 560) hydrogen bonds : angle 3.83923 / 2.62 ( 1623) link_BETA1-3 : bond 0.00387 / 0.20 ( 1) link_BETA1-3 : angle 1.45614 / 1.22 ( 3) link_BETA1-4 : bond 0.00341 / 0.17 ( 7) link_BETA1-4 : angle 1.32929 / 0.88 ( 21) link_BETA1-6 : bond 0.00676 / 0.36 ( 1) link_BETA1-6 : angle 1.55146 / 1.22 ( 3) link_NAG-ASN : bond 0.00362 / 0.18 ( 12) link_NAG-ASN : angle 2.20568 / 1.56 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.84 seconds wall clock time: 61 minutes 26.65 seconds (3686.65 seconds total)