Starting phenix.real_space_refine on Wed Mar 4 07:45:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d8x_30614/03_2026/7d8x_30614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d8x_30614/03_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_30614/03_2026/7d8x_30614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d8x_30614/03_2026/7d8x_30614.map" model { file = "/net/cci-nas-00/data/ceres_data/7d8x_30614/03_2026/7d8x_30614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d8x_30614/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 18 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: 2.27, per 1000 atoms: 0.21 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: 1.13 Conformation dependent library (CDL) restraints added in 540.1 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: 1.92 Time building geometry restraints manager: 1.44 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: 6694 24.45 - 48.90: 197 48.90 - 73.34: 49 73.34 - 97.79: 20 97.79 - 122.24: 15 Dihedral angle restraints: 6975 sinusoidal: 3142 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 6972 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: 2.870 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.230 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: 0.000 Load rotamer database and sin/cos tables:10.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 14.379 122.241 4493 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 covalent geometry : bond 0.01016 (11210) covalent geometry : angle 1.12549 (15281) SS BOND : bond 0.00838 ( 4) SS BOND : angle 2.16524 ( 8) hydrogen bonds : bond 0.18706 ( 560) hydrogen bonds : angle 6.83997 ( 1623) link_BETA1-3 : bond 0.00093 ( 1) link_BETA1-3 : angle 1.05217 ( 3) link_BETA1-4 : bond 0.00564 ( 7) link_BETA1-4 : angle 2.75622 ( 21) link_BETA1-6 : bond 0.00284 ( 1) link_BETA1-6 : angle 1.91090 ( 3) link_NAG-ASN : bond 0.00971 ( 12) link_NAG-ASN : angle 5.10737 ( 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 : 0.315 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: 0.6260 time to fit residues: 139.5471 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 : 0.406 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 163 GLN A 243 ASN A 313 GLN A 355 GLN A 358 ASN A 385 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.094158 restraints weight = 15218.831| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.89 r_work: 0.3020 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11235 Z= 0.134 Angle : 0.691 13.892 15352 Z= 0.335 Chirality : 0.044 0.258 1815 Planarity : 0.005 0.041 1840 Dihedral : 13.058 115.064 2186 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.31 % Allowed : 7.99 % Favored : 89.70 % 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: -0.96 (0.22), residues: 1303 helix: 0.41 (0.19), residues: 706 sheet: -1.10 (0.45), residues: 128 loop : -2.09 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 114 TYR 0.015 0.001 TYR A 337 PHE 0.034 0.002 PHE A 302 TRP 0.017 0.001 TRP C 227 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00282 (11210) covalent geometry : angle 0.66900 (15281) SS BOND : bond 0.00859 ( 4) SS BOND : angle 1.56500 ( 8) hydrogen bonds : bond 0.05191 ( 560) hydrogen bonds : angle 4.48486 ( 1623) link_BETA1-3 : bond 0.01066 ( 1) link_BETA1-3 : angle 1.89594 ( 3) link_BETA1-4 : bond 0.00442 ( 7) link_BETA1-4 : angle 1.57175 ( 21) link_BETA1-6 : bond 0.01302 ( 1) link_BETA1-6 : angle 1.87336 ( 3) link_NAG-ASN : bond 0.00538 ( 12) link_NAG-ASN : angle 3.37003 ( 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 161 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8070 (mppt) REVERT: A 108 MET cc_start: 0.9282 (mmm) cc_final: 0.8871 (tpp) REVERT: A 364 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: A 388 GLU cc_start: 0.8036 (tp30) cc_final: 0.7242 (mp0) REVERT: A 391 ARG cc_start: 0.8340 (ttm110) cc_final: 0.8104 (ttp80) REVERT: A 619 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7716 (ptt-90) REVERT: A 644 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: A 666 LYS cc_start: 0.7953 (tptt) cc_final: 0.7505 (ttpt) REVERT: A 681 ILE cc_start: 0.8609 (mt) cc_final: 0.8402 (mm) REVERT: B 84 MET cc_start: 0.8958 (mtt) cc_final: 0.8705 (mtt) REVERT: B 139 MET cc_start: 0.7784 (tpp) cc_final: 0.7438 (tpt) REVERT: B 157 ARG cc_start: 0.7705 (mtt90) cc_final: 0.6852 (mtt-85) REVERT: B 269 ARG cc_start: 0.7359 (ttt-90) cc_final: 0.7091 (ttt180) REVERT: C 66 ARG cc_start: 0.6655 (ttt90) cc_final: 0.6427 (ttt180) REVERT: C 184 ARG cc_start: 0.8034 (mtp180) cc_final: 0.7778 (mtm180) REVERT: C 241 ARG cc_start: 0.8062 (tmm160) cc_final: 0.7021 (mmp-170) REVERT: D 39 ARG cc_start: 0.7140 (ttm-80) cc_final: 0.6658 (ttm110) REVERT: D 40 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7798 (mm-30) REVERT: D 44 VAL cc_start: 0.6854 (t) cc_final: 0.6499 (m) outliers start: 26 outliers final: 8 residues processed: 154 average time/residue: 0.6066 time to fit residues: 99.8297 Evaluate side-chains 126 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS 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 588 ASP 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 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: 0.9990 chunk 125 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 197 GLN B 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.089295 restraints weight = 15353.901| |-----------------------------------------------------------------------------| r_work (start): 0.3062 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: 3.90 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11235 Z= 0.190 Angle : 0.722 14.646 15352 Z= 0.347 Chirality : 0.046 0.237 1815 Planarity : 0.005 0.045 1840 Dihedral : 11.790 114.894 2184 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.55 % Allowed : 8.97 % Favored : 87.48 % 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: -0.15 (0.23), residues: 1303 helix: 1.16 (0.19), residues: 717 sheet: -1.01 (0.44), residues: 138 loop : -1.90 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 114 TYR 0.019 0.002 TYR A 337 PHE 0.034 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 covalent geometry : bond 0.00450 (11210) covalent geometry : angle 0.70303 (15281) SS BOND : bond 0.00420 ( 4) SS BOND : angle 0.93607 ( 8) hydrogen bonds : bond 0.05340 ( 560) hydrogen bonds : angle 4.23751 ( 1623) link_BETA1-3 : bond 0.00922 ( 1) link_BETA1-3 : angle 1.47161 ( 3) link_BETA1-4 : bond 0.00364 ( 7) link_BETA1-4 : angle 1.87590 ( 21) link_BETA1-6 : bond 0.01383 ( 1) link_BETA1-6 : angle 2.18591 ( 3) link_NAG-ASN : bond 0.00524 ( 12) link_NAG-ASN : angle 3.12782 ( 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 155 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9204 (mmm) cc_final: 0.8793 (tpp) REVERT: A 253 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8622 (t70) REVERT: A 364 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: A 388 GLU cc_start: 0.8123 (tp30) cc_final: 0.7145 (mp0) REVERT: A 391 ARG cc_start: 0.8366 (ttm110) cc_final: 0.8048 (ttm110) REVERT: A 500 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: A 561 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8408 (t) REVERT: A 619 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8073 (ptt-90) REVERT: A 644 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: A 666 LYS cc_start: 0.8067 (tptt) cc_final: 0.7511 (ttpp) REVERT: A 681 ILE cc_start: 0.8596 (mt) cc_final: 0.8384 (mm) REVERT: B 84 MET cc_start: 0.8943 (mtt) cc_final: 0.8687 (mtt) REVERT: B 139 MET cc_start: 0.7770 (tpp) cc_final: 0.7432 (tpt) REVERT: B 157 ARG cc_start: 0.7698 (mtt90) cc_final: 0.6863 (mtt-85) REVERT: B 269 ARG cc_start: 0.7541 (ttt-90) cc_final: 0.7152 (ttt180) REVERT: B 458 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: C 66 ARG cc_start: 0.6720 (ttt90) cc_final: 0.6482 (ttt180) REVERT: C 184 ARG cc_start: 0.8077 (mtp180) cc_final: 0.7786 (mtm180) REVERT: C 241 ARG cc_start: 0.8180 (ttm170) cc_final: 0.6925 (mmp80) REVERT: D 39 ARG cc_start: 0.7215 (ttm-80) cc_final: 0.6623 (ttm110) REVERT: D 40 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7780 (mm-30) REVERT: D 44 VAL cc_start: 0.6863 (t) cc_final: 0.6513 (m) outliers start: 40 outliers final: 15 residues processed: 140 average time/residue: 0.6128 time to fit residues: 91.6728 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 : 0.387 ------------------------------------------------------------------------------- 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 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 B residue 458 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 76 THR 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: 4.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.087476 restraints weight = 15188.187| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.88 r_work: 0.2911 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11235 Z= 0.217 Angle : 0.739 14.902 15352 Z= 0.356 Chirality : 0.048 0.220 1815 Planarity : 0.005 0.053 1840 Dihedral : 11.574 114.915 2184 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.46 % Allowed : 10.21 % Favored : 86.32 % 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: 0.13 (0.24), residues: 1303 helix: 1.42 (0.19), residues: 717 sheet: -1.14 (0.43), residues: 137 loop : -1.72 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 114 TYR 0.018 0.002 TYR A 337 PHE 0.035 0.002 PHE A 302 TRP 0.017 0.002 TRP C 209 HIS 0.006 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00521 (11210) covalent geometry : angle 0.72006 (15281) SS BOND : bond 0.00355 ( 4) SS BOND : angle 0.94091 ( 8) hydrogen bonds : bond 0.05444 ( 560) hydrogen bonds : angle 4.18112 ( 1623) link_BETA1-3 : bond 0.00831 ( 1) link_BETA1-3 : angle 1.06525 ( 3) link_BETA1-4 : bond 0.00398 ( 7) link_BETA1-4 : angle 2.01206 ( 21) link_BETA1-6 : bond 0.01303 ( 1) link_BETA1-6 : angle 2.13272 ( 3) link_NAG-ASN : bond 0.00514 ( 12) link_NAG-ASN : angle 3.13427 ( 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 : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8641 (t70) REVERT: A 351 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8395 (mmmt) REVERT: A 364 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: A 391 ARG cc_start: 0.8443 (ttm170) cc_final: 0.8095 (ttm110) REVERT: A 500 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8593 (tt0) REVERT: A 561 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8493 (t) REVERT: A 644 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: A 666 LYS cc_start: 0.8126 (tptt) cc_final: 0.7568 (ttpp) REVERT: B 84 MET cc_start: 0.8950 (mtt) cc_final: 0.8704 (mtt) REVERT: B 139 MET cc_start: 0.7868 (tpp) cc_final: 0.7542 (tpt) REVERT: B 157 ARG cc_start: 0.7644 (mtt90) cc_final: 0.6821 (mtt-85) REVERT: B 269 ARG cc_start: 0.7558 (ttt-90) cc_final: 0.6972 (ttt180) REVERT: B 458 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: C 66 ARG cc_start: 0.6983 (ttt90) cc_final: 0.6633 (ttt-90) REVERT: C 184 ARG cc_start: 0.8108 (mtp180) cc_final: 0.7811 (mtm180) REVERT: C 241 ARG cc_start: 0.8270 (ttm170) cc_final: 0.6986 (mmp80) REVERT: D 39 ARG cc_start: 0.7290 (ttm-80) cc_final: 0.6656 (ttm110) REVERT: D 40 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7748 (mm-30) REVERT: D 44 VAL cc_start: 0.6868 (t) cc_final: 0.6515 (m) outliers start: 39 outliers final: 19 residues processed: 141 average time/residue: 0.6372 time to fit residues: 96.0332 Evaluate side-chains 139 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 B residue 458 ASP Chi-restraints excluded: chain B residue 459 GLN 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: 0.6980 chunk 34 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.090366 restraints weight = 15137.456| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.89 r_work: 0.2959 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2588 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 : 0.626 14.559 15352 Z= 0.302 Chirality : 0.044 0.239 1815 Planarity : 0.004 0.038 1840 Dihedral : 10.890 112.712 2184 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.02 % Allowed : 11.37 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.63 (0.24), residues: 1303 helix: 1.86 (0.20), residues: 715 sheet: -0.96 (0.44), residues: 140 loop : -1.54 (0.29), 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 0.031 0.001 PHE A 302 TRP 0.011 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00291 (11210) covalent geometry : angle 0.61098 (15281) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.61813 ( 8) hydrogen bonds : bond 0.04347 ( 560) hydrogen bonds : angle 3.98819 ( 1623) link_BETA1-3 : bond 0.00853 ( 1) link_BETA1-3 : angle 1.66287 ( 3) link_BETA1-4 : bond 0.00345 ( 7) link_BETA1-4 : angle 1.64765 ( 21) link_BETA1-6 : bond 0.01551 ( 1) link_BETA1-6 : angle 2.29946 ( 3) link_NAG-ASN : bond 0.00389 ( 12) link_NAG-ASN : angle 2.51125 ( 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: 34 poor density : 115 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9136 (mmm) cc_final: 0.8755 (tpp) REVERT: A 364 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: A 388 GLU cc_start: 0.8149 (tp30) cc_final: 0.7212 (mp0) REVERT: A 391 ARG cc_start: 0.8398 (ttm170) cc_final: 0.8127 (ttm110) REVERT: A 561 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8355 (t) REVERT: A 644 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: A 666 LYS cc_start: 0.8008 (tptt) cc_final: 0.7456 (ttpp) REVERT: B 84 MET cc_start: 0.8947 (mtt) cc_final: 0.8700 (mtt) REVERT: B 139 MET cc_start: 0.7809 (tpp) cc_final: 0.7485 (tpt) REVERT: B 157 ARG cc_start: 0.7600 (mtt90) cc_final: 0.6793 (mtt-85) REVERT: B 269 ARG cc_start: 0.7487 (ttt-90) cc_final: 0.7024 (ttt180) REVERT: C 66 ARG cc_start: 0.6940 (ttt90) cc_final: 0.6648 (ttt180) REVERT: C 184 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7750 (mtm180) REVERT: C 241 ARG cc_start: 0.8249 (ttm170) cc_final: 0.6921 (mmp80) REVERT: D 39 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.6647 (ttm110) REVERT: D 40 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7625 (mm-30) REVERT: D 44 VAL cc_start: 0.6891 (t) cc_final: 0.6572 (m) outliers start: 34 outliers final: 16 residues processed: 136 average time/residue: 0.6048 time to fit residues: 88.0909 Evaluate side-chains 128 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL 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 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 48 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 76 THR 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: 3.9990 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.0570 chunk 122 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3443 r_free = 0.3443 target = 0.116235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.091089 restraints weight = 15207.702| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.89 r_work: 0.2969 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.003 0.037 11235 Z= 0.120 Angle : 0.608 14.291 15352 Z= 0.292 Chirality : 0.043 0.241 1815 Planarity : 0.004 0.043 1840 Dihedral : 10.464 109.491 2184 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.37 % Allowed : 11.81 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.96 (0.24), residues: 1303 helix: 2.16 (0.20), residues: 713 sheet: -0.91 (0.44), residues: 141 loop : -1.41 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 114 TYR 0.015 0.001 TYR A 337 PHE 0.029 0.001 PHE A 302 TRP 0.011 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00267 (11210) covalent geometry : angle 0.59333 (15281) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.56535 ( 8) hydrogen bonds : bond 0.04103 ( 560) hydrogen bonds : angle 3.89879 ( 1623) link_BETA1-3 : bond 0.00902 ( 1) link_BETA1-3 : angle 1.65786 ( 3) link_BETA1-4 : bond 0.00364 ( 7) link_BETA1-4 : angle 1.63982 ( 21) link_BETA1-6 : bond 0.01457 ( 1) link_BETA1-6 : angle 2.44027 ( 3) link_NAG-ASN : bond 0.00425 ( 12) link_NAG-ASN : angle 2.40833 ( 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 155 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7808 (mtp-110) REVERT: A 108 MET cc_start: 0.9095 (mmm) cc_final: 0.8663 (tpp) REVERT: A 114 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7061 (mtp-110) REVERT: A 253 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8648 (t70) REVERT: A 364 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: A 388 GLU cc_start: 0.8149 (tp30) cc_final: 0.7215 (mp0) REVERT: A 391 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8139 (ttm110) REVERT: A 561 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8426 (t) REVERT: A 644 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: A 666 LYS cc_start: 0.7972 (tptt) cc_final: 0.7426 (ttpp) REVERT: B 84 MET cc_start: 0.8941 (mtt) cc_final: 0.8702 (mtt) REVERT: B 139 MET cc_start: 0.7747 (tpp) cc_final: 0.7399 (tpt) REVERT: B 157 ARG cc_start: 0.7583 (mtt90) cc_final: 0.6767 (mtt-85) REVERT: B 269 ARG cc_start: 0.7480 (ttt-90) cc_final: 0.6981 (ttt180) REVERT: B 280 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7352 (pt0) REVERT: C 66 ARG cc_start: 0.7013 (ttt90) cc_final: 0.6669 (ttt180) REVERT: C 184 ARG cc_start: 0.8004 (mtp180) cc_final: 0.7702 (mtm180) REVERT: C 241 ARG cc_start: 0.8221 (ttm170) cc_final: 0.6838 (mmm160) REVERT: D 39 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6746 (ttm110) REVERT: D 40 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7614 (mm-30) REVERT: D 44 VAL cc_start: 0.6864 (t) cc_final: 0.6530 (m) outliers start: 38 outliers final: 18 residues processed: 138 average time/residue: 0.5691 time to fit residues: 84.5044 Evaluate side-chains 132 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 75 VAL 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 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: 3.9990 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.113888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089187 restraints weight = 15053.027| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.84 r_work: 0.2936 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2727 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= 0.161 Angle : 0.658 14.485 15352 Z= 0.316 Chirality : 0.045 0.240 1815 Planarity : 0.004 0.041 1840 Dihedral : 10.495 108.221 2184 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.11 % Allowed : 12.52 % 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: 0.91 (0.24), residues: 1303 helix: 2.09 (0.20), residues: 716 sheet: -1.02 (0.43), residues: 139 loop : -1.36 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 114 TYR 0.016 0.002 TYR A 337 PHE 0.030 0.002 PHE A 302 TRP 0.011 0.001 TRP D 58 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00379 (11210) covalent geometry : angle 0.64197 (15281) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.69127 ( 8) hydrogen bonds : bond 0.04614 ( 560) hydrogen bonds : angle 3.94456 ( 1623) link_BETA1-3 : bond 0.00865 ( 1) link_BETA1-3 : angle 1.85196 ( 3) link_BETA1-4 : bond 0.00333 ( 7) link_BETA1-4 : angle 1.76684 ( 21) link_BETA1-6 : bond 0.01535 ( 1) link_BETA1-6 : angle 2.54569 ( 3) link_NAG-ASN : bond 0.00433 ( 12) link_NAG-ASN : angle 2.59248 ( 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 143 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7785 (mtp-110) REVERT: A 108 MET cc_start: 0.9105 (mmm) cc_final: 0.8679 (tpp) REVERT: A 253 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8678 (t70) REVERT: A 364 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: A 388 GLU cc_start: 0.8178 (tp30) cc_final: 0.7217 (mp0) REVERT: A 391 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8167 (ttm110) REVERT: A 644 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: A 666 LYS cc_start: 0.8026 (tptt) cc_final: 0.7461 (ttpp) REVERT: B 84 MET cc_start: 0.8925 (mtt) cc_final: 0.8686 (mtt) REVERT: B 139 MET cc_start: 0.7819 (tpp) cc_final: 0.7479 (tpt) REVERT: B 157 ARG cc_start: 0.7567 (mtt90) cc_final: 0.6813 (mtt-85) REVERT: B 269 ARG cc_start: 0.7508 (ttt-90) cc_final: 0.7002 (ttt180) REVERT: C 66 ARG cc_start: 0.7038 (ttt90) cc_final: 0.6694 (ttt180) REVERT: C 184 ARG cc_start: 0.8011 (mtp180) cc_final: 0.7694 (mtm180) REVERT: C 241 ARG cc_start: 0.8196 (ttm170) cc_final: 0.6802 (mmm160) REVERT: D 39 ARG cc_start: 0.7251 (ttm-80) cc_final: 0.6697 (ttm110) REVERT: D 40 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7591 (mm-30) REVERT: D 44 VAL cc_start: 0.6861 (t) cc_final: 0.6529 (m) outliers start: 35 outliers final: 20 residues processed: 130 average time/residue: 0.6079 time to fit residues: 84.6154 Evaluate side-chains 131 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 75 VAL 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 273 GLU 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 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 76 THR 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: 2.9990 chunk 99 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3425 r_free = 0.3425 target = 0.114905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.090158 restraints weight = 15281.568| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.87 r_work: 0.2955 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11235 Z= 0.132 Angle : 0.619 14.439 15352 Z= 0.298 Chirality : 0.043 0.241 1815 Planarity : 0.004 0.041 1840 Dihedral : 10.285 105.568 2184 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.31 % Allowed : 13.59 % 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: 1.07 (0.24), residues: 1303 helix: 2.21 (0.20), residues: 716 sheet: -0.96 (0.44), residues: 139 loop : -1.25 (0.30), residues: 448 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 0.030 0.001 PHE A 302 TRP 0.012 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00300 (11210) covalent geometry : angle 0.60397 (15281) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.55889 ( 8) hydrogen bonds : bond 0.04241 ( 560) hydrogen bonds : angle 3.90160 ( 1623) link_BETA1-3 : bond 0.00840 ( 1) link_BETA1-3 : angle 1.80597 ( 3) link_BETA1-4 : bond 0.00341 ( 7) link_BETA1-4 : angle 1.62192 ( 21) link_BETA1-6 : bond 0.01585 ( 1) link_BETA1-6 : angle 2.64939 ( 3) link_NAG-ASN : bond 0.00404 ( 12) link_NAG-ASN : angle 2.42240 ( 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 : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7792 (mtp-110) REVERT: A 108 MET cc_start: 0.9091 (mmm) cc_final: 0.8674 (tpp) REVERT: A 364 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: A 388 GLU cc_start: 0.8170 (tp30) cc_final: 0.7202 (mp0) REVERT: A 391 ARG cc_start: 0.8479 (ttm170) cc_final: 0.8166 (ttm110) REVERT: A 644 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: A 666 LYS cc_start: 0.7981 (tptt) cc_final: 0.7444 (ttpp) REVERT: B 84 MET cc_start: 0.8935 (mtt) cc_final: 0.8689 (mtt) REVERT: B 139 MET cc_start: 0.7810 (tpp) cc_final: 0.7476 (tpt) REVERT: B 157 ARG cc_start: 0.7564 (mtt90) cc_final: 0.6753 (mtt-85) REVERT: B 269 ARG cc_start: 0.7503 (ttt-90) cc_final: 0.6974 (ttt180) REVERT: C 66 ARG cc_start: 0.7065 (ttt90) cc_final: 0.6676 (ttt180) REVERT: C 184 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7660 (mtm180) REVERT: C 241 ARG cc_start: 0.8172 (ttm170) cc_final: 0.6728 (mmm160) REVERT: C 243 LEU cc_start: 0.7910 (mt) cc_final: 0.7688 (mt) REVERT: D 39 ARG cc_start: 0.7242 (ttm-80) cc_final: 0.6697 (ttm110) REVERT: D 40 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7569 (mm-30) REVERT: D 44 VAL cc_start: 0.6864 (t) cc_final: 0.6524 (m) outliers start: 26 outliers final: 21 residues processed: 126 average time/residue: 0.6238 time to fit residues: 84.1162 Evaluate side-chains 131 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 167 LEU 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 273 GLU 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 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 76 THR 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: 2.9990 chunk 117 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 95 optimal weight: 0.0670 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.115266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.090533 restraints weight = 15141.186| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.86 r_work: 0.2959 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2856 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= 0.128 Angle : 0.616 14.380 15352 Z= 0.297 Chirality : 0.043 0.237 1815 Planarity : 0.004 0.041 1840 Dihedral : 10.063 101.917 2184 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.75 % Allowed : 13.06 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.15 (0.24), residues: 1303 helix: 2.27 (0.20), residues: 717 sheet: -0.92 (0.44), residues: 139 loop : -1.22 (0.30), residues: 447 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 0.012 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00290 (11210) covalent geometry : angle 0.60182 (15281) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.53620 ( 8) hydrogen bonds : bond 0.04162 ( 560) hydrogen bonds : angle 3.87611 ( 1623) link_BETA1-3 : bond 0.00899 ( 1) link_BETA1-3 : angle 1.88194 ( 3) link_BETA1-4 : bond 0.00329 ( 7) link_BETA1-4 : angle 1.59553 ( 21) link_BETA1-6 : bond 0.01548 ( 1) link_BETA1-6 : angle 2.78097 ( 3) link_NAG-ASN : bond 0.00393 ( 12) link_NAG-ASN : angle 2.37745 ( 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: 31 poor density : 112 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7804 (mtp-110) REVERT: A 108 MET cc_start: 0.9083 (mmm) cc_final: 0.8678 (tpp) REVERT: A 253 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8657 (t70) REVERT: A 364 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: A 388 GLU cc_start: 0.8163 (tp30) cc_final: 0.7199 (mp0) REVERT: A 391 ARG cc_start: 0.8455 (ttm170) cc_final: 0.8156 (ttm110) REVERT: A 644 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: A 666 LYS cc_start: 0.7950 (tptt) cc_final: 0.7402 (ttpp) REVERT: B 84 MET cc_start: 0.8928 (mtt) cc_final: 0.8680 (mtt) REVERT: B 139 MET cc_start: 0.7820 (tpp) cc_final: 0.7518 (tpt) REVERT: B 157 ARG cc_start: 0.7598 (mtt90) cc_final: 0.6782 (mtt-85) REVERT: B 269 ARG cc_start: 0.7510 (ttt-90) cc_final: 0.6968 (ttt180) REVERT: C 66 ARG cc_start: 0.7055 (ttt90) cc_final: 0.6668 (ttt180) REVERT: C 184 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7647 (mtm180) REVERT: C 241 ARG cc_start: 0.8170 (ttm170) cc_final: 0.6738 (mmm160) REVERT: C 243 LEU cc_start: 0.7910 (mt) cc_final: 0.7690 (mt) REVERT: D 39 ARG cc_start: 0.7237 (ttm-80) cc_final: 0.6697 (ttm110) REVERT: D 40 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7564 (mm-30) REVERT: D 44 VAL cc_start: 0.6882 (t) cc_final: 0.6537 (m) outliers start: 31 outliers final: 23 residues processed: 133 average time/residue: 0.6624 time to fit residues: 94.4886 Evaluate side-chains 133 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 75 VAL 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 273 GLU 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 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 76 THR 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: 0.9980 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 95 optimal weight: 0.0370 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.115064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.090324 restraints weight = 15173.424| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.87 r_work: 0.2956 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11235 Z= 0.132 Angle : 0.624 14.375 15352 Z= 0.300 Chirality : 0.044 0.236 1815 Planarity : 0.004 0.041 1840 Dihedral : 9.955 98.863 2184 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.75 % Allowed : 12.88 % 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: 1.16 (0.24), residues: 1303 helix: 2.28 (0.20), residues: 717 sheet: -0.97 (0.44), residues: 137 loop : -1.22 (0.30), residues: 449 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 0.012 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00303 (11210) covalent geometry : angle 0.60915 (15281) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.58467 ( 8) hydrogen bonds : bond 0.04226 ( 560) hydrogen bonds : angle 3.87590 ( 1623) link_BETA1-3 : bond 0.00852 ( 1) link_BETA1-3 : angle 1.89060 ( 3) link_BETA1-4 : bond 0.00327 ( 7) link_BETA1-4 : angle 1.60712 ( 21) link_BETA1-6 : bond 0.01558 ( 1) link_BETA1-6 : angle 2.89457 ( 3) link_NAG-ASN : bond 0.00395 ( 12) link_NAG-ASN : angle 2.39073 ( 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 140 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7795 (mtp-110) REVERT: A 108 MET cc_start: 0.9078 (mmm) cc_final: 0.8676 (tpp) REVERT: A 253 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8650 (t70) REVERT: A 364 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: A 388 GLU cc_start: 0.8171 (tp30) cc_final: 0.7205 (mp0) REVERT: A 391 ARG cc_start: 0.8457 (ttm170) cc_final: 0.8161 (ttm110) REVERT: A 644 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: A 666 LYS cc_start: 0.7949 (tptt) cc_final: 0.7400 (ttpp) REVERT: B 84 MET cc_start: 0.8939 (mtt) cc_final: 0.8693 (mtt) REVERT: B 139 MET cc_start: 0.7719 (tpp) cc_final: 0.7072 (mtp) REVERT: B 157 ARG cc_start: 0.7588 (mtt90) cc_final: 0.6804 (mtt-85) REVERT: B 269 ARG cc_start: 0.7589 (ttt-90) cc_final: 0.7059 (ttt180) REVERT: C 66 ARG cc_start: 0.7054 (ttt90) cc_final: 0.6669 (ttt180) REVERT: C 184 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7658 (mtm180) REVERT: C 241 ARG cc_start: 0.8199 (ttm170) cc_final: 0.6722 (mmm160) REVERT: D 39 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6698 (ttm110) REVERT: D 40 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7564 (mm-30) REVERT: D 44 VAL cc_start: 0.6869 (t) cc_final: 0.6527 (m) outliers start: 31 outliers final: 22 residues processed: 128 average time/residue: 0.6607 time to fit residues: 90.7318 Evaluate side-chains 134 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 66 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 160 ARG 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 282 LEU Chi-restraints excluded: chain B residue 286 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 76 THR 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: 1.9990 chunk 99 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 0.0040 chunk 63 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 52 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** 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 = 0.3417 r_free = 0.3417 target = 0.114300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.089526 restraints weight = 15182.112| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.86 r_work: 0.2941 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11235 Z= 0.147 Angle : 0.644 14.483 15352 Z= 0.310 Chirality : 0.044 0.230 1815 Planarity : 0.004 0.041 1840 Dihedral : 9.896 94.761 2184 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.13 % Allowed : 13.59 % Favored : 84.28 % 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: 1.14 (0.24), residues: 1303 helix: 2.28 (0.19), residues: 716 sheet: -0.95 (0.44), residues: 135 loop : -1.24 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 114 TYR 0.015 0.001 TYR A 337 PHE 0.030 0.002 PHE A 302 TRP 0.009 0.001 TRP C 209 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00342 (11210) covalent geometry : angle 0.62930 (15281) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.65234 ( 8) hydrogen bonds : bond 0.04431 ( 560) hydrogen bonds : angle 3.90283 ( 1623) link_BETA1-3 : bond 0.00826 ( 1) link_BETA1-3 : angle 1.94634 ( 3) link_BETA1-4 : bond 0.00334 ( 7) link_BETA1-4 : angle 1.69041 ( 21) link_BETA1-6 : bond 0.01508 ( 1) link_BETA1-6 : angle 3.03531 ( 3) link_NAG-ASN : bond 0.00409 ( 12) link_NAG-ASN : angle 2.47981 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3889.93 seconds wall clock time: 66 minutes 52.31 seconds (4012.31 seconds total)