Starting phenix.real_space_refine on Wed Jul 30 03:42:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d8x_30614/07_2025/7d8x_30614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d8x_30614/07_2025/7d8x_30614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d8x_30614/07_2025/7d8x_30614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d8x_30614/07_2025/7d8x_30614.map" model { file = "/net/cci-nas-00/data/ceres_data/7d8x_30614/07_2025/7d8x_30614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d8x_30614/07_2025/7d8x_30614.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.45, per 1000 atoms: 0.68 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: 3.10 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.13 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: 3.12 Time building geometry restraints manager: 3.48 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.080 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:14.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.680 ------------------------------------------------------------------------------- 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 : 3.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.054 0.005 TRP C 227 HIS 0.025 0.004 HIS C 197 PHE 0.052 0.004 PHE C 132 TYR 0.036 0.004 TYR A 565 ARG 0.020 0.002 ARG A 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00971 ( 12) link_NAG-ASN : angle 5.10737 ( 36) link_BETA1-4 : bond 0.00564 ( 7) link_BETA1-4 : angle 2.75622 ( 21) hydrogen bonds : bond 0.18706 ( 560) hydrogen bonds : angle 6.83997 ( 1623) link_BETA1-6 : bond 0.00284 ( 1) link_BETA1-6 : angle 1.91090 ( 3) SS BOND : bond 0.00838 ( 4) SS BOND : angle 2.16524 ( 8) link_BETA1-3 : bond 0.00093 ( 1) link_BETA1-3 : angle 1.05217 ( 3) covalent geometry : bond 0.01016 (11210) covalent geometry : angle 1.12549 (15281) *********************** 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 : 1.098 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: 1.3736 time to fit residues: 307.3962 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 : 1.209 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 313 GLN A 355 GLN A 358 ASN A 454 GLN A 531 ASN A 553 HIS A 606 GLN B 214 HIS B 454 GLN D 8 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.093086 restraints weight = 15004.280| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.87 r_work: 0.2999 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1763 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= 0.147 Angle : 0.709 13.954 15352 Z= 0.343 Chirality : 0.045 0.257 1815 Planarity : 0.005 0.042 1840 Dihedral : 13.287 114.975 2186 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.40 % Allowed : 7.99 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.22), residues: 1303 helix: 0.41 (0.19), residues: 707 sheet: -1.10 (0.44), residues: 129 loop : -2.11 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 209 HIS 0.007 0.001 HIS C 197 PHE 0.035 0.002 PHE A 302 TYR 0.016 0.002 TYR A 337 ARG 0.005 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 12) link_NAG-ASN : angle 3.47014 ( 36) link_BETA1-4 : bond 0.00470 ( 7) link_BETA1-4 : angle 1.66698 ( 21) hydrogen bonds : bond 0.05378 ( 560) hydrogen bonds : angle 4.50004 ( 1623) link_BETA1-6 : bond 0.01475 ( 1) link_BETA1-6 : angle 1.94637 ( 3) SS BOND : bond 0.00538 ( 4) SS BOND : angle 1.57904 ( 8) link_BETA1-3 : bond 0.00990 ( 1) link_BETA1-3 : angle 1.94131 ( 3) covalent geometry : bond 0.00322 (11210) covalent geometry : angle 0.68554 (15281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8102 (mppt) REVERT: A 108 MET cc_start: 0.9286 (mmm) cc_final: 0.8836 (tpp) REVERT: A 364 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: A 388 GLU cc_start: 0.8052 (tp30) cc_final: 0.7244 (mp0) REVERT: A 391 ARG cc_start: 0.8348 (ttm110) cc_final: 0.8111 (ttp80) REVERT: A 619 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7730 (ptt-90) REVERT: A 644 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: A 666 LYS cc_start: 0.8009 (tptt) cc_final: 0.7536 (ttpt) REVERT: A 681 ILE cc_start: 0.8612 (mt) cc_final: 0.8402 (mm) REVERT: B 84 MET cc_start: 0.8950 (mtt) cc_final: 0.8705 (mtt) REVERT: B 139 MET cc_start: 0.7799 (tpp) cc_final: 0.7449 (tpt) REVERT: B 157 ARG cc_start: 0.7786 (mtt90) cc_final: 0.6900 (mtt-85) REVERT: B 269 ARG cc_start: 0.7389 (ttt-90) cc_final: 0.7122 (ttt180) REVERT: C 66 ARG cc_start: 0.6686 (ttt90) cc_final: 0.6448 (ttt180) REVERT: C 98 ASP cc_start: 0.8423 (t70) cc_final: 0.8211 (t0) REVERT: C 184 ARG cc_start: 0.8060 (mtp180) cc_final: 0.7800 (mtm180) REVERT: C 241 ARG cc_start: 0.8090 (ttm170) cc_final: 0.7023 (mmp-170) REVERT: D 39 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6633 (ttm170) REVERT: D 40 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7793 (mm-30) REVERT: D 44 VAL cc_start: 0.6873 (t) cc_final: 0.6518 (m) outliers start: 27 outliers final: 10 residues processed: 152 average time/residue: 1.3881 time to fit residues: 226.9149 Evaluate side-chains 127 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 C residue 57 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 9 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 66 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 385 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 = 0.3475 r_free = 0.3475 target = 0.118275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.093820 restraints weight = 15223.456| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.87 r_work: 0.3015 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11235 Z= 0.117 Angle : 0.621 14.014 15352 Z= 0.299 Chirality : 0.043 0.249 1815 Planarity : 0.004 0.040 1840 Dihedral : 11.381 114.797 2184 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.37 % Allowed : 8.79 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1303 helix: 1.38 (0.20), residues: 708 sheet: -1.01 (0.44), residues: 141 loop : -1.83 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 209 HIS 0.005 0.001 HIS C 197 PHE 0.031 0.001 PHE A 302 TYR 0.014 0.001 TYR A 337 ARG 0.009 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 12) link_NAG-ASN : angle 2.68099 ( 36) link_BETA1-4 : bond 0.00388 ( 7) link_BETA1-4 : angle 1.55053 ( 21) hydrogen bonds : bond 0.04383 ( 560) hydrogen bonds : angle 4.14914 ( 1623) link_BETA1-6 : bond 0.01541 ( 1) link_BETA1-6 : angle 2.15328 ( 3) SS BOND : bond 0.00261 ( 4) SS BOND : angle 0.67907 ( 8) link_BETA1-3 : bond 0.00999 ( 1) link_BETA1-3 : angle 1.46638 ( 3) covalent geometry : bond 0.00250 (11210) covalent geometry : angle 0.60421 (15281) *********************** 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 165 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9197 (mmm) cc_final: 0.8741 (tpp) REVERT: A 253 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8465 (t70) REVERT: A 364 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: A 388 GLU cc_start: 0.8038 (tp30) cc_final: 0.7277 (mp0) REVERT: A 391 ARG cc_start: 0.8304 (ttm110) cc_final: 0.8059 (ttp80) REVERT: A 561 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8335 (t) REVERT: A 619 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8058 (ptt-90) REVERT: A 644 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: A 666 LYS cc_start: 0.7915 (tptt) cc_final: 0.7404 (ttpt) REVERT: A 681 ILE cc_start: 0.8630 (mt) cc_final: 0.8423 (mm) REVERT: B 84 MET cc_start: 0.8942 (mtt) cc_final: 0.8674 (mtt) REVERT: B 139 MET cc_start: 0.7791 (tpp) cc_final: 0.7439 (tpt) REVERT: B 157 ARG cc_start: 0.7654 (mtt90) cc_final: 0.6826 (mtt-85) REVERT: B 269 ARG cc_start: 0.7459 (ttt-90) cc_final: 0.7119 (ttt180) REVERT: C 66 ARG cc_start: 0.6658 (ttt90) cc_final: 0.6410 (ttt180) REVERT: C 184 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7711 (mtm180) REVERT: C 240 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6396 (tt0) REVERT: C 241 ARG cc_start: 0.8158 (ttm170) cc_final: 0.6893 (mmp80) REVERT: D 39 ARG cc_start: 0.7225 (ttm-80) cc_final: 0.6650 (ttm110) REVERT: D 40 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7760 (mm-30) REVERT: D 44 VAL cc_start: 0.6813 (t) cc_final: 0.6379 (m) outliers start: 38 outliers final: 9 residues processed: 151 average time/residue: 1.3421 time to fit residues: 217.9245 Evaluate side-chains 131 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 364 GLU 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 B residue 241 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain D residue 51 SER 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 66 optimal weight: 0.0070 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.116157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.090958 restraints weight = 14959.292| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.88 r_work: 0.2968 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11235 Z= 0.141 Angle : 0.642 14.283 15352 Z= 0.310 Chirality : 0.044 0.234 1815 Planarity : 0.004 0.041 1840 Dihedral : 10.863 113.655 2184 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.84 % Allowed : 10.57 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1303 helix: 1.73 (0.20), residues: 715 sheet: -1.12 (0.44), residues: 144 loop : -1.71 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.017 0.001 TYR A 337 ARG 0.004 0.000 ARG A 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 12) link_NAG-ASN : angle 2.66815 ( 36) link_BETA1-4 : bond 0.00350 ( 7) link_BETA1-4 : angle 1.75125 ( 21) hydrogen bonds : bond 0.04538 ( 560) hydrogen bonds : angle 4.01433 ( 1623) link_BETA1-6 : bond 0.01446 ( 1) link_BETA1-6 : angle 2.27090 ( 3) SS BOND : bond 0.00264 ( 4) SS BOND : angle 0.80081 ( 8) link_BETA1-3 : bond 0.00852 ( 1) link_BETA1-3 : angle 1.28907 ( 3) covalent geometry : bond 0.00326 (11210) covalent geometry : angle 0.62572 (15281) *********************** 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 150 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9165 (mmm) cc_final: 0.8652 (tpp) REVERT: A 253 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8559 (t70) REVERT: A 272 ASP cc_start: 0.7957 (p0) cc_final: 0.7721 (m-30) REVERT: A 364 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: A 388 GLU cc_start: 0.8113 (tp30) cc_final: 0.7181 (mp0) REVERT: A 391 ARG cc_start: 0.8368 (ttm110) cc_final: 0.8074 (ttm110) REVERT: A 500 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: A 561 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8394 (t) REVERT: A 619 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8035 (ptt-90) REVERT: A 644 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: A 666 LYS cc_start: 0.8002 (tptt) cc_final: 0.7616 (ptmm) REVERT: B 84 MET cc_start: 0.8972 (mtt) cc_final: 0.8709 (mtt) REVERT: B 139 MET cc_start: 0.7761 (tpp) cc_final: 0.7408 (tpt) REVERT: B 157 ARG cc_start: 0.7631 (mtt90) cc_final: 0.6811 (mtt-85) REVERT: B 269 ARG cc_start: 0.7559 (ttt-90) cc_final: 0.7085 (ttt180) REVERT: C 66 ARG cc_start: 0.6839 (ttt90) cc_final: 0.6557 (ttt180) REVERT: C 184 ARG cc_start: 0.8030 (mtp180) cc_final: 0.7753 (mtm180) REVERT: C 240 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6370 (tt0) REVERT: C 241 ARG cc_start: 0.8233 (ttm170) cc_final: 0.6937 (mmm160) REVERT: D 39 ARG cc_start: 0.7227 (ttm-80) cc_final: 0.6651 (ttm110) REVERT: D 40 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7834 (mm-30) outliers start: 32 outliers final: 13 residues processed: 139 average time/residue: 1.3746 time to fit residues: 205.1005 Evaluate side-chains 130 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE 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 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 114 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain D residue 51 SER 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 75 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 150 ASN A 444 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.088390 restraints weight = 15107.494| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.89 r_work: 0.2928 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11235 Z= 0.182 Angle : 0.689 14.525 15352 Z= 0.331 Chirality : 0.046 0.232 1815 Planarity : 0.004 0.042 1840 Dihedral : 10.872 112.166 2184 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.29 % Allowed : 11.28 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1303 helix: 1.79 (0.20), residues: 717 sheet: -1.02 (0.45), residues: 136 loop : -1.63 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 209 HIS 0.005 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.017 0.002 TYR A 337 ARG 0.004 0.001 ARG A 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 12) link_NAG-ASN : angle 2.78409 ( 36) link_BETA1-4 : bond 0.00354 ( 7) link_BETA1-4 : angle 1.87890 ( 21) hydrogen bonds : bond 0.04955 ( 560) hydrogen bonds : angle 4.04673 ( 1623) link_BETA1-6 : bond 0.01476 ( 1) link_BETA1-6 : angle 2.42741 ( 3) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.78874 ( 8) link_BETA1-3 : bond 0.00870 ( 1) link_BETA1-3 : angle 1.63342 ( 3) covalent geometry : bond 0.00434 (11210) covalent geometry : angle 0.67256 (15281) *********************** 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 146 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9128 (mmm) cc_final: 0.8712 (tpp) REVERT: A 253 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8569 (t70) REVERT: A 351 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8383 (mmmt) REVERT: A 364 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: A 388 GLU cc_start: 0.8128 (tp30) cc_final: 0.7173 (mp0) REVERT: A 391 ARG cc_start: 0.8462 (ttm170) cc_final: 0.8187 (ttm110) REVERT: A 500 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8584 (tt0) REVERT: A 644 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: A 666 LYS cc_start: 0.8074 (tptt) cc_final: 0.7522 (ttpp) REVERT: B 84 MET cc_start: 0.8940 (mtt) cc_final: 0.8680 (mtt) REVERT: B 139 MET cc_start: 0.7802 (tpp) cc_final: 0.7451 (tpt) REVERT: B 157 ARG cc_start: 0.7580 (mtt90) cc_final: 0.6787 (mtt-85) REVERT: B 269 ARG cc_start: 0.7469 (ttt-90) cc_final: 0.6336 (ttt180) REVERT: B 273 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: C 66 ARG cc_start: 0.6918 (ttt90) cc_final: 0.6623 (ttt180) REVERT: C 184 ARG cc_start: 0.8066 (mtp180) cc_final: 0.7785 (mtm180) REVERT: C 241 ARG cc_start: 0.8219 (ttm170) cc_final: 0.6858 (mmm160) REVERT: D 39 ARG cc_start: 0.7290 (ttm-80) cc_final: 0.6680 (ttm110) REVERT: D 40 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7859 (mm-30) outliers start: 37 outliers final: 18 residues processed: 132 average time/residue: 1.3778 time to fit residues: 195.0273 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 : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER 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 389 SER 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 0.0980 chunk 25 optimal weight: 0.0020 chunk 5 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.095084 restraints weight = 15202.881| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.90 r_work: 0.3034 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11235 Z= 0.100 Angle : 0.559 14.083 15352 Z= 0.270 Chirality : 0.042 0.253 1815 Planarity : 0.003 0.038 1840 Dihedral : 10.083 107.181 2184 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.69 % Allowed : 13.23 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1303 helix: 2.20 (0.20), residues: 716 sheet: -0.95 (0.45), residues: 139 loop : -1.38 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 PHE 0.032 0.001 PHE D 66 TYR 0.014 0.001 TYR A 94 ARG 0.004 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 12) link_NAG-ASN : angle 2.04528 ( 36) link_BETA1-4 : bond 0.00435 ( 7) link_BETA1-4 : angle 1.32428 ( 21) hydrogen bonds : bond 0.03464 ( 560) hydrogen bonds : angle 3.85955 ( 1623) link_BETA1-6 : bond 0.01671 ( 1) link_BETA1-6 : angle 2.50791 ( 3) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.55960 ( 8) link_BETA1-3 : bond 0.00961 ( 1) link_BETA1-3 : angle 1.51302 ( 3) covalent geometry : bond 0.00199 (11210) covalent geometry : angle 0.54717 (15281) *********************** 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 141 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9117 (mmm) cc_final: 0.8698 (tpp) REVERT: A 364 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: A 388 GLU cc_start: 0.8064 (tp30) cc_final: 0.7197 (mp0) REVERT: A 391 ARG cc_start: 0.8362 (ttm170) cc_final: 0.8103 (ttm110) REVERT: A 583 ARG cc_start: 0.7461 (ttm-80) cc_final: 0.6871 (ttt180) REVERT: A 666 LYS cc_start: 0.7882 (tptt) cc_final: 0.7466 (ptmm) REVERT: B 84 MET cc_start: 0.8943 (mtt) cc_final: 0.8696 (mtt) REVERT: B 139 MET cc_start: 0.7734 (tpp) cc_final: 0.7431 (tpt) REVERT: B 157 ARG cc_start: 0.7483 (mtt90) cc_final: 0.6695 (mtt-85) REVERT: B 269 ARG cc_start: 0.7513 (ttt-90) cc_final: 0.6442 (ttt180) REVERT: B 273 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: C 66 ARG cc_start: 0.7060 (ttt90) cc_final: 0.6684 (ttt180) REVERT: C 184 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7642 (mtm180) REVERT: C 241 ARG cc_start: 0.8177 (ttm170) cc_final: 0.6822 (mmm160) REVERT: D 39 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6690 (ttm110) REVERT: D 40 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7725 (mm-30) REVERT: D 100 THR cc_start: 0.8346 (m) cc_final: 0.8036 (p) outliers start: 19 outliers final: 7 residues processed: 130 average time/residue: 1.3534 time to fit residues: 188.9969 Evaluate side-chains 120 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 286 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 28 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 84 optimal weight: 0.1980 chunk 109 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 60 optimal weight: 0.0570 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 GLN ** 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 = 0.3458 r_free = 0.3458 target = 0.117206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.092046 restraints weight = 15305.562| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.89 r_work: 0.2988 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2776 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= 0.124 Angle : 0.594 13.997 15352 Z= 0.286 Chirality : 0.043 0.243 1815 Planarity : 0.004 0.035 1840 Dihedral : 9.983 104.757 2184 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.78 % Allowed : 13.59 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1303 helix: 2.28 (0.20), residues: 715 sheet: -0.89 (0.45), residues: 139 loop : -1.37 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 PHE 0.029 0.001 PHE A 302 TYR 0.014 0.001 TYR A 337 ARG 0.005 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 12) link_NAG-ASN : angle 2.25914 ( 36) link_BETA1-4 : bond 0.00322 ( 7) link_BETA1-4 : angle 1.51385 ( 21) hydrogen bonds : bond 0.03908 ( 560) hydrogen bonds : angle 3.84202 ( 1623) link_BETA1-6 : bond 0.01490 ( 1) link_BETA1-6 : angle 2.60463 ( 3) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.58355 ( 8) link_BETA1-3 : bond 0.00934 ( 1) link_BETA1-3 : angle 1.73562 ( 3) covalent geometry : bond 0.00281 (11210) covalent geometry : angle 0.58106 (15281) *********************** 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 128 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9089 (mmm) cc_final: 0.8669 (tpp) REVERT: A 364 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: A 388 GLU cc_start: 0.8082 (tp30) cc_final: 0.7183 (mp0) REVERT: A 391 ARG cc_start: 0.8376 (ttm170) cc_final: 0.8122 (ttm110) REVERT: A 666 LYS cc_start: 0.7945 (tptt) cc_final: 0.7582 (ptmm) REVERT: B 84 MET cc_start: 0.8956 (mtt) cc_final: 0.8708 (mtt) REVERT: B 139 MET cc_start: 0.7745 (tpp) cc_final: 0.7344 (tpt) REVERT: B 157 ARG cc_start: 0.7553 (mtt90) cc_final: 0.6719 (mtt-85) REVERT: B 269 ARG cc_start: 0.7555 (ttt-90) cc_final: 0.6505 (ttt180) REVERT: B 273 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: B 280 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7148 (pt0) REVERT: C 66 ARG cc_start: 0.7030 (ttt90) cc_final: 0.6654 (ttt180) REVERT: C 184 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7659 (mtm180) REVERT: C 241 ARG cc_start: 0.8167 (ttm170) cc_final: 0.6782 (mmm160) REVERT: D 39 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.6698 (ttm110) REVERT: D 40 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7755 (mm-30) outliers start: 20 outliers final: 10 residues processed: 121 average time/residue: 1.4978 time to fit residues: 194.1166 Evaluate side-chains 116 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 273 GLU 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 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 75 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 109 optimal weight: 0.0270 chunk 61 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 606 GLN ** 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 = 0.3395 r_free = 0.3395 target = 0.112711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.087775 restraints weight = 15074.827| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.85 r_work: 0.2914 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11235 Z= 0.211 Angle : 0.710 14.424 15352 Z= 0.341 Chirality : 0.047 0.232 1815 Planarity : 0.005 0.043 1840 Dihedral : 10.433 104.562 2184 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.13 % Allowed : 13.23 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1303 helix: 2.01 (0.19), residues: 718 sheet: -0.98 (0.45), residues: 135 loop : -1.40 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 209 HIS 0.005 0.001 HIS A 553 PHE 0.031 0.002 PHE A 302 TYR 0.017 0.002 TYR A 173 ARG 0.007 0.001 ARG A 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 12) link_NAG-ASN : angle 2.80192 ( 36) link_BETA1-4 : bond 0.00370 ( 7) link_BETA1-4 : angle 1.93945 ( 21) hydrogen bonds : bond 0.05099 ( 560) hydrogen bonds : angle 4.01098 ( 1623) link_BETA1-6 : bond 0.01440 ( 1) link_BETA1-6 : angle 2.68240 ( 3) SS BOND : bond 0.00290 ( 4) SS BOND : angle 0.83596 ( 8) link_BETA1-3 : bond 0.00834 ( 1) link_BETA1-3 : angle 2.09461 ( 3) covalent geometry : bond 0.00510 (11210) covalent geometry : angle 0.69254 (15281) *********************** 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 132 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9105 (mmm) cc_final: 0.8755 (tpp) REVERT: A 364 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: A 388 GLU cc_start: 0.8239 (tp30) cc_final: 0.7278 (mp0) REVERT: A 391 ARG cc_start: 0.8454 (ttm170) cc_final: 0.8200 (ttm110) REVERT: A 666 LYS cc_start: 0.8067 (tptt) cc_final: 0.7653 (ptmm) REVERT: B 84 MET cc_start: 0.8915 (mtt) cc_final: 0.8682 (mtt) REVERT: B 139 MET cc_start: 0.7795 (tpp) cc_final: 0.7101 (mtp) REVERT: B 157 ARG cc_start: 0.7541 (mtt90) cc_final: 0.6756 (mtt-85) REVERT: B 269 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.6967 (ttt180) REVERT: C 66 ARG cc_start: 0.6934 (ttt90) cc_final: 0.6565 (ttt-90) REVERT: C 184 ARG cc_start: 0.7990 (mtp180) cc_final: 0.7698 (mtm180) REVERT: C 241 ARG cc_start: 0.8154 (ttm170) cc_final: 0.6733 (mmm160) REVERT: C 243 LEU cc_start: 0.7884 (mt) cc_final: 0.7662 (mt) REVERT: D 39 ARG cc_start: 0.7318 (ttm-80) cc_final: 0.6738 (ttm110) REVERT: D 40 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7682 (mm-30) REVERT: D 44 VAL cc_start: 0.6912 (t) cc_final: 0.6576 (m) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 1.3372 time to fit residues: 175.6535 Evaluate side-chains 122 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 155 GLU 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 544 SER Chi-restraints excluded: chain A residue 696 VAL 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 416 ILE 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 83 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3416 r_free = 0.3416 target = 0.114209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089301 restraints weight = 15342.045| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.88 r_work: 0.2943 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2765 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= 0.143 Angle : 0.639 14.455 15352 Z= 0.308 Chirality : 0.044 0.237 1815 Planarity : 0.004 0.042 1840 Dihedral : 10.226 102.177 2184 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.31 % Allowed : 13.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1303 helix: 2.13 (0.19), residues: 717 sheet: -1.05 (0.44), residues: 137 loop : -1.27 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 PHE 0.031 0.001 PHE A 302 TYR 0.014 0.001 TYR A 337 ARG 0.003 0.000 ARG A 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 12) link_NAG-ASN : angle 2.49661 ( 36) link_BETA1-4 : bond 0.00350 ( 7) link_BETA1-4 : angle 1.68469 ( 21) hydrogen bonds : bond 0.04453 ( 560) hydrogen bonds : angle 3.93963 ( 1623) link_BETA1-6 : bond 0.01524 ( 1) link_BETA1-6 : angle 2.72839 ( 3) SS BOND : bond 0.00252 ( 4) SS BOND : angle 0.63359 ( 8) link_BETA1-3 : bond 0.00901 ( 1) link_BETA1-3 : angle 1.85852 ( 3) covalent geometry : bond 0.00332 (11210) covalent geometry : angle 0.62370 (15281) *********************** 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 136 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9074 (mmm) cc_final: 0.8645 (tpp) REVERT: A 364 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: A 388 GLU cc_start: 0.8180 (tp30) cc_final: 0.7213 (mp0) REVERT: A 391 ARG cc_start: 0.8432 (ttm170) cc_final: 0.8170 (ttm110) REVERT: A 666 LYS cc_start: 0.8002 (tptt) cc_final: 0.7599 (ptmm) REVERT: B 84 MET cc_start: 0.8931 (mtt) cc_final: 0.8690 (mtt) REVERT: B 139 MET cc_start: 0.7757 (tpp) cc_final: 0.7362 (tpt) REVERT: B 157 ARG cc_start: 0.7486 (mtt90) cc_final: 0.6718 (mtt-85) REVERT: B 269 ARG cc_start: 0.7497 (ttt-90) cc_final: 0.6953 (ttt180) REVERT: C 66 ARG cc_start: 0.6983 (ttt90) cc_final: 0.6669 (ttt180) REVERT: C 184 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7656 (mtm180) REVERT: C 241 ARG cc_start: 0.8168 (ttm170) cc_final: 0.6709 (mmm160) REVERT: C 243 LEU cc_start: 0.7866 (mt) cc_final: 0.7655 (mt) REVERT: D 39 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.6728 (ttm110) REVERT: D 40 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7550 (mm-30) REVERT: D 44 VAL cc_start: 0.6832 (t) cc_final: 0.6441 (m) outliers start: 26 outliers final: 18 residues processed: 126 average time/residue: 1.3867 time to fit residues: 187.8438 Evaluate side-chains 127 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 155 GLU 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 696 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 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 124 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3434 r_free = 0.3434 target = 0.115467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.090706 restraints weight = 15150.192| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.87 r_work: 0.2964 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11235 Z= 0.128 Angle : 0.612 14.414 15352 Z= 0.295 Chirality : 0.043 0.234 1815 Planarity : 0.004 0.041 1840 Dihedral : 9.925 97.051 2184 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.69 % Allowed : 14.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1303 helix: 2.29 (0.20), residues: 714 sheet: -0.97 (0.44), residues: 140 loop : -1.19 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 PHE 0.030 0.001 PHE A 302 TYR 0.014 0.001 TYR A 337 ARG 0.010 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 12) link_NAG-ASN : angle 2.37373 ( 36) link_BETA1-4 : bond 0.00342 ( 7) link_BETA1-4 : angle 1.58066 ( 21) hydrogen bonds : bond 0.04157 ( 560) hydrogen bonds : angle 3.88956 ( 1623) link_BETA1-6 : bond 0.01524 ( 1) link_BETA1-6 : angle 2.91494 ( 3) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.55679 ( 8) link_BETA1-3 : bond 0.00892 ( 1) link_BETA1-3 : angle 1.80816 ( 3) covalent geometry : bond 0.00292 (11210) covalent geometry : angle 0.59781 (15281) ********************** 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 127 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9080 (mmm) cc_final: 0.8678 (tpp) REVERT: A 364 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: A 388 GLU cc_start: 0.8165 (tp30) cc_final: 0.7221 (mp0) REVERT: A 391 ARG cc_start: 0.8477 (ttm170) cc_final: 0.8164 (ttm110) REVERT: A 666 LYS cc_start: 0.8010 (tptt) cc_final: 0.7586 (ptmm) REVERT: B 84 MET cc_start: 0.8944 (mtt) cc_final: 0.8692 (mtt) REVERT: B 139 MET cc_start: 0.7713 (tpp) cc_final: 0.7298 (tpt) REVERT: B 157 ARG cc_start: 0.7484 (mtt90) cc_final: 0.6684 (mtt-85) REVERT: B 269 ARG cc_start: 0.7472 (ttt-90) cc_final: 0.6974 (ttt180) REVERT: C 66 ARG cc_start: 0.7100 (ttt90) cc_final: 0.6717 (ttt180) REVERT: C 184 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7636 (mtm180) REVERT: C 241 ARG cc_start: 0.8149 (ttm170) cc_final: 0.6726 (mmm160) REVERT: C 243 LEU cc_start: 0.7884 (mt) cc_final: 0.7576 (OUTLIER) REVERT: D 39 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.6742 (ttm110) REVERT: D 40 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7552 (mm-30) REVERT: D 44 VAL cc_start: 0.6858 (t) cc_final: 0.6525 (m) outliers start: 19 outliers final: 18 residues processed: 121 average time/residue: 1.3640 time to fit residues: 177.3247 Evaluate side-chains 123 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 155 GLU 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 696 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 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 106 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3419 r_free = 0.3419 target = 0.114402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.089568 restraints weight = 15161.500| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.87 r_work: 0.2944 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11235 Z= 0.150 Angle : 0.642 14.436 15352 Z= 0.309 Chirality : 0.044 0.228 1815 Planarity : 0.004 0.042 1840 Dihedral : 9.883 93.467 2184 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.87 % Allowed : 13.68 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1303 helix: 2.22 (0.19), residues: 716 sheet: -0.94 (0.44), residues: 135 loop : -1.22 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 58 HIS 0.004 0.001 HIS A 553 PHE 0.030 0.002 PHE D 66 TYR 0.015 0.001 TYR A 337 ARG 0.004 0.000 ARG A 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 12) link_NAG-ASN : angle 2.49176 ( 36) link_BETA1-4 : bond 0.00335 ( 7) link_BETA1-4 : angle 1.69668 ( 21) hydrogen bonds : bond 0.04454 ( 560) hydrogen bonds : angle 3.91426 ( 1623) link_BETA1-6 : bond 0.01480 ( 1) link_BETA1-6 : angle 3.06535 ( 3) SS BOND : bond 0.00254 ( 4) SS BOND : angle 0.68163 ( 8) link_BETA1-3 : bond 0.00864 ( 1) link_BETA1-3 : angle 1.92413 ( 3) covalent geometry : bond 0.00351 (11210) covalent geometry : angle 0.62644 (15281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8301.50 seconds wall clock time: 141 minutes 55.24 seconds (8515.24 seconds total)