Starting phenix.real_space_refine on Fri Sep 11 20:04:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lqg_0944/09_2026/6lqg_0944.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lqg_0944/09_2026/6lqg_0944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6lqg_0944/09_2026/6lqg_0944.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lqg_0944/09_2026/6lqg_0944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lqg_0944/09_2026/6lqg_0944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lqg_0944/09_2026/6lqg_0944.map" model { file = "/net/cci-nas-00/data/ceres_data/6lqg_0944/09_2026/6lqg_0944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lqg_0944/09_2026/6lqg_0944.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 2 5.49 5 S 41 5.16 5 Cl 1 4.86 5 C 7116 2.51 5 N 1712 2.21 5 O 1979 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10855 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: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2453 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'EN9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'CLR': 3, 'PC1': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Time building chain proxies: 2.50, per 1000 atoms: 0.23 Number of scatterers: 10855 At special positions: 0 Unit cell: (110.191, 96.008, 133.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 41 16.00 P 2 15.00 F 4 9.00 O 1979 8.00 N 1712 7.00 C 7116 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 810 " - " ASN A 387 " " NAG A 818 " - " ASN A 506 " " NAG A 819 " - " ASN A 264 " " NAG A 820 " - " ASN A 187 " " NAG A 821 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 546.7 milliseconds 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 57.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.572A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.994A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.007A pdb=" N LYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.878A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.872A pdb=" N ARG A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.577A pdb=" N PHE A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 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 407 removed outlier: 4.044A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.725A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.823A pdb=" N ASN A 464 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.558A pdb=" N LEU A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 502 removed outlier: 3.720A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.922A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 removed outlier: 3.761A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.596A pdb=" N ASP A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.607A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.523A pdb=" N PHE A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.753A pdb=" N THR B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 156 removed outlier: 3.793A pdb=" N ARG B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 removed outlier: 3.913A pdb=" N ILE B 162 " --> pdb=" O CYS B 158 " (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: 3.995A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 404 through 429 removed outlier: 3.658A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 452 through 463 removed outlier: 4.351A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.575A pdb=" N PHE C 18 " --> pdb=" O PHE C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 60 removed outlier: 4.157A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 103 removed outlier: 3.623A pdb=" N TYR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 139 removed outlier: 3.737A pdb=" N MET C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.812A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.756A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.572A pdb=" N SER C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 21 removed outlier: 4.423A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) 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 43 removed outlier: 3.830A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 81 removed outlier: 3.607A pdb=" N ILE D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (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 44 removed outlier: 4.612A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR A 94 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ALA A 122 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 96 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N SER A 124 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A 98 " --> pdb=" O SER A 124 " (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: 6.919A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.913A 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: 6.656A 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 289 572 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3209 1.34 - 1.48: 3123 1.48 - 1.62: 4739 1.62 - 1.76: 2 1.76 - 1.90: 62 Bond restraints: 11135 Sorted by residual: bond pdb=" C29 EN9 B 701 " pdb=" C33 EN9 B 701 " ideal model delta sigma weight residual 1.461 1.609 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C21 EN9 B 701 " pdb=" S02 EN9 B 701 " ideal model delta sigma weight residual 1.772 1.901 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C17 EN9 B 701 " pdb=" C20 EN9 B 701 " ideal model delta sigma weight residual 1.504 1.620 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C33 EN9 B 701 " pdb=" N13 EN9 B 701 " ideal model delta sigma weight residual 1.368 1.463 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" N11 EN9 B 701 " pdb=" S02 EN9 B 701 " ideal model delta sigma weight residual 1.662 1.756 -0.094 2.00e-02 2.50e+03 2.20e+01 ... (remaining 11130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 14672 2.41 - 4.82: 432 4.82 - 7.23: 63 7.23 - 9.64: 21 9.64 - 12.05: 3 Bond angle restraints: 15191 Sorted by residual: angle pdb=" C GLY D 99 " pdb=" N THR D 100 " pdb=" CA THR D 100 " ideal model delta sigma weight residual 120.68 129.91 -9.23 1.52e+00 4.33e-01 3.69e+01 angle pdb=" C GLY A 504 " pdb=" N THR A 505 " pdb=" CA THR A 505 " ideal model delta sigma weight residual 121.54 129.85 -8.31 1.91e+00 2.74e-01 1.89e+01 angle pdb=" O07 EN9 B 701 " pdb=" S02 EN9 B 701 " pdb=" O08 EN9 B 701 " ideal model delta sigma weight residual 119.97 107.92 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CA PRO A 92 " pdb=" C PRO A 92 " pdb=" N PRO A 93 " ideal model delta sigma weight residual 117.93 122.68 -4.75 1.20e+00 6.94e-01 1.57e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 115.31 -4.61 1.22e+00 6.72e-01 1.43e+01 ... (remaining 15186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 6040 17.09 - 34.18: 221 34.18 - 51.27: 53 51.27 - 68.36: 4 68.36 - 85.45: 9 Dihedral angle restraints: 6327 sinusoidal: 2488 harmonic: 3839 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 -165.82 79.82 1 1.00e+01 1.00e-02 7.90e+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 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA VAL C 134 " pdb=" C VAL C 134 " pdb=" N ILE C 135 " pdb=" CA ILE C 135 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1662 0.095 - 0.190: 135 0.190 - 0.285: 7 0.285 - 0.380: 4 0.380 - 0.475: 3 Chirality restraints: 1811 Sorted by residual: 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 -2.02 -0.47 2.00e-01 2.50e+01 5.63e+00 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 -2.00 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C2 NAG A 810 " pdb=" C1 NAG A 810 " pdb=" C3 NAG A 810 " pdb=" N2 NAG A 810 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 1808 not shown) Planarity restraints: 1843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.020 2.00e-02 2.50e+03 1.84e-02 8.46e+00 pdb=" CG TRP C 227 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 36 " -0.020 2.00e-02 2.50e+03 1.62e-02 6.60e+00 pdb=" CG TRP D 36 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP D 36 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 36 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 36 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 36 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 336 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C ASP A 336 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP A 336 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 337 " 0.014 2.00e-02 2.50e+03 ... (remaining 1840 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 1 2.22 - 2.89: 3933 2.89 - 3.56: 14478 3.56 - 4.23: 24363 4.23 - 4.90: 42079 Nonbonded interactions: 84854 Sorted by model distance: nonbonded pdb=" NH1 ARG A 281 " pdb=" O ASP A 283 " model vdw 1.552 3.120 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.257 3.040 nonbonded pdb=" OG SER A 286 " pdb=" O VAL A 291 " model vdw 2.336 3.040 nonbonded pdb=" O GLN B 464 " pdb=" ND2 ASN C 207 " model vdw 2.337 3.120 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.343 3.040 ... (remaining 84849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.130 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.007 0.148 11159 Z= 0.334 Angle : 1.024 12.053 15259 Z= 0.515 Chirality : 0.058 0.475 1811 Planarity : 0.007 0.058 1832 Dihedral : 10.406 85.446 3841 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.27 % Allowed : 1.42 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.18), residues: 1305 helix: -1.81 (0.15), residues: 706 sheet: -1.95 (0.43), residues: 129 loop : -3.20 (0.22), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 429 TYR 0.032 0.002 TYR A 565 PHE 0.029 0.003 PHE C 179 TRP 0.047 0.004 TRP C 227 HIS 0.015 0.002 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.33 (11135) covalent geometry : angle 1.00559 / 0.51 (15191) SS BOND : bond 0.00803 / 0.41 ( 4) SS BOND : angle 1.96244 / 1.01 ( 8) hydrogen bonds : bond 0.13980 / 9.82 ( 572) hydrogen bonds : angle 5.90176 / 4.14 ( 1665) link_BETA1-3 : bond 0.00004 / 0.00 ( 1) link_BETA1-3 : angle 2.30737 / 1.68 ( 3) link_BETA1-4 : bond 0.00663 / 0.39 ( 7) link_BETA1-4 : angle 2.95832 / 1.89 ( 21) link_BETA1-6 : bond 0.00456 / 0.24 ( 1) link_BETA1-6 : angle 1.31331 / 1.03 ( 3) link_NAG-ASN : bond 0.01048 / 0.68 ( 11) link_NAG-ASN : angle 3.50482 / 2.49 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 209 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 688 TYR cc_start: 0.8548 (t80) cc_final: 0.8209 (t80) REVERT: B 115 TYR cc_start: 0.7034 (m-80) cc_final: 0.6814 (m-10) outliers start: 3 outliers final: 3 residues processed: 212 average time/residue: 0.1318 time to fit residues: 37.4132 Evaluate side-chains 122 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 91 ASN A 355 GLN A 358 ASN A 385 GLN A 454 GLN A 531 ASN B 112 GLN B 214 HIS C 68 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095804 restraints weight = 17372.102| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.11 r_work: 0.3003 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11159 Z= 0.137 Angle : 0.631 10.106 15259 Z= 0.307 Chirality : 0.043 0.352 1811 Planarity : 0.005 0.060 1832 Dihedral : 7.181 71.971 1529 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.77 % Allowed : 6.29 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.22), residues: 1305 helix: 0.36 (0.19), residues: 702 sheet: -1.24 (0.44), residues: 132 loop : -2.67 (0.24), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 543 TYR 0.013 0.001 TYR C 187 PHE 0.026 0.002 PHE A 302 TRP 0.020 0.002 TRP C 227 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (11135) covalent geometry : angle 0.61670 / 0.30 (15191) SS BOND : bond 0.00621 / 0.31 ( 4) SS BOND : angle 1.05189 / 0.68 ( 8) hydrogen bonds : bond 0.04756 / 3.21 ( 572) hydrogen bonds : angle 4.21257 / 2.97 ( 1665) link_BETA1-3 : bond 0.00382 / 0.20 ( 1) link_BETA1-3 : angle 2.57330 / 2.05 ( 3) link_BETA1-4 : bond 0.00455 / 0.28 ( 7) link_BETA1-4 : angle 1.79636 / 1.12 ( 21) link_BETA1-6 : bond 0.01126 / 0.59 ( 1) link_BETA1-6 : angle 2.04587 / 1.48 ( 3) link_NAG-ASN : bond 0.00454 / 0.29 ( 11) link_NAG-ASN : angle 2.44138 / 1.90 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8735 (tp40) REVERT: A 109 GLU cc_start: 0.8236 (mt-10) cc_final: 0.8036 (mm-30) REVERT: A 584 GLU cc_start: 0.7811 (mp0) cc_final: 0.7561 (mp0) REVERT: A 688 TYR cc_start: 0.8861 (t80) cc_final: 0.8463 (t80) REVERT: B 115 TYR cc_start: 0.7524 (m-80) cc_final: 0.7122 (m-10) REVERT: B 279 ASN cc_start: 0.7998 (m110) cc_final: 0.7794 (m-40) REVERT: B 419 CYS cc_start: 0.8412 (m) cc_final: 0.8127 (m) REVERT: C 109 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7688 (ttm110) REVERT: C 137 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8082 (mp) REVERT: C 240 GLN cc_start: 0.7593 (mt0) cc_final: 0.7257 (tm-30) outliers start: 20 outliers final: 14 residues processed: 148 average time/residue: 0.1060 time to fit residues: 22.6250 Evaluate side-chains 136 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 535 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.093708 restraints weight = 17385.875| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.11 r_work: 0.2972 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11159 Z= 0.146 Angle : 0.610 11.638 15259 Z= 0.294 Chirality : 0.042 0.340 1811 Planarity : 0.004 0.047 1832 Dihedral : 6.981 71.650 1529 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.84 % Allowed : 6.65 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.23), residues: 1305 helix: 1.12 (0.20), residues: 706 sheet: -1.07 (0.44), residues: 134 loop : -2.38 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 429 TYR 0.013 0.001 TYR C 218 PHE 0.027 0.002 PHE A 302 TRP 0.017 0.001 TRP D 36 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11135) covalent geometry : angle 0.59596 / 0.29 (15191) SS BOND : bond 0.00483 / 0.24 ( 4) SS BOND : angle 0.85470 / 0.57 ( 8) hydrogen bonds : bond 0.04555 / 3.08 ( 572) hydrogen bonds : angle 3.95301 / 2.79 ( 1665) link_BETA1-3 : bond 0.00302 / 0.16 ( 1) link_BETA1-3 : angle 2.19520 / 1.72 ( 3) link_BETA1-4 : bond 0.00352 / 0.23 ( 7) link_BETA1-4 : angle 1.70147 / 1.04 ( 21) link_BETA1-6 : bond 0.01194 / 0.63 ( 1) link_BETA1-6 : angle 1.99899 / 1.40 ( 3) link_NAG-ASN : bond 0.00404 / 0.25 ( 11) link_NAG-ASN : angle 2.34107 / 1.84 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8714 (tp40) REVERT: A 240 PHE cc_start: 0.8070 (m-80) cc_final: 0.7754 (m-80) REVERT: A 688 TYR cc_start: 0.8883 (t80) cc_final: 0.8442 (t80) REVERT: B 115 TYR cc_start: 0.7529 (m-80) cc_final: 0.7118 (m-10) REVERT: C 109 ARG cc_start: 0.7931 (ttm110) cc_final: 0.7707 (ttm110) REVERT: C 137 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8130 (mp) REVERT: C 240 GLN cc_start: 0.7743 (mt0) cc_final: 0.7353 (tm-30) outliers start: 32 outliers final: 24 residues processed: 153 average time/residue: 0.1037 time to fit residues: 22.9685 Evaluate side-chains 146 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 535 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.088252 restraints weight = 17478.156| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.10 r_work: 0.2884 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 11159 Z= 0.294 Angle : 0.753 12.380 15259 Z= 0.362 Chirality : 0.048 0.338 1811 Planarity : 0.005 0.044 1832 Dihedral : 7.488 72.004 1529 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.55 % Allowed : 7.45 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.23), residues: 1305 helix: 1.04 (0.20), residues: 712 sheet: -1.23 (0.42), residues: 140 loop : -2.34 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 429 TYR 0.019 0.002 TYR C 218 PHE 0.033 0.003 PHE A 302 TRP 0.023 0.002 TRP D 58 HIS 0.006 0.002 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.29 (11135) covalent geometry : angle 0.73594 / 0.36 (15191) SS BOND : bond 0.00656 / 0.33 ( 4) SS BOND : angle 1.17814 / 0.77 ( 8) hydrogen bonds : bond 0.05851 / 3.95 ( 572) hydrogen bonds : angle 4.15894 / 2.93 ( 1665) link_BETA1-3 : bond 0.00175 / 0.09 ( 1) link_BETA1-3 : angle 2.20275 / 1.67 ( 3) link_BETA1-4 : bond 0.00279 / 0.18 ( 7) link_BETA1-4 : angle 2.02349 / 1.22 ( 21) link_BETA1-6 : bond 0.01237 / 0.65 ( 1) link_BETA1-6 : angle 2.21973 / 1.61 ( 3) link_NAG-ASN : bond 0.00556 / 0.28 ( 11) link_NAG-ASN : angle 2.99733 / 2.39 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.399 Fit side-chains REVERT: A 63 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8615 (tp-100) REVERT: A 108 MET cc_start: 0.9000 (mmm) cc_final: 0.8597 (mmp) REVERT: A 253 ASP cc_start: 0.9305 (OUTLIER) cc_final: 0.8634 (t70) REVERT: A 310 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 688 TYR cc_start: 0.8915 (t80) cc_final: 0.8424 (t80) REVERT: B 115 TYR cc_start: 0.7509 (m-80) cc_final: 0.7124 (m-10) REVERT: B 249 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8474 (mp) REVERT: B 270 MET cc_start: 0.7380 (mmp) cc_final: 0.7159 (mmt) REVERT: C 109 ARG cc_start: 0.7978 (ttm110) cc_final: 0.7747 (ttm110) REVERT: C 137 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8326 (mp) REVERT: C 240 GLN cc_start: 0.7832 (mt0) cc_final: 0.7444 (tm-30) outliers start: 40 outliers final: 33 residues processed: 149 average time/residue: 0.1051 time to fit residues: 22.8080 Evaluate side-chains 148 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 535 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.091933 restraints weight = 17218.525| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.10 r_work: 0.2943 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11159 Z= 0.124 Angle : 0.602 11.943 15259 Z= 0.289 Chirality : 0.042 0.337 1811 Planarity : 0.003 0.034 1832 Dihedral : 7.092 70.839 1529 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.37 % Allowed : 8.33 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.24), residues: 1305 helix: 1.47 (0.20), residues: 714 sheet: -0.98 (0.43), residues: 138 loop : -2.13 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 269 TYR 0.011 0.001 TYR A 569 PHE 0.025 0.001 PHE A 302 TRP 0.015 0.001 TRP D 36 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11135) covalent geometry : angle 0.58927 / 0.29 (15191) SS BOND : bond 0.00257 / 0.13 ( 4) SS BOND : angle 0.55881 / 0.40 ( 8) hydrogen bonds : bond 0.04480 / 3.01 ( 572) hydrogen bonds : angle 3.86232 / 2.72 ( 1665) link_BETA1-3 : bond 0.00254 / 0.13 ( 1) link_BETA1-3 : angle 2.15210 / 1.68 ( 3) link_BETA1-4 : bond 0.00381 / 0.24 ( 7) link_BETA1-4 : angle 1.64284 / 0.99 ( 21) link_BETA1-6 : bond 0.01116 / 0.59 ( 1) link_BETA1-6 : angle 1.86775 / 1.29 ( 3) link_NAG-ASN : bond 0.00364 / 0.23 ( 11) link_NAG-ASN : angle 2.24448 / 1.76 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8687 (tp40) REVERT: A 253 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8362 (t70) REVERT: A 310 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 688 TYR cc_start: 0.8892 (t80) cc_final: 0.8405 (t80) REVERT: B 115 TYR cc_start: 0.7472 (m-80) cc_final: 0.7085 (m-10) REVERT: B 249 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8445 (mp) REVERT: B 270 MET cc_start: 0.7141 (mmp) cc_final: 0.6885 (mmt) REVERT: C 109 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7782 (ttm110) REVERT: C 137 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8287 (mp) REVERT: C 240 GLN cc_start: 0.7709 (mt0) cc_final: 0.7290 (tm-30) outliers start: 38 outliers final: 27 residues processed: 149 average time/residue: 0.1002 time to fit residues: 22.0823 Evaluate side-chains 147 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 18 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.090913 restraints weight = 17383.014| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.10 r_work: 0.2927 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11159 Z= 0.166 Angle : 0.630 11.839 15259 Z= 0.299 Chirality : 0.043 0.334 1811 Planarity : 0.004 0.034 1832 Dihedral : 7.037 70.665 1528 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.46 % Allowed : 8.69 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1305 helix: 1.56 (0.20), residues: 715 sheet: -0.99 (0.42), residues: 140 loop : -2.07 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.012 0.001 TYR A 569 PHE 0.027 0.002 PHE A 302 TRP 0.014 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (11135) covalent geometry : angle 0.61789 / 0.30 (15191) SS BOND : bond 0.00346 / 0.17 ( 4) SS BOND : angle 0.71614 / 0.46 ( 8) hydrogen bonds : bond 0.04617 / 3.10 ( 572) hydrogen bonds : angle 3.83990 / 2.70 ( 1665) link_BETA1-3 : bond 0.00265 / 0.14 ( 1) link_BETA1-3 : angle 2.04671 / 1.60 ( 3) link_BETA1-4 : bond 0.00301 / 0.20 ( 7) link_BETA1-4 : angle 1.70022 / 1.03 ( 21) link_BETA1-6 : bond 0.01092 / 0.57 ( 1) link_BETA1-6 : angle 1.92183 / 1.35 ( 3) link_NAG-ASN : bond 0.00375 / 0.21 ( 11) link_NAG-ASN : angle 2.30398 / 1.82 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8733 (tp40) REVERT: A 253 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8554 (t70) REVERT: A 310 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 688 TYR cc_start: 0.8908 (t80) cc_final: 0.8396 (t80) REVERT: B 115 TYR cc_start: 0.7506 (m-80) cc_final: 0.7139 (m-10) REVERT: B 249 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8474 (mp) REVERT: C 109 ARG cc_start: 0.8051 (ttm110) cc_final: 0.7837 (ttm110) REVERT: C 137 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8312 (mp) REVERT: C 240 GLN cc_start: 0.7636 (mt0) cc_final: 0.7218 (tm-30) outliers start: 39 outliers final: 32 residues processed: 151 average time/residue: 0.0998 time to fit residues: 22.2734 Evaluate side-chains 153 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088696 restraints weight = 17296.074| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.08 r_work: 0.2893 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11159 Z= 0.237 Angle : 0.695 12.336 15259 Z= 0.330 Chirality : 0.046 0.335 1811 Planarity : 0.004 0.032 1832 Dihedral : 7.253 71.261 1527 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.90 % Allowed : 9.13 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.24), residues: 1305 helix: 1.45 (0.20), residues: 716 sheet: -1.03 (0.42), residues: 140 loop : -2.10 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 342 TYR 0.015 0.002 TYR C 218 PHE 0.030 0.002 PHE A 302 TRP 0.013 0.002 TRP D 36 HIS 0.005 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 (11135) covalent geometry : angle 0.68130 / 0.33 (15191) SS BOND : bond 0.00454 / 0.23 ( 4) SS BOND : angle 0.88535 / 0.57 ( 8) hydrogen bonds : bond 0.05231 / 3.52 ( 572) hydrogen bonds : angle 3.96561 / 2.79 ( 1665) link_BETA1-3 : bond 0.00191 / 0.10 ( 1) link_BETA1-3 : angle 2.06982 / 1.60 ( 3) link_BETA1-4 : bond 0.00242 / 0.16 ( 7) link_BETA1-4 : angle 1.88418 / 1.13 ( 21) link_BETA1-6 : bond 0.01043 / 0.55 ( 1) link_BETA1-6 : angle 2.01046 / 1.43 ( 3) link_NAG-ASN : bond 0.00469 / 0.24 ( 11) link_NAG-ASN : angle 2.57256 / 2.04 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8784 (tp40) REVERT: A 253 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.8552 (t70) REVERT: A 310 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8241 (tm-30) REVERT: A 688 TYR cc_start: 0.8915 (t80) cc_final: 0.8390 (t80) REVERT: B 115 TYR cc_start: 0.7463 (m-80) cc_final: 0.7105 (m-10) REVERT: B 249 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8458 (mp) REVERT: B 269 ARG cc_start: 0.8021 (ttt180) cc_final: 0.7805 (ttt180) REVERT: C 109 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7838 (ttm110) REVERT: C 137 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8344 (mp) REVERT: C 240 GLN cc_start: 0.7692 (mt0) cc_final: 0.7293 (tm-30) outliers start: 44 outliers final: 34 residues processed: 153 average time/residue: 0.1036 time to fit residues: 23.1947 Evaluate side-chains 155 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 75 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.091438 restraints weight = 17228.591| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.08 r_work: 0.2936 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11159 Z= 0.135 Angle : 0.612 11.604 15259 Z= 0.291 Chirality : 0.042 0.333 1811 Planarity : 0.003 0.030 1832 Dihedral : 7.029 70.617 1527 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.46 % Allowed : 10.02 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1305 helix: 1.77 (0.20), residues: 709 sheet: -0.79 (0.43), residues: 138 loop : -1.94 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.012 0.001 TYR A 569 PHE 0.025 0.001 PHE A 302 TRP 0.014 0.001 TRP D 36 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (11135) covalent geometry : angle 0.60106 / 0.29 (15191) SS BOND : bond 0.00250 / 0.13 ( 4) SS BOND : angle 0.54921 / 0.38 ( 8) hydrogen bonds : bond 0.04364 / 2.93 ( 572) hydrogen bonds : angle 3.79178 / 2.67 ( 1665) link_BETA1-3 : bond 0.00278 / 0.15 ( 1) link_BETA1-3 : angle 2.04908 / 1.60 ( 3) link_BETA1-4 : bond 0.00359 / 0.23 ( 7) link_BETA1-4 : angle 1.61538 / 0.97 ( 21) link_BETA1-6 : bond 0.01140 / 0.60 ( 1) link_BETA1-6 : angle 1.88214 / 1.31 ( 3) link_NAG-ASN : bond 0.00329 / 0.20 ( 11) link_NAG-ASN : angle 2.14812 / 1.69 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8755 (tp40) REVERT: A 253 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8541 (t70) REVERT: A 688 TYR cc_start: 0.8897 (t80) cc_final: 0.8358 (t80) REVERT: B 115 TYR cc_start: 0.7416 (m-80) cc_final: 0.7057 (m-10) REVERT: B 249 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 269 ARG cc_start: 0.7957 (ttt180) cc_final: 0.7755 (ttt180) REVERT: C 137 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8328 (mp) REVERT: C 240 GLN cc_start: 0.7550 (mt0) cc_final: 0.7147 (tm-30) outliers start: 39 outliers final: 31 residues processed: 151 average time/residue: 0.0985 time to fit residues: 22.0430 Evaluate side-chains 155 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093449 restraints weight = 17174.738| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.08 r_work: 0.2971 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11159 Z= 0.111 Angle : 0.581 11.248 15259 Z= 0.276 Chirality : 0.041 0.336 1811 Planarity : 0.003 0.029 1832 Dihedral : 6.750 70.320 1527 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.93 % Allowed : 10.28 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1305 helix: 1.98 (0.20), residues: 713 sheet: -0.60 (0.44), residues: 132 loop : -1.87 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 377 TYR 0.011 0.001 TYR A 569 PHE 0.024 0.001 PHE A 302 TRP 0.013 0.001 TRP D 36 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11135) covalent geometry : angle 0.57132 / 0.27 (15191) SS BOND : bond 0.00224 / 0.11 ( 4) SS BOND : angle 0.54710 / 0.39 ( 8) hydrogen bonds : bond 0.03840 / 2.58 ( 572) hydrogen bonds : angle 3.66751 / 2.58 ( 1665) link_BETA1-3 : bond 0.00347 / 0.18 ( 1) link_BETA1-3 : angle 1.90664 / 1.51 ( 3) link_BETA1-4 : bond 0.00407 / 0.25 ( 7) link_BETA1-4 : angle 1.47059 / 0.90 ( 21) link_BETA1-6 : bond 0.01023 / 0.54 ( 1) link_BETA1-6 : angle 1.74802 / 1.23 ( 3) link_NAG-ASN : bond 0.00344 / 0.21 ( 11) link_NAG-ASN : angle 1.93020 / 1.51 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8536 (t70) REVERT: A 688 TYR cc_start: 0.8901 (t80) cc_final: 0.8360 (t80) REVERT: B 115 TYR cc_start: 0.7479 (m-80) cc_final: 0.7115 (m-10) REVERT: B 249 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 269 ARG cc_start: 0.7999 (ttt180) cc_final: 0.7792 (ttt180) REVERT: C 137 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8307 (mp) REVERT: C 240 GLN cc_start: 0.7477 (mt0) cc_final: 0.6988 (tm-30) outliers start: 33 outliers final: 25 residues processed: 149 average time/residue: 0.0972 time to fit residues: 21.6683 Evaluate side-chains 143 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 0.1980 chunk 116 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093287 restraints weight = 17206.312| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.09 r_work: 0.2967 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11159 Z= 0.115 Angle : 0.576 11.521 15259 Z= 0.274 Chirality : 0.041 0.331 1811 Planarity : 0.003 0.028 1832 Dihedral : 6.677 70.382 1527 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.84 % Allowed : 10.55 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1305 helix: 2.09 (0.20), residues: 714 sheet: -0.55 (0.43), residues: 132 loop : -1.78 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 377 TYR 0.014 0.001 TYR B 256 PHE 0.024 0.001 PHE A 302 TRP 0.012 0.001 TRP D 36 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11135) covalent geometry : angle 0.56629 / 0.27 (15191) SS BOND : bond 0.00215 / 0.11 ( 4) SS BOND : angle 0.55459 / 0.37 ( 8) hydrogen bonds : bond 0.03841 / 2.58 ( 572) hydrogen bonds : angle 3.64365 / 2.56 ( 1665) link_BETA1-3 : bond 0.00323 / 0.17 ( 1) link_BETA1-3 : angle 1.83104 / 1.44 ( 3) link_BETA1-4 : bond 0.00391 / 0.25 ( 7) link_BETA1-4 : angle 1.49688 / 0.93 ( 21) link_BETA1-6 : bond 0.00919 / 0.48 ( 1) link_BETA1-6 : angle 1.68758 / 1.22 ( 3) link_NAG-ASN : bond 0.00323 / 0.20 ( 11) link_NAG-ASN : angle 1.94810 / 1.53 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8569 (t70) REVERT: A 470 TRP cc_start: 0.8544 (p90) cc_final: 0.8335 (p90) REVERT: A 688 TYR cc_start: 0.8907 (t80) cc_final: 0.8363 (t80) REVERT: B 115 TYR cc_start: 0.7463 (m-80) cc_final: 0.7093 (m-10) REVERT: B 248 LEU cc_start: 0.9152 (mt) cc_final: 0.8946 (mt) REVERT: B 249 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8440 (mp) REVERT: C 137 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8283 (mp) REVERT: C 240 GLN cc_start: 0.7343 (mt0) cc_final: 0.6897 (tm-30) outliers start: 32 outliers final: 27 residues processed: 148 average time/residue: 0.0810 time to fit residues: 17.9769 Evaluate side-chains 149 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091304 restraints weight = 17370.908| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.08 r_work: 0.2936 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11159 Z= 0.160 Angle : 0.617 11.858 15259 Z= 0.293 Chirality : 0.043 0.333 1811 Planarity : 0.003 0.030 1832 Dihedral : 6.798 70.756 1527 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.10 % Allowed : 10.37 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1305 helix: 2.00 (0.20), residues: 715 sheet: -0.70 (0.42), residues: 136 loop : -1.80 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.028 0.001 TYR B 256 PHE 0.026 0.002 PHE A 302 TRP 0.011 0.001 TRP D 36 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (11135) covalent geometry : angle 0.60545 / 0.29 (15191) SS BOND : bond 0.00306 / 0.15 ( 4) SS BOND : angle 0.64903 / 0.41 ( 8) hydrogen bonds : bond 0.04355 / 2.93 ( 572) hydrogen bonds : angle 3.72533 / 2.62 ( 1665) link_BETA1-3 : bond 0.00264 / 0.14 ( 1) link_BETA1-3 : angle 1.84719 / 1.44 ( 3) link_BETA1-4 : bond 0.00303 / 0.21 ( 7) link_BETA1-4 : angle 1.63327 / 1.01 ( 21) link_BETA1-6 : bond 0.00835 / 0.44 ( 1) link_BETA1-6 : angle 1.71649 / 1.27 ( 3) link_NAG-ASN : bond 0.00352 / 0.20 ( 11) link_NAG-ASN : angle 2.15815 / 1.71 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.34 seconds wall clock time: 47 minutes 41.30 seconds (2861.30 seconds total)