Starting phenix.real_space_refine on Wed Mar 4 06:00:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lqg_0944/03_2026/6lqg_0944.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lqg_0944/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6lqg_0944/03_2026/6lqg_0944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lqg_0944/03_2026/6lqg_0944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lqg_0944/03_2026/6lqg_0944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lqg_0944/03_2026/6lqg_0944.map" } 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-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 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: 2.62, per 1000 atoms: 0.24 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: 1.01 Conformation dependent library (CDL) restraints added in 499.5 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: 0.27 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: 1.50 Time building geometry restraints manager: 1.29 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 - 23.59: 6673 23.59 - 47.17: 179 47.17 - 70.76: 45 70.76 - 94.34: 33 94.34 - 117.93: 18 Dihedral angle restraints: 6948 sinusoidal: 3109 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 6945 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.000 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 14.694 117.931 4462 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 covalent geometry : bond 0.00706 (11135) covalent geometry : angle 1.00559 (15191) SS BOND : bond 0.00803 ( 4) SS BOND : angle 1.96244 ( 8) hydrogen bonds : bond 0.13980 ( 572) hydrogen bonds : angle 5.90176 ( 1665) link_BETA1-3 : bond 0.00004 ( 1) link_BETA1-3 : angle 2.30737 ( 3) link_BETA1-4 : bond 0.00663 ( 7) link_BETA1-4 : angle 2.95832 ( 21) link_BETA1-6 : bond 0.00456 ( 1) link_BETA1-6 : angle 1.31331 ( 3) link_NAG-ASN : bond 0.01048 ( 11) link_NAG-ASN : angle 3.50482 ( 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 : 0.300 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: 0.1386 time to fit residues: 39.1310 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 : 0.379 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 91 ASN A 355 GLN A 358 ASN A 385 GLN A 454 GLN A 531 ASN A 535 GLN B 112 GLN B 214 HIS C 68 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095791 restraints weight = 17384.658| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.12 r_work: 0.3005 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11159 Z= 0.137 Angle : 0.647 9.868 15259 Z= 0.311 Chirality : 0.043 0.246 1811 Planarity : 0.005 0.061 1832 Dihedral : 13.409 106.255 2150 Min Nonbonded Distance : 2.439 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: -1.34 (0.22), residues: 1305 helix: 0.34 (0.19), residues: 702 sheet: -1.25 (0.43), residues: 132 loop : -2.68 (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 0.019 0.002 TRP C 227 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00310 (11135) covalent geometry : angle 0.63173 (15191) SS BOND : bond 0.00406 ( 4) SS BOND : angle 1.22085 ( 8) hydrogen bonds : bond 0.04789 ( 572) hydrogen bonds : angle 4.21762 ( 1665) link_BETA1-3 : bond 0.01002 ( 1) link_BETA1-3 : angle 2.67325 ( 3) link_BETA1-4 : bond 0.00519 ( 7) link_BETA1-4 : angle 1.95869 ( 21) link_BETA1-6 : bond 0.02008 ( 1) link_BETA1-6 : angle 2.62380 ( 3) link_NAG-ASN : bond 0.00486 ( 11) link_NAG-ASN : angle 2.46027 ( 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 : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8733 (tp40) REVERT: A 109 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8031 (mm-30) REVERT: A 240 PHE cc_start: 0.8133 (m-80) cc_final: 0.7797 (m-80) REVERT: A 584 GLU cc_start: 0.7816 (mp0) cc_final: 0.7566 (mp0) REVERT: A 688 TYR cc_start: 0.8865 (t80) cc_final: 0.8466 (t80) REVERT: B 115 TYR cc_start: 0.7529 (m-80) cc_final: 0.7130 (m-10) REVERT: B 139 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8298 (ttm) REVERT: B 279 ASN cc_start: 0.7998 (m110) cc_final: 0.7791 (m-40) REVERT: B 419 CYS cc_start: 0.8426 (m) cc_final: 0.8143 (m) REVERT: C 109 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7687 (ttm110) REVERT: C 137 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8083 (mp) REVERT: C 240 GLN cc_start: 0.7600 (mt0) cc_final: 0.7265 (tm-30) outliers start: 20 outliers final: 14 residues processed: 148 average time/residue: 0.1009 time to fit residues: 21.4041 Evaluate side-chains 137 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 139 MET 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: 0.9980 chunk 81 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.110358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.090649 restraints weight = 17497.595| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.13 r_work: 0.2925 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11159 Z= 0.215 Angle : 0.697 12.152 15259 Z= 0.334 Chirality : 0.045 0.255 1811 Planarity : 0.004 0.049 1832 Dihedral : 11.528 101.328 2150 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.46 % Allowed : 6.38 % Favored : 90.16 % 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 (0.23), residues: 1305 helix: 0.90 (0.20), residues: 713 sheet: -1.16 (0.44), residues: 134 loop : -2.43 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 429 TYR 0.018 0.002 TYR C 218 PHE 0.030 0.002 PHE A 302 TRP 0.020 0.002 TRP D 58 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00521 (11135) covalent geometry : angle 0.68014 (15191) SS BOND : bond 0.00565 ( 4) SS BOND : angle 1.07696 ( 8) hydrogen bonds : bond 0.05270 ( 572) hydrogen bonds : angle 4.06337 ( 1665) link_BETA1-3 : bond 0.00725 ( 1) link_BETA1-3 : angle 1.82459 ( 3) link_BETA1-4 : bond 0.00374 ( 7) link_BETA1-4 : angle 2.10594 ( 21) link_BETA1-6 : bond 0.01485 ( 1) link_BETA1-6 : angle 2.87065 ( 3) link_NAG-ASN : bond 0.00459 ( 11) link_NAG-ASN : angle 2.79846 ( 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 168 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8724 (tp40) REVERT: A 253 ASP cc_start: 0.9291 (OUTLIER) cc_final: 0.8598 (t70) REVERT: A 310 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 688 TYR cc_start: 0.8902 (t80) cc_final: 0.8459 (t80) REVERT: B 115 TYR cc_start: 0.7485 (m-80) cc_final: 0.7069 (m-10) REVERT: B 269 ARG cc_start: 0.8012 (ttt180) cc_final: 0.7772 (ttt180) REVERT: B 467 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8401 (pt) REVERT: C 109 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7698 (ttm110) REVERT: C 137 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8179 (mp) REVERT: C 240 GLN cc_start: 0.7759 (mt0) cc_final: 0.7379 (tm-30) outliers start: 39 outliers final: 29 residues processed: 158 average time/residue: 0.1031 time to fit residues: 23.3406 Evaluate side-chains 148 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 246 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL 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 100 ILE 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 B residue 419 CYS Chi-restraints excluded: chain B residue 467 ILE 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 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 Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.091839 restraints weight = 17358.926| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.12 r_work: 0.2944 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11159 Z= 0.155 Angle : 0.629 11.883 15259 Z= 0.299 Chirality : 0.044 0.268 1811 Planarity : 0.004 0.037 1832 Dihedral : 10.769 98.062 2150 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.46 % Allowed : 7.45 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.23), residues: 1305 helix: 1.29 (0.20), residues: 713 sheet: -1.10 (0.43), residues: 140 loop : -2.25 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 241 TYR 0.012 0.001 TYR C 218 PHE 0.027 0.002 PHE A 302 TRP 0.015 0.001 TRP D 36 HIS 0.003 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00369 (11135) covalent geometry : angle 0.61421 (15191) SS BOND : bond 0.00344 ( 4) SS BOND : angle 0.71344 ( 8) hydrogen bonds : bond 0.04649 ( 572) hydrogen bonds : angle 3.90814 ( 1665) link_BETA1-3 : bond 0.00784 ( 1) link_BETA1-3 : angle 1.48428 ( 3) link_BETA1-4 : bond 0.00353 ( 7) link_BETA1-4 : angle 1.96480 ( 21) link_BETA1-6 : bond 0.01754 ( 1) link_BETA1-6 : angle 2.89104 ( 3) link_NAG-ASN : bond 0.00389 ( 11) link_NAG-ASN : angle 2.43452 ( 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: 39 poor density : 120 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8701 (tp40) REVERT: A 253 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8407 (t70) REVERT: A 310 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8282 (tm-30) REVERT: A 688 TYR cc_start: 0.8876 (t80) cc_final: 0.8398 (t80) REVERT: B 115 TYR cc_start: 0.7456 (m-80) cc_final: 0.7042 (m-10) REVERT: B 249 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8454 (mp) REVERT: B 270 MET cc_start: 0.7256 (mmp) cc_final: 0.6981 (mmt) REVERT: B 467 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8406 (pt) REVERT: C 109 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7772 (ttm110) REVERT: C 137 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8284 (mp) REVERT: C 240 GLN cc_start: 0.7698 (mt0) cc_final: 0.7316 (tm-30) outliers start: 39 outliers final: 30 residues processed: 151 average time/residue: 0.1003 time to fit residues: 22.0414 Evaluate side-chains 149 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 253 ASP Chi-restraints excluded: chain A residue 256 VAL 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 B residue 467 ILE 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 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 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: 0.6980 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 28 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093423 restraints weight = 17201.457| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.12 r_work: 0.2966 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2289 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= 0.124 Angle : 0.592 11.447 15259 Z= 0.280 Chirality : 0.043 0.271 1811 Planarity : 0.003 0.034 1832 Dihedral : 9.965 93.478 2150 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.84 % Allowed : 8.87 % 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: 0.20 (0.24), residues: 1305 helix: 1.63 (0.20), residues: 713 sheet: -0.80 (0.44), residues: 132 loop : -2.07 (0.27), residues: 460 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 C 58 Details of bonding type rmsd covalent geometry : bond 0.00287 (11135) covalent geometry : angle 0.57905 (15191) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.59509 ( 8) hydrogen bonds : bond 0.04097 ( 572) hydrogen bonds : angle 3.76105 ( 1665) link_BETA1-3 : bond 0.00850 ( 1) link_BETA1-3 : angle 1.40727 ( 3) link_BETA1-4 : bond 0.00402 ( 7) link_BETA1-4 : angle 1.83640 ( 21) link_BETA1-6 : bond 0.01749 ( 1) link_BETA1-6 : angle 2.91671 ( 3) link_NAG-ASN : bond 0.00368 ( 11) link_NAG-ASN : angle 2.14372 ( 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 162 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8241 (tm-30) REVERT: A 688 TYR cc_start: 0.8894 (t80) cc_final: 0.8376 (t80) REVERT: B 115 TYR cc_start: 0.7446 (m-80) cc_final: 0.7079 (m-10) REVERT: B 249 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8434 (mp) REVERT: B 269 ARG cc_start: 0.8189 (ttt180) cc_final: 0.7917 (ttt180) REVERT: B 467 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8381 (pt) REVERT: C 109 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7790 (ttm110) REVERT: C 137 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8280 (mp) REVERT: C 155 TYR cc_start: 0.8678 (m-80) cc_final: 0.8320 (m-80) REVERT: C 184 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.8251 (mtp85) REVERT: C 240 GLN cc_start: 0.7554 (mt0) cc_final: 0.7065 (tm-30) outliers start: 32 outliers final: 23 residues processed: 154 average time/residue: 0.0884 time to fit residues: 19.7804 Evaluate side-chains 145 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 VAL 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 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 467 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 18 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.091350 restraints weight = 17378.535| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.13 r_work: 0.2935 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2393 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= 0.170 Angle : 0.631 11.934 15259 Z= 0.297 Chirality : 0.044 0.261 1811 Planarity : 0.004 0.030 1832 Dihedral : 9.784 85.966 2149 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.72 % Allowed : 8.69 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.24), residues: 1305 helix: 1.67 (0.20), residues: 714 sheet: -0.97 (0.43), residues: 140 loop : -2.03 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 429 TYR 0.018 0.001 TYR B 256 PHE 0.027 0.002 PHE A 302 TRP 0.016 0.001 TRP D 58 HIS 0.003 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00408 (11135) covalent geometry : angle 0.61717 (15191) SS BOND : bond 0.00340 ( 4) SS BOND : angle 0.75503 ( 8) hydrogen bonds : bond 0.04517 ( 572) hydrogen bonds : angle 3.80701 ( 1665) link_BETA1-3 : bond 0.00823 ( 1) link_BETA1-3 : angle 1.58962 ( 3) link_BETA1-4 : bond 0.00340 ( 7) link_BETA1-4 : angle 1.93669 ( 21) link_BETA1-6 : bond 0.01487 ( 1) link_BETA1-6 : angle 3.17024 ( 3) link_NAG-ASN : bond 0.00382 ( 11) link_NAG-ASN : angle 2.31403 ( 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 161 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.8639 (t70) REVERT: A 310 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8234 (tm-30) REVERT: A 688 TYR cc_start: 0.8908 (t80) cc_final: 0.8409 (t80) REVERT: B 115 TYR cc_start: 0.7477 (m-80) cc_final: 0.7103 (m-10) REVERT: B 249 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8450 (mp) REVERT: B 270 MET cc_start: 0.7135 (mmp) cc_final: 0.6887 (mmt) REVERT: B 467 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8397 (pt) REVERT: C 109 ARG cc_start: 0.8015 (ttm110) cc_final: 0.7811 (ttm110) REVERT: C 137 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8297 (mp) REVERT: C 240 GLN cc_start: 0.7526 (mt0) cc_final: 0.7004 (tm-30) outliers start: 42 outliers final: 32 residues processed: 151 average time/residue: 0.0968 time to fit residues: 21.3231 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 : 0.383 ------------------------------------------------------------------------------- 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 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 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 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 407 THR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 467 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 3.9990 chunk 38 optimal weight: 0.0370 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.089039 restraints weight = 17343.003| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.12 r_work: 0.2899 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11159 Z= 0.231 Angle : 0.688 12.313 15259 Z= 0.326 Chirality : 0.046 0.243 1811 Planarity : 0.004 0.033 1832 Dihedral : 9.770 75.381 2148 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.72 % Allowed : 9.49 % 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: 0.10 (0.24), residues: 1305 helix: 1.54 (0.20), residues: 714 sheet: -1.06 (0.42), residues: 138 loop : -2.01 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 342 TYR 0.021 0.002 TYR B 256 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 covalent geometry : bond 0.00563 (11135) covalent geometry : angle 0.67178 (15191) SS BOND : bond 0.00431 ( 4) SS BOND : angle 0.90030 ( 8) hydrogen bonds : bond 0.05137 ( 572) hydrogen bonds : angle 3.92274 ( 1665) link_BETA1-3 : bond 0.00835 ( 1) link_BETA1-3 : angle 1.69084 ( 3) link_BETA1-4 : bond 0.00290 ( 7) link_BETA1-4 : angle 2.14562 ( 21) link_BETA1-6 : bond 0.01172 ( 1) link_BETA1-6 : angle 3.69494 ( 3) link_NAG-ASN : bond 0.00455 ( 11) link_NAG-ASN : angle 2.54327 ( 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 161 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.8638 (t70) REVERT: A 310 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 688 TYR cc_start: 0.8929 (t80) cc_final: 0.8410 (t80) REVERT: B 115 TYR cc_start: 0.7521 (m-80) cc_final: 0.7158 (m-10) REVERT: B 249 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8471 (mp) REVERT: B 270 MET cc_start: 0.7238 (mmp) cc_final: 0.7037 (mmt) REVERT: B 467 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8356 (pt) REVERT: C 109 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7845 (ttm110) REVERT: C 137 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8347 (mp) REVERT: C 240 GLN cc_start: 0.7585 (mt0) cc_final: 0.7182 (tm-30) outliers start: 42 outliers final: 31 residues processed: 150 average time/residue: 0.1017 time to fit residues: 22.1697 Evaluate side-chains 150 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 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 B residue 467 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.091088 restraints weight = 17241.411| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.11 r_work: 0.2930 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11159 Z= 0.148 Angle : 0.624 11.688 15259 Z= 0.295 Chirality : 0.044 0.247 1811 Planarity : 0.003 0.030 1832 Dihedral : 9.370 68.604 2148 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.63 % Allowed : 10.02 % Favored : 86.35 % 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: 1.74 (0.20), residues: 715 sheet: -0.83 (0.43), residues: 138 loop : -1.92 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.012 0.001 TYR A 569 PHE 0.025 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 covalent geometry : bond 0.00350 (11135) covalent geometry : angle 0.60909 (15191) SS BOND : bond 0.00264 ( 4) SS BOND : angle 0.58511 ( 8) hydrogen bonds : bond 0.04463 ( 572) hydrogen bonds : angle 3.80627 ( 1665) link_BETA1-3 : bond 0.00902 ( 1) link_BETA1-3 : angle 1.62586 ( 3) link_BETA1-4 : bond 0.00367 ( 7) link_BETA1-4 : angle 1.93411 ( 21) link_BETA1-6 : bond 0.00993 ( 1) link_BETA1-6 : angle 3.92963 ( 3) link_NAG-ASN : bond 0.00375 ( 11) link_NAG-ASN : angle 2.24166 ( 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 162 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8397 (t70) REVERT: A 310 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 688 TYR cc_start: 0.8907 (t80) cc_final: 0.8374 (t80) REVERT: B 115 TYR cc_start: 0.7500 (m-80) cc_final: 0.7126 (m-10) REVERT: B 249 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8470 (mp) REVERT: B 467 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8385 (pt) REVERT: C 109 ARG cc_start: 0.8057 (ttm110) cc_final: 0.7856 (ttm110) REVERT: C 137 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8322 (mp) REVERT: C 155 TYR cc_start: 0.8768 (m-80) cc_final: 0.8433 (m-80) REVERT: C 240 GLN cc_start: 0.7541 (mt0) cc_final: 0.7045 (tm-30) outliers start: 41 outliers final: 32 residues processed: 152 average time/residue: 0.0947 time to fit residues: 21.2434 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 : 0.387 ------------------------------------------------------------------------------- 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 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 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 407 THR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 467 ILE 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 231 THR Chi-restraints excluded: chain C residue 237 ARG 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 Chi-restraints excluded: chain D residue 96 ILE 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: 1.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.092015 restraints weight = 17239.618| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.12 r_work: 0.2947 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2645 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= 0.133 Angle : 0.602 11.550 15259 Z= 0.286 Chirality : 0.043 0.251 1811 Planarity : 0.003 0.029 1832 Dihedral : 8.872 65.474 2148 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.46 % Allowed : 10.20 % Favored : 86.35 % 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: 0.54 (0.24), residues: 1305 helix: 1.90 (0.20), residues: 714 sheet: -0.78 (0.43), residues: 138 loop : -1.87 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.011 0.001 TYR A 569 PHE 0.025 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 covalent geometry : bond 0.00312 (11135) covalent geometry : angle 0.58789 (15191) SS BOND : bond 0.00259 ( 4) SS BOND : angle 0.62211 ( 8) hydrogen bonds : bond 0.04142 ( 572) hydrogen bonds : angle 3.71039 ( 1665) link_BETA1-3 : bond 0.00930 ( 1) link_BETA1-3 : angle 1.63155 ( 3) link_BETA1-4 : bond 0.00403 ( 7) link_BETA1-4 : angle 1.84733 ( 21) link_BETA1-6 : bond 0.00574 ( 1) link_BETA1-6 : angle 4.17148 ( 3) link_NAG-ASN : bond 0.00362 ( 11) link_NAG-ASN : angle 2.12732 ( 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 160 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8575 (t70) REVERT: A 310 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 688 TYR cc_start: 0.8911 (t80) cc_final: 0.8374 (t80) REVERT: B 115 TYR cc_start: 0.7419 (m-80) cc_final: 0.7076 (m-10) REVERT: B 249 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8503 (mp) REVERT: B 467 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8355 (pt) REVERT: C 137 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8322 (mp) REVERT: C 240 GLN cc_start: 0.7502 (mt0) cc_final: 0.7018 (tm-30) outliers start: 39 outliers final: 30 residues processed: 150 average time/residue: 0.0985 time to fit residues: 21.3697 Evaluate side-chains 151 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL 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 270 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 467 ILE 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 231 THR Chi-restraints excluded: chain C residue 237 ARG 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 Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 12 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094271 restraints weight = 17189.675| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.11 r_work: 0.2981 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2725 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= 0.106 Angle : 0.574 11.510 15259 Z= 0.272 Chirality : 0.042 0.244 1811 Planarity : 0.003 0.028 1832 Dihedral : 8.234 65.039 2148 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.66 % Allowed : 11.35 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1305 helix: 2.11 (0.20), residues: 712 sheet: -0.56 (0.44), residues: 132 loop : -1.79 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 109 TYR 0.011 0.001 TYR A 569 PHE 0.024 0.001 PHE A 302 TRP 0.020 0.001 TRP B 165 HIS 0.003 0.000 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00241 (11135) covalent geometry : angle 0.56081 (15191) SS BOND : bond 0.00160 ( 4) SS BOND : angle 0.49475 ( 8) hydrogen bonds : bond 0.03677 ( 572) hydrogen bonds : angle 3.63072 ( 1665) link_BETA1-3 : bond 0.00963 ( 1) link_BETA1-3 : angle 1.54185 ( 3) link_BETA1-4 : bond 0.00436 ( 7) link_BETA1-4 : angle 1.73007 ( 21) link_BETA1-6 : bond 0.00509 ( 1) link_BETA1-6 : angle 3.62266 ( 3) link_NAG-ASN : bond 0.00355 ( 11) link_NAG-ASN : angle 1.98302 ( 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 151 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8572 (t70) REVERT: A 310 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 688 TYR cc_start: 0.8903 (t80) cc_final: 0.8361 (t80) REVERT: B 115 TYR cc_start: 0.7420 (m-80) cc_final: 0.7073 (m-10) REVERT: B 248 LEU cc_start: 0.9148 (mt) cc_final: 0.8943 (mt) REVERT: B 249 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8441 (mp) REVERT: B 467 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8376 (pt) REVERT: C 137 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8274 (mp) REVERT: C 237 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7825 (ttp80) REVERT: C 240 GLN cc_start: 0.7338 (mt0) cc_final: 0.6874 (tm-30) outliers start: 30 outliers final: 24 residues processed: 142 average time/residue: 0.0934 time to fit residues: 19.7300 Evaluate side-chains 146 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 282 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 467 ILE 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 231 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.091938 restraints weight = 17345.693| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.11 r_work: 0.2946 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11159 Z= 0.149 Angle : 0.605 11.938 15259 Z= 0.288 Chirality : 0.043 0.249 1811 Planarity : 0.003 0.030 1832 Dihedral : 8.174 64.907 2148 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.84 % Allowed : 11.26 % Favored : 85.90 % 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: 0.76 (0.24), residues: 1305 helix: 2.10 (0.20), residues: 713 sheet: -0.74 (0.43), residues: 132 loop : -1.77 (0.28), residues: 460 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 0.026 0.002 PHE A 302 TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00358 (11135) covalent geometry : angle 0.59165 (15191) SS BOND : bond 0.00270 ( 4) SS BOND : angle 0.62360 ( 8) hydrogen bonds : bond 0.04180 ( 572) hydrogen bonds : angle 3.68070 ( 1665) link_BETA1-3 : bond 0.00937 ( 1) link_BETA1-3 : angle 1.61073 ( 3) link_BETA1-4 : bond 0.00365 ( 7) link_BETA1-4 : angle 1.91607 ( 21) link_BETA1-6 : bond 0.00298 ( 1) link_BETA1-6 : angle 3.23470 ( 3) link_NAG-ASN : bond 0.00365 ( 11) link_NAG-ASN : angle 2.15464 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.57 seconds wall clock time: 44 minutes 22.26 seconds (2662.26 seconds total)