Starting phenix.real_space_refine on Tue Jun 10 05:17:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lqg_0944/06_2025/6lqg_0944.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lqg_0944/06_2025/6lqg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6lqg_0944/06_2025/6lqg_0944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lqg_0944/06_2025/6lqg_0944.map" model { file = "/net/cci-nas-00/data/ceres_data/6lqg_0944/06_2025/6lqg_0944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lqg_0944/06_2025/6lqg_0944.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.10, per 1000 atoms: 0.65 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: 2.66 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.95 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: 3.19 Time building geometry restraints manager: 3.13 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: 1.630 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.610 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.870 ------------------------------------------------------------------------------- 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 : 3.77 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (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 TRP 0.047 0.004 TRP C 227 HIS 0.015 0.002 HIS C 197 PHE 0.029 0.003 PHE C 179 TYR 0.032 0.002 TYR A 565 ARG 0.010 0.001 ARG A 429 Details of bonding type rmsd link_NAG-ASN : bond 0.01048 ( 11) link_NAG-ASN : angle 3.50482 ( 33) link_BETA1-4 : bond 0.00663 ( 7) link_BETA1-4 : angle 2.95832 ( 21) hydrogen bonds : bond 0.13980 ( 572) hydrogen bonds : angle 5.90176 ( 1665) link_BETA1-6 : bond 0.00456 ( 1) link_BETA1-6 : angle 1.31331 ( 3) SS BOND : bond 0.00803 ( 4) SS BOND : angle 1.96244 ( 8) link_BETA1-3 : bond 0.00004 ( 1) link_BETA1-3 : angle 2.30737 ( 3) covalent geometry : bond 0.00706 (11135) covalent geometry : angle 1.00559 (15191) *********************** 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 : 1.167 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: 0.2877 time to fit residues: 80.8922 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 : 1.161 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.113506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.094372 restraints weight = 17169.312| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.07 r_work: 0.2980 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11159 Z= 0.162 Angle : 0.673 10.171 15259 Z= 0.322 Chirality : 0.045 0.252 1811 Planarity : 0.005 0.059 1832 Dihedral : 13.260 106.998 2150 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.86 % Allowed : 6.29 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1305 helix: 0.31 (0.19), residues: 706 sheet: -1.37 (0.43), residues: 134 loop : -2.66 (0.24), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 227 HIS 0.006 0.001 HIS C 197 PHE 0.028 0.002 PHE A 302 TYR 0.011 0.002 TYR B 256 ARG 0.004 0.001 ARG A 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 11) link_NAG-ASN : angle 2.59654 ( 33) link_BETA1-4 : bond 0.00523 ( 7) link_BETA1-4 : angle 2.02387 ( 21) hydrogen bonds : bond 0.05016 ( 572) hydrogen bonds : angle 4.20999 ( 1665) link_BETA1-6 : bond 0.01553 ( 1) link_BETA1-6 : angle 2.44950 ( 3) SS BOND : bond 0.00793 ( 4) SS BOND : angle 1.08640 ( 8) link_BETA1-3 : bond 0.00834 ( 1) link_BETA1-3 : angle 2.64444 ( 3) covalent geometry : bond 0.00381 (11135) covalent geometry : angle 0.65654 (15191) *********************** 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 153 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8721 (tp40) REVERT: A 688 TYR cc_start: 0.8881 (t80) cc_final: 0.8453 (t80) REVERT: B 115 TYR cc_start: 0.7519 (m-80) cc_final: 0.7121 (m-10) REVERT: B 419 CYS cc_start: 0.8442 (m) cc_final: 0.8179 (m) REVERT: C 109 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7631 (ttm110) REVERT: C 137 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8074 (mp) REVERT: C 240 GLN cc_start: 0.7583 (mt0) cc_final: 0.7273 (tm-30) outliers start: 21 outliers final: 17 residues processed: 145 average time/residue: 0.2331 time to fit residues: 48.2704 Evaluate side-chains 132 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 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 22 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.114413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.095018 restraints weight = 17309.667| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.11 r_work: 0.2995 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11159 Z= 0.122 Angle : 0.602 11.509 15259 Z= 0.287 Chirality : 0.042 0.252 1811 Planarity : 0.004 0.046 1832 Dihedral : 11.153 103.457 2150 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.48 % Allowed : 7.00 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1305 helix: 1.18 (0.20), residues: 706 sheet: -1.05 (0.44), residues: 134 loop : -2.34 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 36 HIS 0.004 0.001 HIS C 197 PHE 0.027 0.001 PHE A 302 TYR 0.011 0.001 TYR A 569 ARG 0.003 0.000 ARG C 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 11) link_NAG-ASN : angle 2.19295 ( 33) link_BETA1-4 : bond 0.00476 ( 7) link_BETA1-4 : angle 1.87938 ( 21) hydrogen bonds : bond 0.04267 ( 572) hydrogen bonds : angle 3.91845 ( 1665) link_BETA1-6 : bond 0.01804 ( 1) link_BETA1-6 : angle 2.77634 ( 3) SS BOND : bond 0.00352 ( 4) SS BOND : angle 0.79617 ( 8) link_BETA1-3 : bond 0.00797 ( 1) link_BETA1-3 : angle 1.90530 ( 3) covalent geometry : bond 0.00273 (11135) covalent geometry : angle 0.58817 (15191) *********************** 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 155 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8384 (t70) REVERT: A 688 TYR cc_start: 0.8869 (t80) cc_final: 0.8420 (t80) REVERT: B 115 TYR cc_start: 0.7515 (m-80) cc_final: 0.7089 (m-10) REVERT: B 139 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8181 (ttm) REVERT: C 109 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7705 (ttm110) REVERT: C 137 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8122 (mp) REVERT: C 240 GLN cc_start: 0.7722 (mt0) cc_final: 0.7364 (tm-30) outliers start: 28 outliers final: 18 residues processed: 147 average time/residue: 0.2322 time to fit residues: 48.9138 Evaluate side-chains 138 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 ASN 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 511 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain C residue 51 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 146 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 10 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.108672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.088885 restraints weight = 17395.159| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.11 r_work: 0.2897 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11159 Z= 0.266 Angle : 0.735 12.664 15259 Z= 0.351 Chirality : 0.048 0.265 1811 Planarity : 0.005 0.044 1832 Dihedral : 10.986 95.983 2150 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.72 % Allowed : 7.27 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1305 helix: 1.15 (0.20), residues: 711 sheet: -1.23 (0.43), residues: 138 loop : -2.29 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 58 HIS 0.007 0.001 HIS C 197 PHE 0.033 0.003 PHE A 302 TYR 0.017 0.002 TYR C 218 ARG 0.005 0.001 ARG A 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 11) link_NAG-ASN : angle 2.93476 ( 33) link_BETA1-4 : bond 0.00268 ( 7) link_BETA1-4 : angle 2.24465 ( 21) hydrogen bonds : bond 0.05636 ( 572) hydrogen bonds : angle 4.07684 ( 1665) link_BETA1-6 : bond 0.01626 ( 1) link_BETA1-6 : angle 3.15420 ( 3) SS BOND : bond 0.00599 ( 4) SS BOND : angle 1.11062 ( 8) link_BETA1-3 : bond 0.00675 ( 1) link_BETA1-3 : angle 1.57421 ( 3) covalent geometry : bond 0.00643 (11135) covalent geometry : angle 0.71718 (15191) *********************** 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 168 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 1.415 Fit side-chains REVERT: A 253 ASP cc_start: 0.9304 (OUTLIER) cc_final: 0.8638 (t70) REVERT: A 310 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 688 TYR cc_start: 0.8904 (t80) cc_final: 0.8377 (t80) REVERT: B 115 TYR cc_start: 0.7480 (m-80) cc_final: 0.7088 (m-10) REVERT: B 249 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8471 (mp) REVERT: C 109 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7704 (ttm110) REVERT: C 132 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8620 (t80) REVERT: C 137 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8317 (mp) REVERT: C 240 GLN cc_start: 0.7821 (mt0) cc_final: 0.7434 (tm-30) outliers start: 42 outliers final: 31 residues processed: 156 average time/residue: 0.2948 time to fit residues: 65.7387 Evaluate side-chains 148 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 401 SER Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 80 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 123 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.113078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093362 restraints weight = 17240.013| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.11 r_work: 0.2966 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11159 Z= 0.118 Angle : 0.597 11.697 15259 Z= 0.283 Chirality : 0.042 0.267 1811 Planarity : 0.003 0.034 1832 Dihedral : 10.101 93.009 2149 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.48 % Allowed : 9.66 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1305 helix: 1.57 (0.20), residues: 714 sheet: -0.88 (0.44), residues: 138 loop : -2.07 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 36 HIS 0.003 0.001 HIS A 553 PHE 0.024 0.001 PHE A 302 TYR 0.011 0.001 TYR A 569 ARG 0.002 0.000 ARG C 241 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 11) link_NAG-ASN : angle 2.13058 ( 33) link_BETA1-4 : bond 0.00437 ( 7) link_BETA1-4 : angle 1.84323 ( 21) hydrogen bonds : bond 0.04172 ( 572) hydrogen bonds : angle 3.79633 ( 1665) link_BETA1-6 : bond 0.01895 ( 1) link_BETA1-6 : angle 2.94082 ( 3) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.55499 ( 8) link_BETA1-3 : bond 0.00839 ( 1) link_BETA1-3 : angle 1.25666 ( 3) covalent geometry : bond 0.00265 (11135) covalent geometry : angle 0.58384 (15191) *********************** 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 150 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8359 (t70) REVERT: A 310 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 688 TYR cc_start: 0.8872 (t80) cc_final: 0.8395 (t80) REVERT: B 115 TYR cc_start: 0.7480 (m-80) cc_final: 0.7125 (m-10) REVERT: B 249 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 109 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7776 (ttm110) REVERT: C 132 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8493 (t80) REVERT: C 137 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8236 (mp) REVERT: C 226 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8281 (tp) REVERT: C 240 GLN cc_start: 0.7591 (mt0) cc_final: 0.7145 (tm-30) outliers start: 28 outliers final: 18 residues processed: 142 average time/residue: 0.2218 time to fit residues: 46.2225 Evaluate side-chains 140 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 91 ASN Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 11 optimal weight: 0.0570 chunk 12 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 93 optimal weight: 0.0040 overall best weight: 0.4110 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.114502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094729 restraints weight = 17297.353| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.13 r_work: 0.2996 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11159 Z= 0.103 Angle : 0.572 11.462 15259 Z= 0.269 Chirality : 0.042 0.262 1811 Planarity : 0.003 0.030 1832 Dihedral : 9.432 86.272 2148 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.22 % Allowed : 9.66 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1305 helix: 1.90 (0.20), residues: 714 sheet: -0.67 (0.46), residues: 120 loop : -1.85 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 36 HIS 0.003 0.000 HIS C 58 PHE 0.024 0.001 PHE A 302 TYR 0.014 0.001 TYR B 256 ARG 0.002 0.000 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 11) link_NAG-ASN : angle 1.93557 ( 33) link_BETA1-4 : bond 0.00463 ( 7) link_BETA1-4 : angle 1.70606 ( 21) hydrogen bonds : bond 0.03691 ( 572) hydrogen bonds : angle 3.65008 ( 1665) link_BETA1-6 : bond 0.01589 ( 1) link_BETA1-6 : angle 3.04657 ( 3) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.58015 ( 8) link_BETA1-3 : bond 0.00957 ( 1) link_BETA1-3 : angle 1.41442 ( 3) covalent geometry : bond 0.00226 (11135) covalent geometry : angle 0.56062 (15191) *********************** 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 145 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 688 TYR cc_start: 0.8889 (t80) cc_final: 0.8410 (t80) REVERT: B 115 TYR cc_start: 0.7489 (m-80) cc_final: 0.7099 (m-10) REVERT: B 249 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8459 (mp) REVERT: B 269 ARG cc_start: 0.8019 (ttt180) cc_final: 0.7801 (ttt180) REVERT: B 270 MET cc_start: 0.7043 (mmp) cc_final: 0.6793 (mmt) REVERT: C 109 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7858 (ttm110) REVERT: C 132 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8475 (t80) REVERT: C 137 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8272 (mp) REVERT: C 237 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.8149 (ttp-170) REVERT: C 240 GLN cc_start: 0.7483 (mt0) cc_final: 0.6968 (tm-30) outliers start: 25 outliers final: 17 residues processed: 140 average time/residue: 0.2904 time to fit residues: 63.6091 Evaluate side-chains 135 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 2.070 ------------------------------------------------------------------------------- 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 91 ASN Chi-restraints excluded: chain A residue 147 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 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7835 > 50: distance: 16 - 33: 37.431 distance: 27 - 33: 33.612 distance: 33 - 34: 39.967 distance: 34 - 35: 40.532 distance: 34 - 37: 21.371 distance: 35 - 36: 56.537 distance: 35 - 41: 39.929 distance: 37 - 38: 44.489 distance: 37 - 39: 60.714 distance: 38 - 40: 41.564 distance: 41 - 42: 55.187 distance: 42 - 45: 40.184 distance: 43 - 44: 56.547 distance: 43 - 49: 40.970 distance: 45 - 46: 39.206 distance: 46 - 47: 40.204 distance: 46 - 48: 39.714 distance: 49 - 50: 64.910 distance: 50 - 51: 7.177 distance: 50 - 53: 57.755 distance: 51 - 52: 53.764 distance: 53 - 54: 57.814 distance: 53 - 55: 67.832 distance: 57 - 58: 68.697 distance: 58 - 59: 39.796 distance: 58 - 62: 48.135 distance: 60 - 61: 56.063 distance: 62 - 63: 11.194 distance: 63 - 64: 69.575 distance: 64 - 65: 56.254 distance: 66 - 67: 69.212 distance: 67 - 68: 9.581 distance: 67 - 69: 67.532 distance: 68 - 70: 40.086 distance: 69 - 71: 3.719 distance: 70 - 72: 41.105 distance: 71 - 72: 39.309 distance: 72 - 73: 69.069 distance: 74 - 75: 69.296 distance: 74 - 80: 38.907 distance: 75 - 76: 40.321 distance: 75 - 78: 57.319 distance: 76 - 77: 50.750 distance: 76 - 81: 57.685 distance: 78 - 79: 56.863 distance: 79 - 80: 56.999 distance: 81 - 82: 50.208 distance: 82 - 83: 22.703 distance: 82 - 85: 39.561 distance: 83 - 84: 43.297 distance: 83 - 90: 21.939 distance: 86 - 87: 41.312 distance: 87 - 88: 39.446 distance: 87 - 89: 56.303 distance: 91 - 92: 39.572 distance: 91 - 94: 39.326 distance: 92 - 93: 40.300 distance: 92 - 104: 39.238 distance: 95 - 96: 59.916 distance: 95 - 97: 57.725 distance: 96 - 98: 38.779 distance: 97 - 99: 34.467 distance: 97 - 100: 12.314 distance: 98 - 99: 27.295 distance: 99 - 101: 30.746 distance: 100 - 102: 6.650 distance: 101 - 103: 42.620 distance: 102 - 103: 14.668 distance: 104 - 105: 38.128 distance: 105 - 106: 3.170 distance: 105 - 108: 54.965 distance: 106 - 107: 56.155 distance: 106 - 112: 4.799 distance: 109 - 110: 56.822 distance: 109 - 111: 56.658 distance: 112 - 113: 5.731 distance: 113 - 114: 52.633 distance: 113 - 116: 3.928 distance: 114 - 118: 34.412 distance: 115 - 138: 37.760 distance: 116 - 117: 69.513