Starting phenix.real_space_refine on Tue May 13 20:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mnh_48423/05_2025/9mnh_48423.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mnh_48423/05_2025/9mnh_48423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mnh_48423/05_2025/9mnh_48423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mnh_48423/05_2025/9mnh_48423.map" model { file = "/net/cci-nas-00/data/ceres_data/9mnh_48423/05_2025/9mnh_48423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mnh_48423/05_2025/9mnh_48423.cif" } resolution = 4.03 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= 0.002 sd= 0.114 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6864 2.51 5 N 1758 2.21 5 O 2193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10875 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3495 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 21, 'TRANS': 439} Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3495 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 21, 'TRANS': 439} Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3495 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 21, 'TRANS': 439} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.18, per 1000 atoms: 0.66 Number of scatterers: 10875 At special positions: 0 Unit cell: (112.2, 112.2, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2193 8.00 N 1758 7.00 C 6864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 334 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 357 " distance=2.02 Simple disulfide: pdb=" SG CYS A 381 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 411 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 334 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 411 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 334 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 381 " - pdb=" SG CYS C 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 411 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " BETA1-6 " NAG E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG G 1 " - " FUC G 4 " " NAG I 1 " - " FUC I 4 " NAG-ASN " NAG A 601 " - " ASN A 434 " " NAG A 602 " - " ASN A 353 " " NAG A 603 " - " ASN A 458 " " NAG B 601 " - " ASN B 434 " " NAG B 602 " - " ASN B 353 " " NAG B 603 " - " ASN B 458 " " NAG C 601 " - " ASN C 434 " " NAG C 602 " - " ASN C 353 " " NAG C 603 " - " ASN C 458 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 93 " " NAG F 1 " - " ASN B 61 " " NAG G 1 " - " ASN B 93 " " NAG H 1 " - " ASN C 61 " " NAG I 1 " - " ASN C 93 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2574 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 21 sheets defined 37.8% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.569A pdb=" N LEU A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.729A pdb=" N THR A 63 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 64 " --> pdb=" O ASN A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 60 through 64' Processing helix chain 'A' and resid 69 through 95 removed outlier: 4.078A pdb=" N TYR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix removed outlier: 3.771A pdb=" N VAL A 95 " --> pdb=" O MET A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 118 through 140 removed outlier: 3.523A pdb=" N VAL A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN A 133 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASN A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.742A pdb=" N ASN A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 208 removed outlier: 3.623A pdb=" N THR A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.508A pdb=" N LEU A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.842A pdb=" N LEU A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.128A pdb=" N LEU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 446 through 478 Processing helix chain 'B' and resid 23 through 31 removed outlier: 3.540A pdb=" N LEU B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.792A pdb=" N THR B 63 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 64 " --> pdb=" O ASN B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 60 through 64' Processing helix chain 'B' and resid 69 through 94 removed outlier: 4.094A pdb=" N TYR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Proline residue: B 83 - end of helix removed outlier: 3.570A pdb=" N SER B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 140 removed outlier: 5.303A pdb=" N GLN B 133 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 185 through 208 removed outlier: 3.562A pdb=" N THR B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 213 removed outlier: 3.598A pdb=" N ARG B 213 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.857A pdb=" N LEU B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.315A pdb=" N LEU B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 446 through 479 removed outlier: 3.977A pdb=" N THR B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 476 " --> pdb=" O ASN B 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 31 removed outlier: 3.713A pdb=" N LEU C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.670A pdb=" N THR C 63 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 60 through 64' Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.067A pdb=" N TYR C 73 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA C 79 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Proline residue: C 83 - end of helix removed outlier: 3.656A pdb=" N SER C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.555A pdb=" N GLY C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 115' Processing helix chain 'C' and resid 118 through 140 removed outlier: 5.239A pdb=" N GLN C 133 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 171 through 176 removed outlier: 3.620A pdb=" N ASN C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 208 removed outlier: 3.544A pdb=" N THR C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 207 " --> pdb=" O GLN C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.969A pdb=" N LEU C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 252 removed outlier: 4.493A pdb=" N LEU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 247 through 252' Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 357 Processing helix chain 'C' and resid 448 through 479 removed outlier: 3.545A pdb=" N ASN C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 476 " --> pdb=" O ASN C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing sheet with id=AA1, first strand: chain 'A' and resid 279 through 281 Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281 removed outlier: 5.612A pdb=" N LYS A 34 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE A 291 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N HIS A 36 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 311 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 54 removed outlier: 3.766A pdb=" N THR A 47 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 271 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA5, first strand: chain 'A' and resid 155 through 156 Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 297 removed outlier: 4.010A pdb=" N LEU A 301 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AA8, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.927A pdb=" N LYS A 393 " --> pdb=" O CYS A 388 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET A 420 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 279 through 281 removed outlier: 5.595A pdb=" N LYS B 34 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE B 291 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS B 36 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 311 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 279 through 281 Processing sheet with id=AB2, first strand: chain 'B' and resid 47 through 54 removed outlier: 3.662A pdb=" N THR B 47 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 271 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR B 257 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 95 through 96 removed outlier: 6.780A pdb=" N VAL B 109 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS C 388 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS C 393 " --> pdb=" O CYS C 388 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AB5, first strand: chain 'B' and resid 155 through 156 Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 297 removed outlier: 4.009A pdb=" N LEU B 301 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 393 through 394 removed outlier: 3.958A pdb=" N LYS B 393 " --> pdb=" O CYS B 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 279 through 281 removed outlier: 5.533A pdb=" N LYS C 34 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE C 291 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N HIS C 36 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 311 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AC1, first strand: chain 'C' and resid 47 through 54 removed outlier: 3.767A pdb=" N THR C 47 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE C 271 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N THR C 257 " --> pdb=" O ASN C 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 155 through 156 Processing sheet with id=AC3, first strand: chain 'C' and resid 295 through 297 removed outlier: 3.980A pdb=" N LEU C 301 " --> pdb=" O VAL C 362 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1302 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: 3.81 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3298 1.34 - 1.46: 1999 1.46 - 1.58: 5641 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11028 Sorted by residual: bond pdb=" N VAL C 95 " pdb=" CA VAL C 95 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.27e-02 6.20e+03 1.05e+01 bond pdb=" N LYS A 463 " pdb=" CA LYS A 463 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 9.97e+00 bond pdb=" N ILE C 104 " pdb=" CA ILE C 104 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.33e+00 bond pdb=" C SER C 462 " pdb=" N LYS C 463 " ideal model delta sigma weight residual 1.335 1.376 -0.040 1.38e-02 5.25e+03 8.61e+00 bond pdb=" N ILE C 108 " pdb=" CA ILE C 108 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.50e+00 ... (remaining 11023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 14601 2.79 - 5.57: 345 5.57 - 8.36: 65 8.36 - 11.14: 8 11.14 - 13.93: 2 Bond angle restraints: 15021 Sorted by residual: angle pdb=" C ASN A 101 " pdb=" CA ASN A 101 " pdb=" CB ASN A 101 " ideal model delta sigma weight residual 116.54 110.37 6.17 1.15e+00 7.56e-01 2.88e+01 angle pdb=" C ALA A 107 " pdb=" CA ALA A 107 " pdb=" CB ALA A 107 " ideal model delta sigma weight residual 116.63 111.21 5.42 1.16e+00 7.43e-01 2.18e+01 angle pdb=" CG1 ILE B 173 " pdb=" CB ILE B 173 " pdb=" CG2 ILE B 173 " ideal model delta sigma weight residual 110.70 96.77 13.93 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C LEU A 177 " pdb=" N VAL A 178 " pdb=" CA VAL A 178 " ideal model delta sigma weight residual 120.33 123.98 -3.65 8.00e-01 1.56e+00 2.08e+01 angle pdb=" C PRO B 100 " pdb=" N ASN B 101 " pdb=" CA ASN B 101 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 ... (remaining 15016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 6309 15.25 - 30.50: 644 30.50 - 45.75: 130 45.75 - 61.00: 49 61.00 - 76.25: 23 Dihedral angle restraints: 7155 sinusoidal: 3159 harmonic: 3996 Sorted by residual: dihedral pdb=" CA ASN B 456 " pdb=" C ASN B 456 " pdb=" N ILE B 457 " pdb=" CA ILE B 457 " ideal model delta harmonic sigma weight residual 180.00 151.02 28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLN C 419 " pdb=" C GLN C 419 " pdb=" N MET C 420 " pdb=" CA MET C 420 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CB CYS C 65 " pdb=" SG CYS C 65 " pdb=" SG CYS C 186 " pdb=" CB CYS C 186 " ideal model delta sinusoidal sigma weight residual 93.00 48.10 44.90 1 1.00e+01 1.00e-02 2.80e+01 ... (remaining 7152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1725 0.093 - 0.185: 209 0.185 - 0.278: 16 0.278 - 0.370: 2 0.370 - 0.463: 1 Chirality restraints: 1953 Sorted by residual: chirality pdb=" CB ILE B 104 " pdb=" CA ILE B 104 " pdb=" CG1 ILE B 104 " pdb=" CG2 ILE B 104 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CB ILE B 173 " pdb=" CA ILE B 173 " pdb=" CG1 ILE B 173 " pdb=" CG2 ILE B 173 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C2 NAG G 1 " pdb=" C1 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" N2 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.18 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1950 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 462 " -0.039 2.00e-02 2.50e+03 7.51e-02 5.64e+01 pdb=" C SER C 462 " 0.130 2.00e-02 2.50e+03 pdb=" O SER C 462 " -0.049 2.00e-02 2.50e+03 pdb=" N LYS C 463 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 462 " 0.033 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C SER A 462 " -0.112 2.00e-02 2.50e+03 pdb=" O SER A 462 " 0.042 2.00e-02 2.50e+03 pdb=" N LYS A 463 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 462 " 0.032 2.00e-02 2.50e+03 6.21e-02 3.85e+01 pdb=" C SER B 462 " -0.107 2.00e-02 2.50e+03 pdb=" O SER B 462 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS B 463 " 0.036 2.00e-02 2.50e+03 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2375 2.79 - 3.32: 9700 3.32 - 3.85: 17667 3.85 - 4.37: 18854 4.37 - 4.90: 32560 Nonbonded interactions: 81156 Sorted by model distance: nonbonded pdb=" O ASP C 476 " pdb=" OG1 THR C 479 " model vdw 2.267 3.040 nonbonded pdb=" OE1 GLN C 397 " pdb=" OG1 THR C 404 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLN B 397 " pdb=" OG1 THR B 404 " model vdw 2.288 3.040 nonbonded pdb=" OE1 GLN A 397 " pdb=" OG1 THR A 404 " model vdw 2.293 3.040 nonbonded pdb=" O ASN A 456 " pdb=" OG1 THR A 460 " model vdw 2.300 3.040 ... (remaining 81151 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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 group one per residue 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: 2.270 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.440 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.005 0.060 11073 Z= 0.245 Angle : 1.077 20.152 15141 Z= 0.522 Chirality : 0.059 0.463 1953 Planarity : 0.007 0.075 1863 Dihedral : 13.650 76.245 4536 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.48 % Favored : 92.37 % Rotamer: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.06 % 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: -2.41 (0.19), residues: 1377 helix: -1.59 (0.20), residues: 455 sheet: -0.41 (0.31), residues: 240 loop : -2.03 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 302 HIS 0.002 0.001 HIS C 129 PHE 0.011 0.001 PHE C 229 TYR 0.019 0.002 TYR C 426 ARG 0.002 0.001 ARG A 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 15) link_NAG-ASN : angle 5.88778 ( 45) link_BETA1-4 : bond 0.01129 ( 12) link_BETA1-4 : angle 3.88955 ( 36) hydrogen bonds : bond 0.18614 ( 463) hydrogen bonds : angle 6.88370 ( 1302) link_BETA1-6 : bond 0.00469 ( 3) link_BETA1-6 : angle 1.48330 ( 9) SS BOND : bond 0.00278 ( 15) SS BOND : angle 0.92639 ( 30) covalent geometry : bond 0.00451 (11028) covalent geometry : angle 1.01280 (15021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.2172 time to fit residues: 17.2585 Evaluate side-chains 45 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.4980 chunk 104 optimal weight: 0.0670 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN B 139 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.058388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.046618 restraints weight = 51030.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046141 restraints weight = 56616.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.046388 restraints weight = 63511.140| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11073 Z= 0.119 Angle : 0.651 14.580 15141 Z= 0.306 Chirality : 0.046 0.208 1953 Planarity : 0.004 0.042 1863 Dihedral : 7.235 59.308 2055 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % 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: -1.55 (0.21), residues: 1377 helix: -0.34 (0.23), residues: 467 sheet: -0.21 (0.33), residues: 217 loop : -1.80 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 302 HIS 0.001 0.000 HIS C 36 PHE 0.006 0.001 PHE C 208 TYR 0.009 0.001 TYR A 366 ARG 0.003 0.000 ARG A 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 15) link_NAG-ASN : angle 3.85664 ( 45) link_BETA1-4 : bond 0.00792 ( 12) link_BETA1-4 : angle 2.89442 ( 36) hydrogen bonds : bond 0.04831 ( 463) hydrogen bonds : angle 5.32789 ( 1302) link_BETA1-6 : bond 0.00377 ( 3) link_BETA1-6 : angle 1.31181 ( 9) SS BOND : bond 0.00192 ( 15) SS BOND : angle 0.54845 ( 30) covalent geometry : bond 0.00242 (11028) covalent geometry : angle 0.60043 (15021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 0.1974 time to fit residues: 16.5810 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 101 optimal weight: 0.0970 chunk 88 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.057824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044099 restraints weight = 51314.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.044607 restraints weight = 41285.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044796 restraints weight = 34946.632| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11073 Z= 0.118 Angle : 0.645 17.679 15141 Z= 0.297 Chirality : 0.046 0.315 1953 Planarity : 0.003 0.036 1863 Dihedral : 6.853 58.857 2055 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.05 (0.21), residues: 1377 helix: 0.35 (0.24), residues: 464 sheet: -0.06 (0.33), residues: 215 loop : -1.66 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 302 HIS 0.002 0.001 HIS C 129 PHE 0.005 0.001 PHE C 229 TYR 0.010 0.001 TYR C 426 ARG 0.003 0.000 ARG C 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 15) link_NAG-ASN : angle 4.34417 ( 45) link_BETA1-4 : bond 0.00649 ( 12) link_BETA1-4 : angle 2.64521 ( 36) hydrogen bonds : bond 0.04196 ( 463) hydrogen bonds : angle 5.04553 ( 1302) link_BETA1-6 : bond 0.00412 ( 3) link_BETA1-6 : angle 1.25619 ( 9) SS BOND : bond 0.00186 ( 15) SS BOND : angle 0.45267 ( 30) covalent geometry : bond 0.00253 (11028) covalent geometry : angle 0.58703 (15021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2191 time to fit residues: 16.9074 Evaluate side-chains 41 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 453 GLN B 452 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.056263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.044568 restraints weight = 50612.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044438 restraints weight = 61166.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.044652 restraints weight = 62932.763| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11073 Z= 0.164 Angle : 0.673 13.188 15141 Z= 0.314 Chirality : 0.047 0.306 1953 Planarity : 0.003 0.038 1863 Dihedral : 6.905 59.422 2055 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.74 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.22), residues: 1377 helix: 0.63 (0.24), residues: 463 sheet: -0.56 (0.31), residues: 241 loop : -1.60 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 302 HIS 0.005 0.001 HIS C 129 PHE 0.007 0.001 PHE A 229 TYR 0.011 0.001 TYR A 269 ARG 0.003 0.000 ARG C 359 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 15) link_NAG-ASN : angle 3.54917 ( 45) link_BETA1-4 : bond 0.00681 ( 12) link_BETA1-4 : angle 2.58108 ( 36) hydrogen bonds : bond 0.04271 ( 463) hydrogen bonds : angle 5.14596 ( 1302) link_BETA1-6 : bond 0.00417 ( 3) link_BETA1-6 : angle 1.21380 ( 9) SS BOND : bond 0.00271 ( 15) SS BOND : angle 0.67699 ( 30) covalent geometry : bond 0.00375 (11028) covalent geometry : angle 0.63377 (15021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.224 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2001 time to fit residues: 15.1074 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 82 optimal weight: 9.9990 chunk 126 optimal weight: 0.0570 chunk 84 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN C 101 ASN ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.056934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045130 restraints weight = 51414.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.045038 restraints weight = 58935.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045382 restraints weight = 56266.179| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11073 Z= 0.115 Angle : 0.640 18.393 15141 Z= 0.292 Chirality : 0.046 0.356 1953 Planarity : 0.003 0.036 1863 Dihedral : 6.705 59.761 2055 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.52 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: -0.78 (0.22), residues: 1377 helix: 0.88 (0.24), residues: 463 sheet: -0.61 (0.30), residues: 241 loop : -1.49 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 302 HIS 0.002 0.001 HIS C 129 PHE 0.006 0.001 PHE B 229 TYR 0.011 0.001 TYR C 426 ARG 0.001 0.000 ARG A 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 15) link_NAG-ASN : angle 4.24626 ( 45) link_BETA1-4 : bond 0.00641 ( 12) link_BETA1-4 : angle 2.47325 ( 36) hydrogen bonds : bond 0.03774 ( 463) hydrogen bonds : angle 4.93608 ( 1302) link_BETA1-6 : bond 0.00348 ( 3) link_BETA1-6 : angle 1.22359 ( 9) SS BOND : bond 0.00189 ( 15) SS BOND : angle 0.38467 ( 30) covalent geometry : bond 0.00252 (11028) covalent geometry : angle 0.58520 (15021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.292 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2007 time to fit residues: 15.7543 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 40 optimal weight: 0.0270 chunk 89 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.057586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.044750 restraints weight = 51325.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044884 restraints weight = 52084.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.045005 restraints weight = 50097.999| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11073 Z= 0.103 Angle : 0.634 15.125 15141 Z= 0.289 Chirality : 0.046 0.450 1953 Planarity : 0.003 0.034 1863 Dihedral : 6.676 59.628 2055 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.23 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: -0.63 (0.22), residues: 1377 helix: 1.09 (0.25), residues: 463 sheet: -0.57 (0.31), residues: 241 loop : -1.46 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP C 302 HIS 0.002 0.000 HIS C 129 PHE 0.004 0.001 PHE C 229 TYR 0.012 0.001 TYR B 40 ARG 0.002 0.000 ARG C 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 15) link_NAG-ASN : angle 3.85951 ( 45) link_BETA1-4 : bond 0.00641 ( 12) link_BETA1-4 : angle 2.42667 ( 36) hydrogen bonds : bond 0.03386 ( 463) hydrogen bonds : angle 4.78508 ( 1302) link_BETA1-6 : bond 0.00292 ( 3) link_BETA1-6 : angle 1.32466 ( 9) SS BOND : bond 0.00210 ( 15) SS BOND : angle 0.86234 ( 30) covalent geometry : bond 0.00219 (11028) covalent geometry : angle 0.58588 (15021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.167 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1940 time to fit residues: 14.9657 Evaluate side-chains 43 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.056977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044212 restraints weight = 52234.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044484 restraints weight = 52379.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.044635 restraints weight = 53677.351| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11073 Z= 0.130 Angle : 0.646 13.677 15141 Z= 0.299 Chirality : 0.047 0.388 1953 Planarity : 0.003 0.034 1863 Dihedral : 6.695 59.012 2055 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.59 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -0.64 (0.22), residues: 1377 helix: 1.06 (0.25), residues: 468 sheet: -0.57 (0.31), residues: 239 loop : -1.47 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 302 HIS 0.003 0.001 HIS C 129 PHE 0.005 0.001 PHE A 350 TYR 0.014 0.001 TYR B 40 ARG 0.002 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 15) link_NAG-ASN : angle 3.70283 ( 45) link_BETA1-4 : bond 0.00674 ( 12) link_BETA1-4 : angle 2.38802 ( 36) hydrogen bonds : bond 0.03609 ( 463) hydrogen bonds : angle 4.84558 ( 1302) link_BETA1-6 : bond 0.00459 ( 3) link_BETA1-6 : angle 1.39483 ( 9) SS BOND : bond 0.00314 ( 15) SS BOND : angle 0.73601 ( 30) covalent geometry : bond 0.00295 (11028) covalent geometry : angle 0.60317 (15021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2088 time to fit residues: 16.0298 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 67.7519 > 50: distance: 7 - 136: 24.657 distance: 19 - 139: 28.534 distance: 22 - 155: 13.174 distance: 36 - 158: 34.728 distance: 97 - 160: 12.787 distance: 98 - 151: 30.468 distance: 101 - 148: 9.895 distance: 124 - 130: 25.427 distance: 130 - 131: 55.428 distance: 131 - 132: 28.987 distance: 131 - 134: 35.890 distance: 132 - 133: 22.834 distance: 132 - 136: 40.936 distance: 134 - 135: 33.705 distance: 136 - 137: 25.578 distance: 137 - 138: 28.041 distance: 137 - 140: 28.041 distance: 138 - 139: 36.550 distance: 138 - 148: 19.137 distance: 140 - 141: 20.365 distance: 141 - 142: 8.236 distance: 141 - 143: 8.194 distance: 142 - 144: 8.389 distance: 143 - 145: 13.271 distance: 144 - 146: 3.448 distance: 145 - 146: 6.506 distance: 146 - 147: 5.640 distance: 148 - 149: 21.974 distance: 149 - 150: 33.335 distance: 149 - 152: 19.627 distance: 150 - 151: 38.312 distance: 150 - 155: 25.690 distance: 152 - 153: 20.036 distance: 152 - 154: 7.174 distance: 155 - 156: 28.944 distance: 156 - 157: 33.380 distance: 156 - 159: 29.567 distance: 157 - 158: 35.038 distance: 157 - 161: 44.262 distance: 159 - 160: 19.597 distance: 161 - 162: 39.150 distance: 162 - 163: 49.563 distance: 162 - 165: 12.118 distance: 163 - 164: 9.636 distance: 163 - 169: 52.704 distance: 165 - 166: 19.660 distance: 166 - 167: 33.430 distance: 166 - 168: 25.999 distance: 169 - 170: 9.578 distance: 170 - 171: 19.465 distance: 170 - 173: 40.132 distance: 171 - 172: 40.249 distance: 171 - 180: 40.431 distance: 173 - 174: 51.348 distance: 174 - 175: 24.773 distance: 175 - 176: 31.824 distance: 176 - 177: 22.028 distance: 177 - 178: 12.985 distance: 177 - 179: 4.423 distance: 180 - 181: 27.618 distance: 181 - 182: 42.502 distance: 181 - 184: 22.657 distance: 182 - 183: 24.313 distance: 182 - 188: 44.103 distance: 184 - 185: 12.464 distance: 185 - 186: 12.604 distance: 185 - 187: 7.711 distance: 188 - 189: 6.640 distance: 189 - 190: 43.576 distance: 189 - 192: 17.240 distance: 190 - 191: 35.062 distance: 190 - 200: 13.704 distance: 192 - 193: 7.433 distance: 193 - 194: 6.549 distance: 193 - 195: 8.284 distance: 194 - 196: 4.957 distance: 195 - 197: 3.427 distance: 196 - 198: 3.121 distance: 197 - 198: 5.665 distance: 198 - 199: 6.527 distance: 200 - 201: 34.910 distance: 201 - 202: 6.247 distance: 201 - 204: 28.486 distance: 202 - 203: 40.903 distance: 202 - 206: 8.760 distance: 204 - 205: 16.440 distance: 206 - 207: 10.355 distance: 207 - 208: 28.933 distance: 207 - 210: 44.045 distance: 208 - 209: 30.102 distance: 208 - 214: 10.316 distance: 210 - 211: 35.043 distance: 211 - 212: 46.884 distance: 211 - 213: 31.231