Starting phenix.real_space_refine on Wed Sep 17 19:58:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mnh_48423/09_2025/9mnh_48423.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mnh_48423/09_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_48423/09_2025/9mnh_48423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mnh_48423/09_2025/9mnh_48423.map" model { file = "/net/cci-nas-00/data/ceres_data/9mnh_48423/09_2025/9mnh_48423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mnh_48423/09_2025/9mnh_48423.cif" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.92, per 1000 atoms: 0.27 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: 0.98 Conformation dependent library (CDL) restraints added in 477.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.55 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: 1.84 Time building geometry restraints manager: 1.24 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: 0.01 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: 2.310 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.610 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.700 ------------------------------------------------------------------------------- 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 : 3.91 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.001 ARG A 92 TYR 0.019 0.002 TYR C 426 PHE 0.011 0.001 PHE C 229 TRP 0.009 0.001 TRP C 302 HIS 0.002 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00451 (11028) covalent geometry : angle 1.01280 (15021) SS BOND : bond 0.00278 ( 15) SS BOND : angle 0.92639 ( 30) hydrogen bonds : bond 0.18614 ( 463) hydrogen bonds : angle 6.88370 ( 1302) link_BETA1-4 : bond 0.01129 ( 12) link_BETA1-4 : angle 3.88955 ( 36) link_BETA1-6 : bond 0.00469 ( 3) link_BETA1-6 : angle 1.48330 ( 9) link_NAG-ASN : bond 0.00733 ( 15) link_NAG-ASN : angle 5.88778 ( 45) *********************** 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 : 0.430 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: 0.1043 time to fit residues: 8.2062 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 : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3320 r_free = 0.3320 target = 0.058180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046385 restraints weight = 51321.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.045983 restraints weight = 56687.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.046382 restraints weight = 58767.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046415 restraints weight = 50292.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046504 restraints weight = 47106.825| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11073 Z= 0.122 Angle : 0.657 14.708 15141 Z= 0.309 Chirality : 0.046 0.207 1953 Planarity : 0.004 0.043 1863 Dihedral : 7.237 59.220 2055 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 0.33 % Allowed : 4.66 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.21), residues: 1377 helix: -0.35 (0.23), residues: 467 sheet: -0.17 (0.33), residues: 215 loop : -1.80 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.009 0.001 TYR A 366 PHE 0.006 0.001 PHE C 105 TRP 0.007 0.001 TRP C 302 HIS 0.001 0.000 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00251 (11028) covalent geometry : angle 0.60587 (15021) SS BOND : bond 0.00195 ( 15) SS BOND : angle 0.54213 ( 30) hydrogen bonds : bond 0.04900 ( 463) hydrogen bonds : angle 5.37053 ( 1302) link_BETA1-4 : bond 0.00773 ( 12) link_BETA1-4 : angle 2.96663 ( 36) link_BETA1-6 : bond 0.00299 ( 3) link_BETA1-6 : angle 1.26580 ( 9) link_NAG-ASN : bond 0.00545 ( 15) link_NAG-ASN : angle 3.87689 ( 45) *********************** 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 : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 0.0760 time to fit residues: 6.4804 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 : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 7 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 0.0270 chunk 88 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 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 = 0.3322 r_free = 0.3322 target = 0.058288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044604 restraints weight = 51731.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.045128 restraints weight = 40226.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045227 restraints weight = 34823.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.045451 restraints weight = 30599.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.045529 restraints weight = 28153.428| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11073 Z= 0.107 Angle : 0.641 18.342 15141 Z= 0.293 Chirality : 0.046 0.320 1953 Planarity : 0.003 0.035 1863 Dihedral : 6.895 58.769 2055 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.21), residues: 1377 helix: 0.31 (0.24), residues: 464 sheet: 0.01 (0.33), residues: 219 loop : -1.66 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 336 TYR 0.010 0.001 TYR C 426 PHE 0.006 0.001 PHE C 229 TRP 0.005 0.001 TRP C 302 HIS 0.002 0.000 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00220 (11028) covalent geometry : angle 0.58109 (15021) SS BOND : bond 0.00243 ( 15) SS BOND : angle 0.53033 ( 30) hydrogen bonds : bond 0.04102 ( 463) hydrogen bonds : angle 5.02583 ( 1302) link_BETA1-4 : bond 0.00669 ( 12) link_BETA1-4 : angle 2.65745 ( 36) link_BETA1-6 : bond 0.00366 ( 3) link_BETA1-6 : angle 1.26625 ( 9) link_NAG-ASN : bond 0.00492 ( 15) link_NAG-ASN : angle 4.38296 ( 45) *********************** 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 : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 MET cc_start: 0.8196 (mmp) cc_final: 0.7961 (mmp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0999 time to fit residues: 7.6274 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 : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 103 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.0960 ------------------------------------------------------------------------------- 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** 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 = 0.3297 r_free = 0.3297 target = 0.057463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044697 restraints weight = 51445.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044834 restraints weight = 52781.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.045074 restraints weight = 50233.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045201 restraints weight = 42719.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045258 restraints weight = 40669.659| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11073 Z= 0.130 Angle : 0.640 13.641 15141 Z= 0.296 Chirality : 0.046 0.289 1953 Planarity : 0.003 0.036 1863 Dihedral : 6.851 59.581 2055 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.16 % Favored : 94.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.22), residues: 1377 helix: 0.69 (0.24), residues: 463 sheet: -0.48 (0.31), residues: 241 loop : -1.57 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.010 0.001 TYR C 426 PHE 0.005 0.001 PHE A 229 TRP 0.010 0.001 TRP C 302 HIS 0.004 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00291 (11028) covalent geometry : angle 0.59623 (15021) SS BOND : bond 0.00720 ( 15) SS BOND : angle 0.64883 ( 30) hydrogen bonds : bond 0.03940 ( 463) hydrogen bonds : angle 4.99277 ( 1302) link_BETA1-4 : bond 0.00659 ( 12) link_BETA1-4 : angle 2.57598 ( 36) link_BETA1-6 : bond 0.00586 ( 3) link_BETA1-6 : angle 1.27434 ( 9) link_NAG-ASN : bond 0.00606 ( 15) link_NAG-ASN : angle 3.61464 ( 45) *********************** 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 47 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0793 time to fit residues: 6.1899 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 : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 101 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045311 restraints weight = 51491.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045604 restraints weight = 48552.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.045944 restraints weight = 43267.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045955 restraints weight = 39684.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046041 restraints weight = 35607.467| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11073 Z= 0.102 Angle : 0.623 19.045 15141 Z= 0.283 Chirality : 0.046 0.377 1953 Planarity : 0.003 0.033 1863 Dihedral : 6.623 59.447 2055 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.37 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.22), residues: 1377 helix: 1.00 (0.25), residues: 463 sheet: -0.48 (0.31), residues: 241 loop : -1.49 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 142 TYR 0.011 0.001 TYR C 426 PHE 0.005 0.001 PHE C 229 TRP 0.007 0.001 TRP C 302 HIS 0.001 0.000 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00215 (11028) covalent geometry : angle 0.56509 (15021) SS BOND : bond 0.00162 ( 15) SS BOND : angle 0.40995 ( 30) hydrogen bonds : bond 0.03518 ( 463) hydrogen bonds : angle 4.78407 ( 1302) link_BETA1-4 : bond 0.00653 ( 12) link_BETA1-4 : angle 2.46694 ( 36) link_BETA1-6 : bond 0.00350 ( 3) link_BETA1-6 : angle 1.21298 ( 9) link_NAG-ASN : bond 0.00486 ( 15) link_NAG-ASN : angle 4.33948 ( 45) *********************** 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 46 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.441 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0891 time to fit residues: 6.6669 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 : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 128 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.057392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044770 restraints weight = 51537.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044955 restraints weight = 50294.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.045166 restraints weight = 46560.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045238 restraints weight = 44063.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045338 restraints weight = 38615.528| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1953 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= 0.127 Angle : 0.646 15.330 15141 Z= 0.296 Chirality : 0.046 0.419 1953 Planarity : 0.003 0.034 1863 Dihedral : 6.621 59.434 2055 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.52 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.22), residues: 1377 helix: 1.12 (0.25), residues: 462 sheet: -0.46 (0.31), residues: 239 loop : -1.45 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 359 TYR 0.016 0.001 TYR B 40 PHE 0.004 0.001 PHE A 290 TRP 0.007 0.001 TRP C 302 HIS 0.003 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00287 (11028) covalent geometry : angle 0.59932 (15021) SS BOND : bond 0.00311 ( 15) SS BOND : angle 0.67636 ( 30) hydrogen bonds : bond 0.03568 ( 463) hydrogen bonds : angle 4.83641 ( 1302) link_BETA1-4 : bond 0.00629 ( 12) link_BETA1-4 : angle 2.41251 ( 36) link_BETA1-6 : bond 0.00270 ( 3) link_BETA1-6 : angle 1.37266 ( 9) link_NAG-ASN : bond 0.00486 ( 15) link_NAG-ASN : angle 3.88675 ( 45) *********************** 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 : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0861 time to fit residues: 6.5979 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 : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 95 optimal weight: 0.0670 chunk 130 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.6524 ------------------------------------------------------------------------------- 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 C 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.044078 restraints weight = 51136.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.043833 restraints weight = 56221.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.044077 restraints weight = 59262.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.044290 restraints weight = 46803.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.044408 restraints weight = 44059.368| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11073 Z= 0.165 Angle : 0.678 13.561 15141 Z= 0.316 Chirality : 0.048 0.410 1953 Planarity : 0.003 0.043 1863 Dihedral : 6.733 58.330 2055 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.22), residues: 1377 helix: 0.95 (0.24), residues: 468 sheet: -0.56 (0.31), residues: 239 loop : -1.48 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 359 TYR 0.019 0.001 TYR B 40 PHE 0.007 0.001 PHE A 350 TRP 0.011 0.001 TRP C 302 HIS 0.004 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00383 (11028) covalent geometry : angle 0.63825 (15021) SS BOND : bond 0.00390 ( 15) SS BOND : angle 0.83578 ( 30) hydrogen bonds : bond 0.03950 ( 463) hydrogen bonds : angle 5.02184 ( 1302) link_BETA1-4 : bond 0.00682 ( 12) link_BETA1-4 : angle 2.37081 ( 36) link_BETA1-6 : bond 0.00406 ( 3) link_BETA1-6 : angle 1.22081 ( 9) link_NAG-ASN : bond 0.00477 ( 15) link_NAG-ASN : angle 3.69353 ( 45) *********************** 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 48 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.443 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0786 time to fit residues: 6.2277 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 76 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 61 optimal weight: 0.0020 chunk 72 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 288 GLN A 453 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN ** 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 = 0.3296 r_free = 0.3296 target = 0.057450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044747 restraints weight = 50814.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.044840 restraints weight = 49424.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.045040 restraints weight = 53725.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045203 restraints weight = 42192.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045229 restraints weight = 40274.212| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11073 Z= 0.106 Angle : 0.625 12.760 15141 Z= 0.288 Chirality : 0.046 0.319 1953 Planarity : 0.003 0.033 1863 Dihedral : 6.670 58.770 2055 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.52 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.22), residues: 1377 helix: 1.09 (0.25), residues: 473 sheet: -0.54 (0.30), residues: 239 loop : -1.41 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 313 TYR 0.012 0.001 TYR B 40 PHE 0.006 0.001 PHE B 229 TRP 0.006 0.001 TRP C 302 HIS 0.002 0.000 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00230 (11028) covalent geometry : angle 0.58513 (15021) SS BOND : bond 0.00191 ( 15) SS BOND : angle 0.61899 ( 30) hydrogen bonds : bond 0.03363 ( 463) hydrogen bonds : angle 4.76866 ( 1302) link_BETA1-4 : bond 0.00657 ( 12) link_BETA1-4 : angle 2.33516 ( 36) link_BETA1-6 : bond 0.00370 ( 3) link_BETA1-6 : angle 1.20844 ( 9) link_NAG-ASN : bond 0.00517 ( 15) link_NAG-ASN : angle 3.48573 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 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 : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0876 time to fit residues: 6.7425 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 : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 72 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 87 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 0.0980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.057588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.044963 restraints weight = 51070.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.044990 restraints weight = 48171.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045249 restraints weight = 45726.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045281 restraints weight = 44471.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.045390 restraints weight = 38776.397| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2295 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= 0.110 Angle : 0.660 19.670 15141 Z= 0.298 Chirality : 0.050 0.851 1953 Planarity : 0.003 0.032 1863 Dihedral : 6.676 58.803 2055 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.22), residues: 1377 helix: 1.09 (0.25), residues: 474 sheet: -0.51 (0.31), residues: 239 loop : -1.39 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 359 TYR 0.011 0.001 TYR B 40 PHE 0.005 0.001 PHE A 350 TRP 0.010 0.001 TRP C 302 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00238 (11028) covalent geometry : angle 0.60127 (15021) SS BOND : bond 0.00192 ( 15) SS BOND : angle 0.51150 ( 30) hydrogen bonds : bond 0.03318 ( 463) hydrogen bonds : angle 4.79773 ( 1302) link_BETA1-4 : bond 0.00633 ( 12) link_BETA1-4 : angle 2.26850 ( 36) link_BETA1-6 : bond 0.00340 ( 3) link_BETA1-6 : angle 1.19159 ( 9) link_NAG-ASN : bond 0.00666 ( 15) link_NAG-ASN : angle 4.62539 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 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 : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0879 time to fit residues: 6.9142 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 : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 115 optimal weight: 0.0670 chunk 78 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- 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 C 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.055996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045412 restraints weight = 50353.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.045243 restraints weight = 66951.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.045539 restraints weight = 67771.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045635 restraints weight = 54817.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.045664 restraints weight = 56098.862| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11073 Z= 0.182 Angle : 0.722 19.190 15141 Z= 0.335 Chirality : 0.050 0.631 1953 Planarity : 0.004 0.034 1863 Dihedral : 6.651 58.870 2055 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.32 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.22), residues: 1377 helix: 0.81 (0.24), residues: 480 sheet: -0.59 (0.31), residues: 238 loop : -1.43 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 92 TYR 0.019 0.001 TYR B 40 PHE 0.007 0.001 PHE A 290 TRP 0.012 0.001 TRP A 302 HIS 0.005 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00427 (11028) covalent geometry : angle 0.67306 (15021) SS BOND : bond 0.00316 ( 15) SS BOND : angle 0.49673 ( 30) hydrogen bonds : bond 0.04051 ( 463) hydrogen bonds : angle 5.12902 ( 1302) link_BETA1-4 : bond 0.00645 ( 12) link_BETA1-4 : angle 2.23741 ( 36) link_BETA1-6 : bond 0.00377 ( 3) link_BETA1-6 : angle 1.40392 ( 9) link_NAG-ASN : bond 0.00675 ( 15) link_NAG-ASN : angle 4.42875 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 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 45 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.415 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0886 time to fit residues: 6.5516 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 : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 0.0070 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.057135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.044736 restraints weight = 50103.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.044706 restraints weight = 54683.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044948 restraints weight = 51645.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.045054 restraints weight = 47612.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045204 restraints weight = 41547.406| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11073 Z= 0.108 Angle : 0.656 19.781 15141 Z= 0.299 Chirality : 0.048 0.509 1953 Planarity : 0.003 0.031 1863 Dihedral : 6.557 56.687 2055 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.22), residues: 1377 helix: 1.01 (0.24), residues: 480 sheet: -0.52 (0.31), residues: 238 loop : -1.38 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.013 0.001 TYR B 40 PHE 0.005 0.001 PHE C 229 TRP 0.007 0.001 TRP C 302 HIS 0.002 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00236 (11028) covalent geometry : angle 0.60248 (15021) SS BOND : bond 0.00193 ( 15) SS BOND : angle 0.48392 ( 30) hydrogen bonds : bond 0.03345 ( 463) hydrogen bonds : angle 4.85278 ( 1302) link_BETA1-4 : bond 0.00640 ( 12) link_BETA1-4 : angle 2.21947 ( 36) link_BETA1-6 : bond 0.00348 ( 3) link_BETA1-6 : angle 1.21030 ( 9) link_NAG-ASN : bond 0.00660 ( 15) link_NAG-ASN : angle 4.36952 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1390.90 seconds wall clock time: 25 minutes 5.36 seconds (1505.36 seconds total)