Starting phenix.real_space_refine on Thu Jul 31 15:06:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9e_44380/07_2025/9b9e_44380.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9e_44380/07_2025/9b9e_44380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b9e_44380/07_2025/9b9e_44380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9e_44380/07_2025/9b9e_44380.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9e_44380/07_2025/9b9e_44380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9e_44380/07_2025/9b9e_44380.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 72 5.16 5 C 8538 2.51 5 N 2250 2.21 5 O 2682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13542 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3512 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain: "B" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3512 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain: "C" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3512 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain: "D" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Time building chain proxies: 9.65, per 1000 atoms: 0.71 Number of scatterers: 13542 At special positions: 0 Unit cell: (114.4, 119.2, 120.8, 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 72 16.00 O 2682 8.00 N 2250 7.00 C 8538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.04 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 95 " distance=2.04 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 NAG-ASN " NAG A 501 " - " ASN A 464 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 67 " " NAG B 501 " - " ASN B 414 " " NAG B 502 " - " ASN B 99 " " NAG B 503 " - " ASN B 464 " " NAG B 504 " - " ASN B 67 " " NAG C 501 " - " ASN C 414 " " NAG C 502 " - " ASN C 99 " " NAG C 503 " - " ASN C 464 " " NAG C 504 " - " ASN C 67 " Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 24 sheets defined 35.5% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.870A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.760A pdb=" N GLY A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 4.316A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.791A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.530A pdb=" N THR A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.956A pdb=" N ALA A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.685A pdb=" N GLY A 236 " --> pdb=" O GLN A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.507A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.900A pdb=" N CYS A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.744A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 481 removed outlier: 4.399A pdb=" N SER A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.912A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.814A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 100 removed outlier: 3.757A pdb=" N GLY B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Proline residue: B 89 - end of helix removed outlier: 4.185A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.733A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.819A pdb=" N THR B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 215 removed outlier: 3.883A pdb=" N ALA B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 236 removed outlier: 3.701A pdb=" N GLY B 236 " --> pdb=" O GLN B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.543A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 removed outlier: 4.003A pdb=" N CYS B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 442 removed outlier: 4.709A pdb=" N GLY B 442 " --> pdb=" O TYR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 481 removed outlier: 4.070A pdb=" N SER B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.828A pdb=" N LYS C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.811A pdb=" N SER C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 100 removed outlier: 3.791A pdb=" N GLY C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 4.175A pdb=" N ILE C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.684A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.583A pdb=" N SER C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.679A pdb=" N THR C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.896A pdb=" N ALA C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 233 through 236 removed outlier: 3.716A pdb=" N GLY C 236 " --> pdb=" O GLN C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 238 through 245 removed outlier: 3.551A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 removed outlier: 3.988A pdb=" N CYS C 355 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.749A pdb=" N GLY C 442 " --> pdb=" O TYR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 481 removed outlier: 4.059A pdb=" N SER C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.909A pdb=" N PHE D 28 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER D 29 " --> pdb=" O ARG D 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 25 through 29' Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.599A pdb=" N THR D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.811A pdb=" N PHE E 28 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER E 29 " --> pdb=" O ARG E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 29' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.524A pdb=" N THR E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.813A pdb=" N PHE F 28 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER F 29 " --> pdb=" O ARG F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.541A pdb=" N THR F 90 " --> pdb=" O PRO F 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 332 through 333 removed outlier: 7.905A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N LYS A 47 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N GLN A 289 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 162 removed outlier: 11.530A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.637A pdb=" N VAL A 113 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N SER C 428 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET A 115 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 249 removed outlier: 7.220A pdb=" N VAL D 47 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG D 49 " --> pdb=" O MET D 33 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET D 33 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY D 9 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N SER D 123 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL D 11 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 248 through 249 removed outlier: 7.220A pdb=" N VAL D 47 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG D 49 " --> pdb=" O MET D 33 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET D 33 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'A' and resid 419 through 422 removed outlier: 4.594A pdb=" N ILE A 426 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 332 through 333 removed outlier: 7.868A pdb=" N VAL B 338 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS B 45 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N CYS B 340 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS B 47 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU B 295 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR B 43 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 293 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS B 45 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ALA B 291 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N LYS B 47 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N GLN B 289 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 162 removed outlier: 11.569A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 248 through 249 removed outlier: 7.301A pdb=" N VAL E 47 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET E 33 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY E 9 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER E 123 " --> pdb=" O GLY E 9 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL E 11 " --> pdb=" O SER E 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 248 through 249 removed outlier: 7.301A pdb=" N VAL E 47 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET E 33 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB6, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB7, first strand: chain 'B' and resid 419 through 422 removed outlier: 4.491A pdb=" N ILE B 426 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 332 through 333 removed outlier: 7.917A pdb=" N VAL C 338 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS C 45 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N CYS C 340 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS C 47 " --> pdb=" O CYS C 340 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU C 295 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR C 43 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE C 293 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS C 45 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ALA C 291 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N LYS C 47 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N GLN C 289 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 162 removed outlier: 11.570A pdb=" N THR C 168 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP C 56 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR C 170 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 263 " --> pdb=" O TYR C 281 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 248 through 249 removed outlier: 7.347A pdb=" N VAL F 47 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP F 35 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET F 33 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY F 9 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N SER F 123 " --> pdb=" O GLY F 9 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL F 11 " --> pdb=" O SER F 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 248 through 249 removed outlier: 7.347A pdb=" N VAL F 47 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP F 35 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET F 33 " --> pdb=" O ARG F 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AC4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'F' and resid 4 through 6 639 hydrogen bonds defined for protein. 1698 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: 4.90 Time building geometry restraints manager: 4.17 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: 4381 1.34 - 1.46: 2570 1.46 - 1.58: 6699 1.58 - 1.70: 0 1.70 - 1.81: 108 Bond restraints: 13758 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" CB CYS B 355 " pdb=" SG CYS B 355 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" CB CYS C 355 " pdb=" SG CYS C 355 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.79e+00 ... (remaining 13753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 17408 1.72 - 3.43: 1105 3.43 - 5.15: 124 5.15 - 6.87: 32 6.87 - 8.58: 15 Bond angle restraints: 18684 Sorted by residual: angle pdb=" N ASN B 51 " pdb=" CA ASN B 51 " pdb=" C ASN B 51 " ideal model delta sigma weight residual 109.81 118.39 -8.58 2.21e+00 2.05e-01 1.51e+01 angle pdb=" N ASN C 51 " pdb=" CA ASN C 51 " pdb=" C ASN C 51 " ideal model delta sigma weight residual 109.81 118.15 -8.34 2.21e+00 2.05e-01 1.42e+01 angle pdb=" C ILE C 48 " pdb=" N LYS C 49 " pdb=" CA LYS C 49 " ideal model delta sigma weight residual 120.82 126.36 -5.54 1.47e+00 4.63e-01 1.42e+01 angle pdb=" C ILE B 48 " pdb=" N LYS B 49 " pdb=" CA LYS B 49 " ideal model delta sigma weight residual 120.82 126.25 -5.43 1.47e+00 4.63e-01 1.36e+01 angle pdb=" N GLY C 358 " pdb=" CA GLY C 358 " pdb=" C GLY C 358 " ideal model delta sigma weight residual 115.27 120.21 -4.94 1.41e+00 5.03e-01 1.23e+01 ... (remaining 18679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7947 17.94 - 35.88: 442 35.88 - 53.83: 96 53.83 - 71.77: 18 71.77 - 89.71: 17 Dihedral angle restraints: 8520 sinusoidal: 3471 harmonic: 5049 Sorted by residual: dihedral pdb=" CB CYS C 355 " pdb=" SG CYS C 355 " pdb=" SG CYS C 363 " pdb=" CB CYS C 363 " ideal model delta sinusoidal sigma weight residual -86.00 -135.01 49.01 1 1.00e+01 1.00e-02 3.30e+01 dihedral pdb=" CB CYS B 355 " pdb=" SG CYS B 355 " pdb=" SG CYS B 363 " pdb=" CB CYS B 363 " ideal model delta sinusoidal sigma weight residual -86.00 -134.77 48.77 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 363 " pdb=" CB CYS A 363 " ideal model delta sinusoidal sigma weight residual -86.00 -133.78 47.78 1 1.00e+01 1.00e-02 3.15e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1626 0.063 - 0.125: 558 0.125 - 0.188: 56 0.188 - 0.251: 12 0.251 - 0.313: 4 Chirality restraints: 2256 Sorted by residual: chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 99 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ASN A 99 " pdb=" N ASN A 99 " pdb=" C ASN A 99 " pdb=" CB ASN A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ASN B 99 " pdb=" N ASN B 99 " pdb=" C ASN B 99 " pdb=" CB ASN B 99 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2253 not shown) Planarity restraints: 2373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 99 " -0.030 2.00e-02 2.50e+03 2.91e-02 1.06e+01 pdb=" CG ASN A 99 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 99 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 99 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 206 " 0.012 2.00e-02 2.50e+03 2.13e-02 9.04e+00 pdb=" CG TYR A 206 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 206 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 206 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 206 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR A 206 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 49 " 0.223 9.50e-02 1.11e+02 1.00e-01 7.27e+00 pdb=" NE ARG F 49 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG F 49 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG F 49 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG F 49 " 0.002 2.00e-02 2.50e+03 ... (remaining 2370 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4316 2.84 - 3.36: 13195 3.36 - 3.87: 20996 3.87 - 4.39: 23697 4.39 - 4.90: 41395 Nonbonded interactions: 103599 Sorted by model distance: nonbonded pdb=" OG1 THR B 334 " pdb=" O SER B 337 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR C 334 " pdb=" O SER C 337 " model vdw 2.343 3.040 nonbonded pdb=" OG1 THR A 334 " pdb=" O SER A 337 " model vdw 2.367 3.040 nonbonded pdb=" OD1 ASP B 413 " pdb=" OG1 THR B 415 " model vdw 2.420 3.040 nonbonded pdb=" O ASN A 320 " pdb=" OG1 THR A 321 " model vdw 2.421 3.040 ... (remaining 103594 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 8.320 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: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 35.530 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.008 0.056 13788 Z= 0.329 Angle : 0.977 13.358 18756 Z= 0.539 Chirality : 0.060 0.313 2256 Planarity : 0.007 0.100 2361 Dihedral : 12.544 89.710 5226 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -1.31 (0.18), residues: 1728 helix: -1.47 (0.21), residues: 480 sheet: -0.14 (0.24), residues: 411 loop : -0.74 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP F 114 HIS 0.005 0.002 HIS C 372 PHE 0.016 0.002 PHE B 376 TYR 0.032 0.005 TYR A 206 ARG 0.019 0.003 ARG F 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 12) link_NAG-ASN : angle 5.66119 ( 36) hydrogen bonds : bond 0.19958 ( 591) hydrogen bonds : angle 8.88990 ( 1698) SS BOND : bond 0.00485 ( 18) SS BOND : angle 2.10137 ( 36) covalent geometry : bond 0.00792 (13758) covalent geometry : angle 0.94181 (18684) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7967 (tp30) cc_final: 0.6724 (tt0) REVERT: A 139 LYS cc_start: 0.8061 (tptt) cc_final: 0.7318 (mtpt) REVERT: A 160 LYS cc_start: 0.9149 (tttt) cc_final: 0.8861 (tttm) REVERT: A 190 ILE cc_start: 0.8946 (mt) cc_final: 0.8581 (mm) REVERT: A 197 LEU cc_start: 0.7291 (tt) cc_final: 0.7079 (mp) REVERT: A 443 ILE cc_start: 0.7500 (tt) cc_final: 0.7198 (tp) REVERT: B 136 GLU cc_start: 0.8048 (tp30) cc_final: 0.6993 (tt0) REVERT: B 139 LYS cc_start: 0.7959 (tptt) cc_final: 0.7314 (mtpt) REVERT: B 160 LYS cc_start: 0.9078 (tttt) cc_final: 0.8758 (tttp) REVERT: C 136 GLU cc_start: 0.7994 (tp30) cc_final: 0.6779 (tt0) REVERT: C 139 LYS cc_start: 0.7989 (tptt) cc_final: 0.7471 (mtpt) REVERT: C 160 LYS cc_start: 0.9064 (tttt) cc_final: 0.8607 (ttmm) REVERT: C 205 LYS cc_start: 0.7990 (tptt) cc_final: 0.7693 (tptm) REVERT: C 322 LEU cc_start: 0.6918 (mt) cc_final: 0.6697 (tt) REVERT: C 443 ILE cc_start: 0.7450 (tt) cc_final: 0.7199 (tp) REVERT: E 114 TRP cc_start: 0.8598 (m100) cc_final: 0.8351 (m-90) REVERT: F 114 TRP cc_start: 0.8581 (m100) cc_final: 0.8074 (m100) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2736 time to fit residues: 93.5665 Evaluate side-chains 142 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126326 restraints weight = 16913.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125484 restraints weight = 22084.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126039 restraints weight = 22143.569| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13788 Z= 0.154 Angle : 0.643 8.294 18756 Z= 0.341 Chirality : 0.049 0.200 2256 Planarity : 0.005 0.045 2361 Dihedral : 5.867 53.998 2121 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.19 % Allowed : 9.17 % Favored : 89.64 % 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: -0.17 (0.20), residues: 1728 helix: 0.07 (0.24), residues: 465 sheet: 0.16 (0.26), residues: 372 loop : -0.22 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 114 HIS 0.004 0.001 HIS F 58 PHE 0.011 0.002 PHE F 46 TYR 0.013 0.002 TYR B 135 ARG 0.003 0.001 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 12) link_NAG-ASN : angle 3.58789 ( 36) hydrogen bonds : bond 0.04961 ( 591) hydrogen bonds : angle 5.94119 ( 1698) SS BOND : bond 0.00182 ( 18) SS BOND : angle 1.51567 ( 36) covalent geometry : bond 0.00350 (13758) covalent geometry : angle 0.62084 (18684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7251 (tp30) cc_final: 0.6771 (tt0) REVERT: A 190 ILE cc_start: 0.9267 (mt) cc_final: 0.8929 (mm) REVERT: A 336 ARG cc_start: 0.7452 (mmm160) cc_final: 0.7187 (tpt170) REVERT: B 136 GLU cc_start: 0.7380 (tp30) cc_final: 0.7038 (tt0) REVERT: B 190 ILE cc_start: 0.9066 (mt) cc_final: 0.8759 (mm) REVERT: B 238 ASN cc_start: 0.8824 (t0) cc_final: 0.8372 (t0) REVERT: B 411 MET cc_start: 0.6874 (ttp) cc_final: 0.6539 (ttp) REVERT: C 136 GLU cc_start: 0.7325 (tp30) cc_final: 0.6911 (tt0) REVERT: C 190 ILE cc_start: 0.9113 (mt) cc_final: 0.8814 (mm) REVERT: C 238 ASN cc_start: 0.8897 (t0) cc_final: 0.8424 (t0) outliers start: 18 outliers final: 10 residues processed: 189 average time/residue: 0.2796 time to fit residues: 75.2475 Evaluate side-chains 140 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain F residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.0270 chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128938 restraints weight = 16891.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127966 restraints weight = 28849.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128381 restraints weight = 24978.100| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13788 Z= 0.135 Angle : 0.567 7.643 18756 Z= 0.298 Chirality : 0.047 0.193 2256 Planarity : 0.004 0.043 2361 Dihedral : 5.476 51.796 2121 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.65 % Allowed : 11.55 % Favored : 86.80 % 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: -0.09 (0.20), residues: 1728 helix: 0.38 (0.25), residues: 465 sheet: 0.18 (0.25), residues: 402 loop : -0.31 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 114 HIS 0.003 0.001 HIS E 58 PHE 0.010 0.001 PHE B 376 TYR 0.012 0.001 TYR B 206 ARG 0.002 0.000 ARG E 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 12) link_NAG-ASN : angle 2.87660 ( 36) hydrogen bonds : bond 0.04367 ( 591) hydrogen bonds : angle 5.44047 ( 1698) SS BOND : bond 0.00381 ( 18) SS BOND : angle 1.24950 ( 36) covalent geometry : bond 0.00304 (13758) covalent geometry : angle 0.55080 (18684) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.507 Fit side-chains REVERT: A 136 GLU cc_start: 0.7274 (tp30) cc_final: 0.6686 (tt0) REVERT: A 190 ILE cc_start: 0.9200 (mt) cc_final: 0.8861 (mm) REVERT: A 336 ARG cc_start: 0.7466 (mmm160) cc_final: 0.7176 (tpt170) REVERT: A 411 MET cc_start: 0.6896 (ttp) cc_final: 0.6619 (ttp) REVERT: B 190 ILE cc_start: 0.8934 (mt) cc_final: 0.8647 (mm) REVERT: B 411 MET cc_start: 0.6874 (ttp) cc_final: 0.6536 (ttp) REVERT: C 136 GLU cc_start: 0.7357 (tp30) cc_final: 0.6869 (tt0) REVERT: C 190 ILE cc_start: 0.9004 (mt) cc_final: 0.8737 (mm) REVERT: C 238 ASN cc_start: 0.8774 (t0) cc_final: 0.8408 (t0) outliers start: 25 outliers final: 17 residues processed: 156 average time/residue: 0.2845 time to fit residues: 64.5195 Evaluate side-chains 138 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 17 optimal weight: 0.6980 chunk 145 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124967 restraints weight = 16825.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124585 restraints weight = 16669.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124868 restraints weight = 16432.678| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13788 Z= 0.136 Angle : 0.562 8.643 18756 Z= 0.293 Chirality : 0.046 0.190 2256 Planarity : 0.004 0.043 2361 Dihedral : 5.364 52.612 2121 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.24 % Allowed : 12.01 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1728 helix: 0.44 (0.25), residues: 465 sheet: 0.01 (0.24), residues: 408 loop : -0.34 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 114 HIS 0.003 0.001 HIS E 58 PHE 0.010 0.001 PHE B 376 TYR 0.010 0.001 TYR A 292 ARG 0.002 0.000 ARG A 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 12) link_NAG-ASN : angle 2.70910 ( 36) hydrogen bonds : bond 0.04120 ( 591) hydrogen bonds : angle 5.25556 ( 1698) SS BOND : bond 0.00231 ( 18) SS BOND : angle 1.38442 ( 36) covalent geometry : bond 0.00322 (13758) covalent geometry : angle 0.54669 (18684) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.655 Fit side-chains REVERT: A 136 GLU cc_start: 0.7362 (tp30) cc_final: 0.6665 (tt0) REVERT: A 190 ILE cc_start: 0.9182 (mt) cc_final: 0.8854 (mm) REVERT: A 336 ARG cc_start: 0.7532 (mmm160) cc_final: 0.7233 (tpt170) REVERT: A 352 MET cc_start: 0.9033 (tpt) cc_final: 0.8743 (tpp) REVERT: A 411 MET cc_start: 0.6961 (ttp) cc_final: 0.6673 (ttp) REVERT: B 190 ILE cc_start: 0.8898 (mt) cc_final: 0.8634 (mm) REVERT: B 218 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8381 (tt) REVERT: B 411 MET cc_start: 0.6928 (ttp) cc_final: 0.6584 (ttp) REVERT: C 136 GLU cc_start: 0.7450 (tp30) cc_final: 0.6817 (tt0) REVERT: C 190 ILE cc_start: 0.8944 (mt) cc_final: 0.8673 (mm) REVERT: C 238 ASN cc_start: 0.8753 (t0) cc_final: 0.8407 (t0) outliers start: 34 outliers final: 24 residues processed: 149 average time/residue: 0.2870 time to fit residues: 61.6619 Evaluate side-chains 144 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 143 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126209 restraints weight = 16955.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125331 restraints weight = 27974.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125491 restraints weight = 24695.916| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13788 Z= 0.147 Angle : 0.557 7.419 18756 Z= 0.292 Chirality : 0.047 0.191 2256 Planarity : 0.004 0.041 2361 Dihedral : 5.348 52.821 2121 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.51 % Allowed : 12.74 % Favored : 84.75 % 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: -0.21 (0.20), residues: 1728 helix: 0.48 (0.25), residues: 465 sheet: -0.06 (0.24), residues: 420 loop : -0.42 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 114 HIS 0.004 0.001 HIS F 58 PHE 0.010 0.001 PHE B 376 TYR 0.011 0.001 TYR A 292 ARG 0.005 0.000 ARG A 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 12) link_NAG-ASN : angle 2.62935 ( 36) hydrogen bonds : bond 0.04149 ( 591) hydrogen bonds : angle 5.15067 ( 1698) SS BOND : bond 0.00360 ( 18) SS BOND : angle 1.18274 ( 36) covalent geometry : bond 0.00358 (13758) covalent geometry : angle 0.54363 (18684) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 1.422 Fit side-chains REVERT: A 190 ILE cc_start: 0.9177 (mt) cc_final: 0.8836 (mm) REVERT: A 336 ARG cc_start: 0.7559 (mmm160) cc_final: 0.7188 (tpt170) REVERT: A 353 ARG cc_start: 0.8123 (ttm110) cc_final: 0.7915 (ttm110) REVERT: A 411 MET cc_start: 0.6893 (ttp) cc_final: 0.6633 (ttp) REVERT: B 190 ILE cc_start: 0.8828 (mt) cc_final: 0.8577 (mm) REVERT: B 218 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8412 (tt) REVERT: B 411 MET cc_start: 0.6920 (ttp) cc_final: 0.6617 (ttp) REVERT: C 136 GLU cc_start: 0.7372 (tp30) cc_final: 0.6848 (tt0) REVERT: C 190 ILE cc_start: 0.8967 (mt) cc_final: 0.8705 (mm) REVERT: C 218 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8430 (tt) outliers start: 38 outliers final: 29 residues processed: 150 average time/residue: 0.2586 time to fit residues: 57.2778 Evaluate side-chains 145 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120287 restraints weight = 17383.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119971 restraints weight = 17405.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120191 restraints weight = 16546.335| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13788 Z= 0.197 Angle : 0.607 7.183 18756 Z= 0.319 Chirality : 0.048 0.185 2256 Planarity : 0.005 0.046 2361 Dihedral : 5.584 53.180 2121 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.51 % Allowed : 13.99 % Favored : 83.50 % 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: -0.50 (0.20), residues: 1728 helix: 0.31 (0.25), residues: 465 sheet: -0.26 (0.26), residues: 369 loop : -0.63 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 114 HIS 0.004 0.001 HIS D 58 PHE 0.012 0.002 PHE F 46 TYR 0.014 0.002 TYR B 292 ARG 0.004 0.000 ARG A 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 12) link_NAG-ASN : angle 2.82072 ( 36) hydrogen bonds : bond 0.04635 ( 591) hydrogen bonds : angle 5.31805 ( 1698) SS BOND : bond 0.00306 ( 18) SS BOND : angle 1.31169 ( 36) covalent geometry : bond 0.00488 (13758) covalent geometry : angle 0.59221 (18684) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.707 Fit side-chains REVERT: A 190 ILE cc_start: 0.9214 (mt) cc_final: 0.8898 (mm) REVERT: A 336 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7155 (tpt170) REVERT: A 353 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7945 (ttm110) REVERT: B 190 ILE cc_start: 0.8886 (mt) cc_final: 0.8616 (mm) REVERT: B 218 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8465 (tt) REVERT: B 411 MET cc_start: 0.7038 (ttp) cc_final: 0.6737 (ttp) REVERT: C 136 GLU cc_start: 0.7418 (tp30) cc_final: 0.6851 (tt0) REVERT: C 190 ILE cc_start: 0.8974 (mt) cc_final: 0.8708 (mm) REVERT: C 218 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8380 (tt) outliers start: 38 outliers final: 29 residues processed: 153 average time/residue: 0.2780 time to fit residues: 63.5991 Evaluate side-chains 150 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 30 optimal weight: 0.0060 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 161 optimal weight: 0.3980 chunk 149 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.136859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128390 restraints weight = 16846.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127403 restraints weight = 28040.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127851 restraints weight = 24636.357| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13788 Z= 0.109 Angle : 0.504 6.746 18756 Z= 0.265 Chirality : 0.045 0.172 2256 Planarity : 0.004 0.043 2361 Dihedral : 5.175 53.207 2121 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.31 % Allowed : 14.98 % Favored : 82.71 % 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: -0.27 (0.20), residues: 1728 helix: 0.61 (0.25), residues: 465 sheet: -0.18 (0.24), residues: 420 loop : -0.53 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 52 HIS 0.004 0.001 HIS F 58 PHE 0.010 0.001 PHE B 376 TYR 0.008 0.001 TYR C 292 ARG 0.003 0.000 ARG A 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 12) link_NAG-ASN : angle 2.47789 ( 36) hydrogen bonds : bond 0.03688 ( 591) hydrogen bonds : angle 4.98327 ( 1698) SS BOND : bond 0.00173 ( 18) SS BOND : angle 1.16398 ( 36) covalent geometry : bond 0.00251 (13758) covalent geometry : angle 0.49079 (18684) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 1.617 Fit side-chains REVERT: A 68 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.6834 (ppp) REVERT: A 190 ILE cc_start: 0.9140 (mt) cc_final: 0.8850 (mm) REVERT: A 336 ARG cc_start: 0.7523 (mmm160) cc_final: 0.7132 (tpt170) REVERT: B 190 ILE cc_start: 0.8633 (mt) cc_final: 0.8433 (mm) REVERT: B 218 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8431 (tt) REVERT: C 136 GLU cc_start: 0.7359 (tp30) cc_final: 0.6820 (tt0) REVERT: C 190 ILE cc_start: 0.8878 (mt) cc_final: 0.8634 (mm) REVERT: E 82 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6890 (mtp) outliers start: 35 outliers final: 25 residues processed: 153 average time/residue: 0.2489 time to fit residues: 57.3227 Evaluate side-chains 149 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 7 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139116 restraints weight = 16302.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.139885 restraints weight = 13012.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140171 restraints weight = 11014.433| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13788 Z= 0.135 Angle : 0.531 7.161 18756 Z= 0.278 Chirality : 0.046 0.175 2256 Planarity : 0.004 0.043 2361 Dihedral : 5.192 53.248 2121 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.57 % Allowed : 15.05 % Favored : 82.38 % 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: -0.34 (0.20), residues: 1728 helix: 0.62 (0.26), residues: 465 sheet: -0.20 (0.26), residues: 372 loop : -0.63 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 114 HIS 0.003 0.001 HIS D 58 PHE 0.010 0.001 PHE B 376 TYR 0.010 0.001 TYR A 292 ARG 0.005 0.000 ARG A 365 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 12) link_NAG-ASN : angle 2.50701 ( 36) hydrogen bonds : bond 0.03883 ( 591) hydrogen bonds : angle 4.98465 ( 1698) SS BOND : bond 0.00178 ( 18) SS BOND : angle 1.20827 ( 36) covalent geometry : bond 0.00326 (13758) covalent geometry : angle 0.51760 (18684) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 1.449 Fit side-chains REVERT: A 68 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.6886 (ppp) REVERT: A 190 ILE cc_start: 0.9147 (mt) cc_final: 0.8843 (mm) REVERT: A 336 ARG cc_start: 0.7604 (mmm160) cc_final: 0.7169 (tpt170) REVERT: B 218 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8505 (tt) REVERT: C 68 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.6691 (ppp) REVERT: C 136 GLU cc_start: 0.7562 (tp30) cc_final: 0.6905 (tt0) REVERT: C 190 ILE cc_start: 0.8881 (mt) cc_final: 0.8621 (mm) outliers start: 39 outliers final: 32 residues processed: 150 average time/residue: 0.2431 time to fit residues: 54.9776 Evaluate side-chains 155 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 79 optimal weight: 0.0270 chunk 168 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124910 restraints weight = 16899.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123940 restraints weight = 23303.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124632 restraints weight = 20788.528| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13788 Z= 0.109 Angle : 0.501 6.788 18756 Z= 0.262 Chirality : 0.045 0.172 2256 Planarity : 0.004 0.043 2361 Dihedral : 5.034 53.188 2121 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.44 % Allowed : 15.38 % Favored : 82.18 % 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: -0.21 (0.20), residues: 1728 helix: 0.75 (0.26), residues: 465 sheet: -0.15 (0.24), residues: 420 loop : -0.55 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 114 HIS 0.003 0.001 HIS D 58 PHE 0.012 0.001 PHE F 28 TYR 0.008 0.001 TYR B 292 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 12) link_NAG-ASN : angle 2.39493 ( 36) hydrogen bonds : bond 0.03559 ( 591) hydrogen bonds : angle 4.85558 ( 1698) SS BOND : bond 0.00217 ( 18) SS BOND : angle 1.16670 ( 36) covalent geometry : bond 0.00254 (13758) covalent geometry : angle 0.48766 (18684) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.572 Fit side-chains REVERT: A 68 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.6789 (ppp) REVERT: A 190 ILE cc_start: 0.9111 (mt) cc_final: 0.8840 (mm) REVERT: A 336 ARG cc_start: 0.7540 (mmm160) cc_final: 0.7136 (tpt170) REVERT: B 68 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7392 (ppp) REVERT: B 218 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8494 (tt) REVERT: C 68 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.6564 (ppp) REVERT: C 136 GLU cc_start: 0.7405 (tp30) cc_final: 0.6853 (tt0) REVERT: C 190 ILE cc_start: 0.8847 (mt) cc_final: 0.8618 (mm) REVERT: D 33 MET cc_start: 0.7295 (mmm) cc_final: 0.7067 (mtp) REVERT: E 28 PHE cc_start: 0.8236 (t80) cc_final: 0.8027 (t80) outliers start: 37 outliers final: 31 residues processed: 152 average time/residue: 0.2324 time to fit residues: 53.9618 Evaluate side-chains 154 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 93 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121445 restraints weight = 17168.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120476 restraints weight = 24238.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121281 restraints weight = 23034.593| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13788 Z= 0.168 Angle : 0.561 6.852 18756 Z= 0.294 Chirality : 0.047 0.179 2256 Planarity : 0.004 0.045 2361 Dihedral : 5.288 53.129 2121 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.44 % Allowed : 15.51 % Favored : 82.05 % 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: -0.43 (0.20), residues: 1728 helix: 0.53 (0.25), residues: 465 sheet: -0.21 (0.25), residues: 390 loop : -0.69 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 114 HIS 0.004 0.001 HIS D 58 PHE 0.010 0.002 PHE F 28 TYR 0.013 0.002 TYR C 292 ARG 0.005 0.000 ARG A 365 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 12) link_NAG-ASN : angle 2.57607 ( 36) hydrogen bonds : bond 0.04170 ( 591) hydrogen bonds : angle 5.06801 ( 1698) SS BOND : bond 0.00186 ( 18) SS BOND : angle 1.35413 ( 36) covalent geometry : bond 0.00416 (13758) covalent geometry : angle 0.54744 (18684) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.616 Fit side-chains REVERT: A 68 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.6952 (ppp) REVERT: A 190 ILE cc_start: 0.9176 (mt) cc_final: 0.8882 (mm) REVERT: A 336 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7174 (tpt170) REVERT: B 68 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7458 (ppp) REVERT: B 218 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8521 (tt) REVERT: B 411 MET cc_start: 0.6913 (ttp) cc_final: 0.6658 (ttp) REVERT: C 68 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.6719 (ppp) REVERT: C 136 GLU cc_start: 0.7446 (tp30) cc_final: 0.6945 (tt0) REVERT: C 190 ILE cc_start: 0.8932 (mt) cc_final: 0.8690 (mm) REVERT: E 28 PHE cc_start: 0.8288 (t80) cc_final: 0.8071 (t80) outliers start: 37 outliers final: 30 residues processed: 151 average time/residue: 0.2287 time to fit residues: 53.0907 Evaluate side-chains 156 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 33 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123410 restraints weight = 17110.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122364 restraints weight = 26038.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122992 restraints weight = 23306.629| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13788 Z= 0.146 Angle : 0.541 6.788 18756 Z= 0.283 Chirality : 0.046 0.176 2256 Planarity : 0.004 0.045 2361 Dihedral : 5.271 53.198 2121 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.31 % Allowed : 15.97 % Favored : 81.72 % 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: -0.49 (0.20), residues: 1728 helix: 0.59 (0.26), residues: 447 sheet: -0.27 (0.24), residues: 420 loop : -0.78 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 114 HIS 0.004 0.001 HIS F 58 PHE 0.010 0.001 PHE B 376 TYR 0.011 0.001 TYR C 292 ARG 0.004 0.000 ARG A 365 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 12) link_NAG-ASN : angle 2.57558 ( 36) hydrogen bonds : bond 0.04024 ( 591) hydrogen bonds : angle 5.03902 ( 1698) SS BOND : bond 0.00172 ( 18) SS BOND : angle 1.36424 ( 36) covalent geometry : bond 0.00358 (13758) covalent geometry : angle 0.52694 (18684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4245.00 seconds wall clock time: 74 minutes 45.35 seconds (4485.35 seconds total)