Starting phenix.real_space_refine on Fri Jul 3 18:38:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uc2_26442/07_2026/7uc2_26442.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uc2_26442/07_2026/7uc2_26442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uc2_26442/07_2026/7uc2_26442.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uc2_26442/07_2026/7uc2_26442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uc2_26442/07_2026/7uc2_26442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uc2_26442/07_2026/7uc2_26442.map" model { file = "/net/cci-nas-00/data/ceres_data/7uc2_26442/07_2026/7uc2_26442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uc2_26442/07_2026/7uc2_26442.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.193 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 80 5.16 5 C 10008 2.51 5 N 2720 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15820 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3852 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 451} Chain breaks: 1 Chain: "B" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3852 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 451} Chain breaks: 1 Chain: "C" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3852 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 451} Chain breaks: 1 Chain: "D" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3852 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 451} Chain breaks: 1 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 3.78, per 1000 atoms: 0.24 Number of scatterers: 15820 At special positions: 0 Unit cell: (92.13, 137.78, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 24 15.00 O 2988 8.00 N 2720 7.00 C 10008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 659.7 milliseconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 6 sheets defined 42.7% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 41 through 58 removed outlier: 4.981A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.591A pdb=" N GLN A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Proline residue: A 86 - end of helix removed outlier: 3.925A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.895A pdb=" N ARG A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 201 through 204 removed outlier: 3.591A pdb=" N GLY A 204 " --> pdb=" O HIS A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 204' Processing helix chain 'A' and resid 205 through 217 removed outlier: 4.713A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.796A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 476 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.087A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 5.325A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.522A pdb=" N ARG B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.776A pdb=" N LEU B 203 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 204 " --> pdb=" O HIS B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 204' Processing helix chain 'B' and resid 205 through 217 removed outlier: 4.712A pdb=" N MET B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.828A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.653A pdb=" N CYS B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 315 through 320 removed outlier: 3.900A pdb=" N ALA B 318 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 454 through 476 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.115A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 5.285A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 176 through 189 Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 205 through 217 removed outlier: 4.667A pdb=" N MET C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.931A pdb=" N GLU C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 280 through 293 Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 315 through 320 removed outlier: 3.507A pdb=" N ALA C 318 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 447 Processing helix chain 'C' and resid 454 through 476 Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 489 through 500 removed outlier: 4.015A pdb=" N ASP C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 removed outlier: 5.240A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.544A pdb=" N ARG D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 157 Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 205 through 217 removed outlier: 4.642A pdb=" N MET D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 removed outlier: 3.714A pdb=" N PHE D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.228A pdb=" N ARG D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 315 through 320 removed outlier: 3.972A pdb=" N ALA D 318 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 489 through 500 removed outlier: 4.122A pdb=" N ASP D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.406A pdb=" N ILE A 33 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR A 139 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 35 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG A 136 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE A 168 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 138 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A 199 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 169 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG A 198 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 480 through 483 removed outlier: 6.361A pdb=" N ALA A 367 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL A 400 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL B 400 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA B 231 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ARG B 357 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 235 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLY B 359 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE B 237 " --> pdb=" O GLY B 359 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 109 removed outlier: 8.729A pdb=" N SER B 106 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 67 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL B 108 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLY B 69 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE B 33 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TYR B 139 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 35 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE B 168 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE B 138 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.808A pdb=" N THR C 31 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU C 137 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 33 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR C 139 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 35 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG C 136 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE C 168 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE C 138 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE C 199 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 169 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG C 198 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 480 through 483 removed outlier: 6.653A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL C 400 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL D 400 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA D 367 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.498A pdb=" N ARG D 136 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE D 168 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE D 138 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TYR D 197 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 167 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D 199 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 169 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG D 198 " --> pdb=" O VAL D 453 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1944 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: 2.81 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2585 1.31 - 1.43: 4400 1.43 - 1.56: 9034 1.56 - 1.68: 41 1.68 - 1.81: 132 Bond restraints: 16192 Sorted by residual: bond pdb=" C1B NAP C 602 " pdb=" C2B NAP C 602 " ideal model delta sigma weight residual 1.528 1.302 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1B NAP A 602 " pdb=" C2B NAP A 602 " ideal model delta sigma weight residual 1.528 1.302 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1B NAP D 602 " pdb=" C2B NAP D 602 " ideal model delta sigma weight residual 1.528 1.304 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1B NAP B 602 " pdb=" C2B NAP B 602 " ideal model delta sigma weight residual 1.528 1.304 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1B NAP C 601 " pdb=" C2B NAP C 601 " ideal model delta sigma weight residual 1.528 1.306 0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 16187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 21561 2.76 - 5.53: 293 5.53 - 8.29: 74 8.29 - 11.06: 19 11.06 - 13.82: 33 Bond angle restraints: 21980 Sorted by residual: angle pdb=" N THR C 423 " pdb=" CA THR C 423 " pdb=" C THR C 423 " ideal model delta sigma weight residual 109.72 121.84 -12.12 1.60e+00 3.91e-01 5.74e+01 angle pdb=" N1A NAP D 601 " pdb=" C6A NAP D 601 " pdb=" N6A NAP D 601 " ideal model delta sigma weight residual 119.30 105.48 13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N1A NAP A 602 " pdb=" C6A NAP A 602 " pdb=" N6A NAP A 602 " ideal model delta sigma weight residual 119.30 105.55 13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N1A NAP B 602 " pdb=" C6A NAP B 602 " pdb=" N6A NAP B 602 " ideal model delta sigma weight residual 119.30 105.56 13.74 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N1A NAP B 601 " pdb=" C6A NAP B 601 " pdb=" N6A NAP B 601 " ideal model delta sigma weight residual 119.30 105.58 13.72 3.00e+00 1.11e-01 2.09e+01 ... (remaining 21975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 7951 17.19 - 34.38: 1127 34.38 - 51.57: 400 51.57 - 68.76: 109 68.76 - 85.95: 49 Dihedral angle restraints: 9636 sinusoidal: 4104 harmonic: 5532 Sorted by residual: dihedral pdb=" CA SER D 157 " pdb=" C SER D 157 " pdb=" N CYS D 158 " pdb=" CA CYS D 158 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ALA C 367 " pdb=" C ALA C 367 " pdb=" N GLU C 368 " pdb=" CA GLU C 368 " ideal model delta harmonic sigma weight residual -180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA SER C 157 " pdb=" C SER C 157 " pdb=" N CYS C 158 " pdb=" CA CYS C 158 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 9633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2041 0.071 - 0.142: 268 0.142 - 0.214: 8 0.214 - 0.285: 7 0.285 - 0.356: 16 Chirality restraints: 2340 Sorted by residual: chirality pdb=" C2B NAP B 602 " pdb=" C1B NAP B 602 " pdb=" C3B NAP B 602 " pdb=" O2B NAP B 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C2B NAP D 602 " pdb=" C1B NAP D 602 " pdb=" C3B NAP D 602 " pdb=" O2B NAP D 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.41 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C2B NAP C 602 " pdb=" C1B NAP C 602 " pdb=" C3B NAP C 602 " pdb=" O2B NAP C 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2337 not shown) Planarity restraints: 2808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 143 " -0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO B 144 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 144 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 144 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 85 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO A 86 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 86 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 86 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 85 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 86 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 86 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 86 " 0.027 5.00e-02 4.00e+02 ... (remaining 2805 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1267 2.74 - 3.28: 15365 3.28 - 3.82: 28625 3.82 - 4.36: 35438 4.36 - 4.90: 58535 Nonbonded interactions: 139230 Sorted by model distance: nonbonded pdb=" OH TYR A 139 " pdb=" OH TYR A 437 " model vdw 2.199 3.040 nonbonded pdb=" O TRP D 462 " pdb=" OG1 THR D 466 " model vdw 2.216 3.040 nonbonded pdb=" O TRP C 462 " pdb=" OG1 THR C 466 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR B 139 " pdb=" OH TYR B 437 " model vdw 2.234 3.040 nonbonded pdb=" OE1 GLU C 419 " pdb=" OH TYR C 507 " model vdw 2.243 3.040 ... (remaining 139225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.780 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 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 : 0.009 0.226 16192 Z= 0.476 Angle : 0.943 13.820 21980 Z= 0.385 Chirality : 0.054 0.356 2340 Planarity : 0.005 0.067 2808 Dihedral : 19.348 85.951 6076 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.02 % Allowed : 23.08 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1884 helix: 1.11 (0.21), residues: 704 sheet: -0.16 (0.26), residues: 416 loop : 0.34 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 120 TYR 0.024 0.001 TYR D 249 PHE 0.015 0.001 PHE B 88 TRP 0.026 0.002 TRP A 53 HIS 0.003 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00948 / 0.48 (16192) covalent geometry : angle 0.94326 / 0.39 (21980) hydrogen bonds : bond 0.14083 / 9.29 ( 678) hydrogen bonds : angle 6.74997 / 4.75 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: B 424 TYR cc_start: 0.5485 (OUTLIER) cc_final: 0.4807 (p90) REVERT: C 30 ASP cc_start: 0.7836 (m-30) cc_final: 0.7388 (t0) REVERT: C 424 TYR cc_start: 0.3844 (OUTLIER) cc_final: 0.2220 (t80) outliers start: 17 outliers final: 7 residues processed: 231 average time/residue: 0.6180 time to fit residues: 156.7054 Evaluate side-chains 227 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 133 GLN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106143 restraints weight = 18975.000| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.85 r_work: 0.3135 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16192 Z= 0.136 Angle : 0.540 9.016 21980 Z= 0.282 Chirality : 0.043 0.199 2340 Planarity : 0.004 0.060 2808 Dihedral : 10.283 72.819 2283 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.94 % Allowed : 20.43 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1884 helix: 1.20 (0.21), residues: 696 sheet: -0.32 (0.25), residues: 420 loop : 0.32 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 120 TYR 0.017 0.001 TYR C 118 PHE 0.017 0.001 PHE D 88 TRP 0.014 0.001 TRP A 164 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16192) covalent geometry : angle 0.54013 / 0.28 (21980) hydrogen bonds : bond 0.04152 / 2.74 ( 678) hydrogen bonds : angle 5.48993 / 3.91 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.769 Fit side-chains REVERT: A 317 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7360 (mm-30) REVERT: B 413 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.6640 (t80) REVERT: B 424 TYR cc_start: 0.5208 (OUTLIER) cc_final: 0.4477 (p90) REVERT: C 30 ASP cc_start: 0.7906 (m-30) cc_final: 0.7373 (t0) REVERT: C 252 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: D 99 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7611 (mm-30) REVERT: D 413 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.6857 (t80) outliers start: 49 outliers final: 13 residues processed: 251 average time/residue: 0.6185 time to fit residues: 170.8677 Evaluate side-chains 230 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 136 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 155 HIS C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.142603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103963 restraints weight = 19299.419| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.85 r_work: 0.3107 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16192 Z= 0.177 Angle : 0.559 9.190 21980 Z= 0.289 Chirality : 0.044 0.150 2340 Planarity : 0.005 0.062 2808 Dihedral : 9.423 59.638 2271 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.43 % Allowed : 20.19 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1884 helix: 1.20 (0.21), residues: 696 sheet: -0.38 (0.25), residues: 420 loop : 0.29 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 439 TYR 0.019 0.002 TYR D 118 PHE 0.015 0.001 PHE B 101 TRP 0.015 0.002 TRP A 164 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (16192) covalent geometry : angle 0.55872 / 0.29 (21980) hydrogen bonds : bond 0.04361 / 2.87 ( 678) hydrogen bonds : angle 5.42016 / 3.87 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7656 (mptm) REVERT: A 317 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: B 119 GLN cc_start: 0.8121 (mm110) cc_final: 0.7509 (mm-40) REVERT: B 317 GLU cc_start: 0.7209 (tp30) cc_final: 0.6964 (tp30) REVERT: B 413 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.6696 (t80) REVERT: B 424 TYR cc_start: 0.5301 (OUTLIER) cc_final: 0.4606 (p90) REVERT: C 466 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8587 (m) REVERT: D 42 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6774 (p0) REVERT: D 99 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7612 (mm-30) REVERT: D 413 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7248 (t80) outliers start: 57 outliers final: 24 residues processed: 259 average time/residue: 0.5823 time to fit residues: 165.5610 Evaluate side-chains 247 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 104 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104521 restraints weight = 19128.145| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.84 r_work: 0.3114 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16192 Z= 0.160 Angle : 0.544 9.153 21980 Z= 0.283 Chirality : 0.043 0.227 2340 Planarity : 0.005 0.061 2808 Dihedral : 9.100 59.991 2268 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.61 % Allowed : 20.73 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1884 helix: 1.21 (0.21), residues: 696 sheet: -0.47 (0.25), residues: 428 loop : 0.30 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 120 TYR 0.020 0.001 TYR D 118 PHE 0.019 0.001 PHE B 101 TRP 0.015 0.002 TRP A 164 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (16192) covalent geometry : angle 0.54446 / 0.28 (21980) hydrogen bonds : bond 0.04109 / 2.70 ( 678) hydrogen bonds : angle 5.34108 / 3.82 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: B 413 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6830 (t80) REVERT: B 419 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: B 424 TYR cc_start: 0.5234 (OUTLIER) cc_final: 0.4539 (p90) REVERT: C 239 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: C 424 TYR cc_start: 0.3698 (OUTLIER) cc_final: 0.1833 (t80) REVERT: C 466 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8576 (m) REVERT: D 42 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6775 (p0) REVERT: D 99 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7393 (mm-30) REVERT: D 133 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7267 (pm20) REVERT: D 249 TYR cc_start: 0.7614 (t80) cc_final: 0.7359 (t80) REVERT: D 297 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: D 413 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7334 (t80) outliers start: 60 outliers final: 24 residues processed: 263 average time/residue: 0.5823 time to fit residues: 167.9569 Evaluate side-chains 248 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 424 TYR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 166 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103472 restraints weight = 19164.873| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.74 r_work: 0.3109 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16192 Z= 0.150 Angle : 0.537 9.280 21980 Z= 0.278 Chirality : 0.043 0.146 2340 Planarity : 0.004 0.057 2808 Dihedral : 8.926 59.340 2268 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.03 % Allowed : 20.91 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1884 helix: 1.23 (0.21), residues: 696 sheet: -0.50 (0.25), residues: 428 loop : 0.29 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 120 TYR 0.020 0.001 TYR B 118 PHE 0.021 0.001 PHE B 101 TRP 0.015 0.001 TRP A 164 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (16192) covalent geometry : angle 0.53676 / 0.28 (21980) hydrogen bonds : bond 0.03973 / 2.61 ( 678) hydrogen bonds : angle 5.29349 / 3.79 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 222 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7663 (mptm) REVERT: A 182 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7536 (ttm170) REVERT: B 88 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6794 (t80) REVERT: B 119 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7080 (mm-40) REVERT: B 133 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: B 182 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6885 (ttt-90) REVERT: B 413 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.6861 (t80) REVERT: B 419 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: B 424 TYR cc_start: 0.5294 (OUTLIER) cc_final: 0.4577 (p90) REVERT: C 239 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: C 404 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8240 (ppp) REVERT: C 424 TYR cc_start: 0.3705 (OUTLIER) cc_final: 0.1827 (t80) REVERT: C 466 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8577 (m) REVERT: D 37 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7604 (mtt) REVERT: D 42 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6805 (p0) REVERT: D 99 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7414 (mm-30) REVERT: D 133 GLN cc_start: 0.7496 (pm20) cc_final: 0.7264 (pm20) REVERT: D 297 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: D 421 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8189 (m-30) outliers start: 67 outliers final: 30 residues processed: 267 average time/residue: 0.5909 time to fit residues: 172.7973 Evaluate side-chains 258 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 424 TYR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 135 optimal weight: 0.2980 chunk 91 optimal weight: 8.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 178 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.143033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103105 restraints weight = 18823.455| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.74 r_work: 0.3103 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16192 Z= 0.171 Angle : 0.552 9.264 21980 Z= 0.286 Chirality : 0.044 0.248 2340 Planarity : 0.005 0.054 2808 Dihedral : 8.887 58.502 2268 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.27 % Allowed : 21.21 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1884 helix: 1.18 (0.21), residues: 696 sheet: -0.52 (0.25), residues: 428 loop : 0.28 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 120 TYR 0.020 0.002 TYR D 118 PHE 0.024 0.001 PHE B 101 TRP 0.015 0.002 TRP A 164 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (16192) covalent geometry : angle 0.55242 / 0.29 (21980) hydrogen bonds : bond 0.04116 / 2.70 ( 678) hydrogen bonds : angle 5.32708 / 3.81 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 215 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7628 (mptm) REVERT: A 182 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7494 (ttm170) REVERT: B 88 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6777 (t80) REVERT: B 119 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7048 (mm-40) REVERT: B 182 ARG cc_start: 0.7116 (ttp-110) cc_final: 0.6841 (ttt-90) REVERT: B 413 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.6853 (t80) REVERT: B 419 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: B 424 TYR cc_start: 0.5282 (OUTLIER) cc_final: 0.4557 (p90) REVERT: C 239 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: C 404 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8290 (ppp) REVERT: C 424 TYR cc_start: 0.3631 (OUTLIER) cc_final: 0.1833 (t80) REVERT: C 466 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8573 (m) REVERT: D 42 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6766 (p0) REVERT: D 99 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7322 (mm-30) REVERT: D 102 PHE cc_start: 0.8206 (m-80) cc_final: 0.7850 (m-80) REVERT: D 133 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: D 297 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: D 413 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7710 (t80) REVERT: D 421 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8160 (m-30) outliers start: 71 outliers final: 33 residues processed: 263 average time/residue: 0.6046 time to fit residues: 174.4616 Evaluate side-chains 257 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 424 TYR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 185 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103635 restraints weight = 18786.711| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.79 r_work: 0.3092 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16192 Z= 0.195 Angle : 0.574 9.868 21980 Z= 0.298 Chirality : 0.044 0.188 2340 Planarity : 0.005 0.059 2808 Dihedral : 8.868 59.514 2268 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.09 % Allowed : 21.21 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1884 helix: 1.05 (0.20), residues: 700 sheet: -0.53 (0.25), residues: 428 loop : 0.23 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 120 TYR 0.024 0.002 TYR D 118 PHE 0.029 0.002 PHE B 101 TRP 0.016 0.002 TRP A 164 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (16192) covalent geometry : angle 0.57449 / 0.30 (21980) hydrogen bonds : bond 0.04321 / 2.83 ( 678) hydrogen bonds : angle 5.39030 / 3.85 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7672 (mptm) REVERT: A 182 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7515 (ttm170) REVERT: A 246 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7155 (ptt-90) REVERT: A 413 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7582 (t80) REVERT: B 88 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.6857 (t80) REVERT: B 119 GLN cc_start: 0.7762 (mm-40) cc_final: 0.6990 (mm-40) REVERT: B 182 ARG cc_start: 0.7207 (ttp-110) cc_final: 0.7003 (ttm-80) REVERT: B 413 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.6867 (t80) REVERT: B 419 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8509 (pm20) REVERT: B 424 TYR cc_start: 0.5311 (OUTLIER) cc_final: 0.4585 (p90) REVERT: C 239 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: C 404 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8372 (ppp) REVERT: C 424 TYR cc_start: 0.3742 (OUTLIER) cc_final: 0.1922 (t80) REVERT: C 466 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8598 (m) REVERT: D 42 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6822 (p0) REVERT: D 99 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7438 (mm-30) REVERT: D 249 TYR cc_start: 0.7556 (t80) cc_final: 0.7351 (t80) REVERT: D 297 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: D 413 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8016 (t80) REVERT: D 421 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8154 (m-30) outliers start: 68 outliers final: 30 residues processed: 260 average time/residue: 0.6173 time to fit residues: 176.1067 Evaluate side-chains 254 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 424 TYR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 111 optimal weight: 6.9990 chunk 51 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101411 restraints weight = 18962.737| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.74 r_work: 0.3068 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16192 Z= 0.226 Angle : 0.600 9.826 21980 Z= 0.311 Chirality : 0.046 0.232 2340 Planarity : 0.005 0.071 2808 Dihedral : 8.902 57.249 2268 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.91 % Allowed : 21.63 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1884 helix: 0.96 (0.20), residues: 700 sheet: -0.52 (0.25), residues: 428 loop : 0.19 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 120 TYR 0.026 0.002 TYR D 118 PHE 0.033 0.002 PHE B 101 TRP 0.016 0.002 TRP A 164 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (16192) covalent geometry : angle 0.59971 / 0.31 (21980) hydrogen bonds : bond 0.04581 / 3.00 ( 678) hydrogen bonds : angle 5.49319 / 3.92 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 213 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7635 (mptm) REVERT: A 182 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7502 (ttm170) REVERT: A 246 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7151 (ptt-90) REVERT: A 413 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7668 (t80) REVERT: B 119 GLN cc_start: 0.7774 (mm-40) cc_final: 0.6985 (mm-40) REVERT: B 133 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: B 398 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8153 (pt0) REVERT: B 413 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.6894 (t80) REVERT: B 419 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: B 424 TYR cc_start: 0.5287 (OUTLIER) cc_final: 0.4589 (p90) REVERT: C 239 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: C 404 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8444 (ppp) REVERT: C 424 TYR cc_start: 0.3709 (OUTLIER) cc_final: 0.1888 (t80) REVERT: C 466 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8606 (m) REVERT: D 42 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6854 (p0) REVERT: D 246 ARG cc_start: 0.7118 (ppt170) cc_final: 0.6788 (mtp-110) REVERT: D 297 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: D 398 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: D 421 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8186 (m-30) outliers start: 65 outliers final: 33 residues processed: 259 average time/residue: 0.6110 time to fit residues: 173.5465 Evaluate side-chains 256 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 424 TYR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 103 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 ASN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106266 restraints weight = 18865.030| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.80 r_work: 0.3141 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16192 Z= 0.113 Angle : 0.524 9.282 21980 Z= 0.273 Chirality : 0.042 0.144 2340 Planarity : 0.004 0.059 2808 Dihedral : 8.616 58.083 2268 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.00 % Allowed : 22.72 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1884 helix: 1.15 (0.21), residues: 696 sheet: -0.59 (0.25), residues: 428 loop : 0.25 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 120 TYR 0.024 0.001 TYR D 118 PHE 0.040 0.001 PHE B 101 TRP 0.018 0.001 TRP A 164 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (16192) covalent geometry : angle 0.52399 / 0.27 (21980) hydrogen bonds : bond 0.03623 / 2.38 ( 678) hydrogen bonds : angle 5.24228 / 3.76 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7498 (ttm170) REVERT: A 246 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7232 (ptt-90) REVERT: A 419 GLU cc_start: 0.8523 (pm20) cc_final: 0.8267 (pt0) REVERT: B 88 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6702 (t80) REVERT: B 119 GLN cc_start: 0.7763 (mm-40) cc_final: 0.6949 (mm-40) REVERT: B 260 MET cc_start: 0.9045 (ttm) cc_final: 0.8776 (mtt) REVERT: B 398 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: B 413 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.6760 (t80) REVERT: B 419 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8447 (pm20) REVERT: B 424 TYR cc_start: 0.5343 (OUTLIER) cc_final: 0.4606 (p90) REVERT: C 85 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7442 (mm-30) REVERT: C 239 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: C 404 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8309 (ppp) REVERT: C 466 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8554 (m) REVERT: D 133 GLN cc_start: 0.7397 (pm20) cc_final: 0.7116 (pm20) REVERT: D 297 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: D 421 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: D 466 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8633 (m) outliers start: 50 outliers final: 18 residues processed: 251 average time/residue: 0.6092 time to fit residues: 167.6972 Evaluate side-chains 238 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 99 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 104 optimal weight: 30.0000 chunk 82 optimal weight: 8.9990 chunk 11 optimal weight: 0.0050 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 102 optimal weight: 5.9990 overall best weight: 2.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105684 restraints weight = 18817.609| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.82 r_work: 0.3128 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16192 Z= 0.133 Angle : 0.535 9.299 21980 Z= 0.278 Chirality : 0.043 0.224 2340 Planarity : 0.004 0.067 2808 Dihedral : 8.588 56.609 2268 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.28 % Allowed : 23.68 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1884 helix: 1.13 (0.21), residues: 696 sheet: -0.56 (0.25), residues: 428 loop : 0.25 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 120 TYR 0.023 0.001 TYR D 118 PHE 0.043 0.001 PHE B 101 TRP 0.020 0.002 TRP A 53 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (16192) covalent geometry : angle 0.53473 / 0.28 (21980) hydrogen bonds : bond 0.03762 / 2.47 ( 678) hydrogen bonds : angle 5.22444 / 3.74 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7496 (ttm170) REVERT: A 246 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7205 (ptt-90) REVERT: A 419 GLU cc_start: 0.8574 (pm20) cc_final: 0.8283 (pt0) REVERT: B 119 GLN cc_start: 0.7800 (mm-40) cc_final: 0.6987 (mm-40) REVERT: B 182 ARG cc_start: 0.7455 (ttt-90) cc_final: 0.6657 (ttp-110) REVERT: B 260 MET cc_start: 0.9098 (ttm) cc_final: 0.8814 (mtt) REVERT: B 398 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: B 413 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.6772 (t80) REVERT: B 419 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: B 424 TYR cc_start: 0.5267 (OUTLIER) cc_final: 0.4567 (p90) REVERT: C 85 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7427 (mm-30) REVERT: C 239 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: C 249 TYR cc_start: 0.7913 (m-10) cc_final: 0.7713 (m-80) REVERT: C 404 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8221 (ppp) REVERT: C 466 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8561 (m) REVERT: D 133 GLN cc_start: 0.7452 (pm20) cc_final: 0.7175 (pm20) REVERT: D 297 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: D 421 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: D 466 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8682 (m) outliers start: 38 outliers final: 19 residues processed: 239 average time/residue: 0.6142 time to fit residues: 161.3012 Evaluate side-chains 239 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 77 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 83 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.141991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103726 restraints weight = 19021.556| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.76 r_work: 0.3104 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16192 Z= 0.184 Angle : 0.570 9.626 21980 Z= 0.296 Chirality : 0.044 0.150 2340 Planarity : 0.005 0.067 2808 Dihedral : 8.676 56.688 2268 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.40 % Allowed : 23.44 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1884 helix: 1.08 (0.20), residues: 696 sheet: -0.53 (0.26), residues: 428 loop : 0.21 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 120 TYR 0.024 0.002 TYR D 118 PHE 0.044 0.002 PHE B 101 TRP 0.024 0.002 TRP A 53 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (16192) covalent geometry : angle 0.56987 / 0.30 (21980) hydrogen bonds : bond 0.04199 / 2.76 ( 678) hydrogen bonds : angle 5.34654 / 3.82 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5679.97 seconds wall clock time: 97 minutes 27.85 seconds (5847.85 seconds total)