Starting phenix.real_space_refine on Wed Mar 4 18:39:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uc2_26442/03_2026/7uc2_26442.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uc2_26442/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7uc2_26442/03_2026/7uc2_26442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uc2_26442/03_2026/7uc2_26442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uc2_26442/03_2026/7uc2_26442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uc2_26442/03_2026/7uc2_26442.map" } 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-5986/lib/python3.9/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: 3.36, per 1000 atoms: 0.21 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: 1.28 Conformation dependent library (CDL) restraints added in 736.1 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: 0.56 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: 2.74 Time building geometry restraints manager: 1.73 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: 8092 17.19 - 34.38: 1246 34.38 - 51.57: 473 51.57 - 68.76: 141 68.76 - 85.95: 52 Dihedral angle restraints: 10004 sinusoidal: 4472 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 10001 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.100 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 20.166 85.951 6444 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 covalent geometry : bond 0.00948 (16192) covalent geometry : angle 0.94326 (21980) hydrogen bonds : bond 0.14083 ( 678) hydrogen bonds : angle 6.74997 ( 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 : 0.636 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: 0.7224 time to fit residues: 181.8376 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 : 0.598 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106395 restraints weight = 18974.250| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.84 r_work: 0.3137 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16192 Z= 0.136 Angle : 0.543 9.059 21980 Z= 0.281 Chirality : 0.043 0.202 2340 Planarity : 0.004 0.060 2808 Dihedral : 13.284 72.763 2651 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.94 % Allowed : 20.55 % Favored : 76.50 % 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: -0.31 (0.25), residues: 420 loop : 0.32 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 120 TYR 0.018 0.001 TYR C 118 PHE 0.017 0.001 PHE D 88 TRP 0.014 0.001 TRP A 164 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00304 (16192) covalent geometry : angle 0.54309 (21980) hydrogen bonds : bond 0.04188 ( 678) hydrogen bonds : angle 5.46993 ( 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 270 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 0.637 Fit side-chains REVERT: A 317 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7325 (mm-30) REVERT: B 413 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.6638 (t80) REVERT: B 424 TYR cc_start: 0.5196 (OUTLIER) cc_final: 0.4472 (p90) REVERT: C 30 ASP cc_start: 0.7909 (m-30) cc_final: 0.7374 (t0) REVERT: C 252 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8303 (pt0) REVERT: D 99 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 413 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.6873 (t80) outliers start: 49 outliers final: 13 residues processed: 252 average time/residue: 0.7211 time to fit residues: 198.6485 Evaluate side-chains 233 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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: 9.9990 chunk 172 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102292 restraints weight = 19283.387| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.74 r_work: 0.3096 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16192 Z= 0.184 Angle : 0.564 9.326 21980 Z= 0.293 Chirality : 0.044 0.152 2340 Planarity : 0.005 0.061 2808 Dihedral : 12.635 60.782 2639 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.67 % Allowed : 20.07 % Favored : 76.26 % 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: 0.57 (0.20), residues: 1884 helix: 1.19 (0.21), residues: 696 sheet: -0.44 (0.25), residues: 428 loop : 0.32 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 120 TYR 0.019 0.002 TYR D 118 PHE 0.016 0.001 PHE B 88 TRP 0.015 0.002 TRP A 164 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00428 (16192) covalent geometry : angle 0.56401 (21980) hydrogen bonds : bond 0.04444 ( 678) hydrogen bonds : angle 5.43007 ( 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 283 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7687 (mptm) REVERT: B 119 GLN cc_start: 0.8128 (mm110) cc_final: 0.7534 (mm-40) REVERT: B 317 GLU cc_start: 0.7237 (tp30) cc_final: 0.6979 (tp30) REVERT: B 413 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.6792 (t80) REVERT: B 424 TYR cc_start: 0.5324 (OUTLIER) cc_final: 0.4617 (p90) REVERT: C 466 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8589 (m) REVERT: D 42 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6765 (p0) REVERT: D 99 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7603 (mm-30) REVERT: D 413 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7339 (t80) outliers start: 61 outliers final: 27 residues processed: 263 average time/residue: 0.7359 time to fit residues: 211.4383 Evaluate side-chains 247 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 252 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 473 GLU 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 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 262 ASN 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 422 LEU 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: 30.0000 chunk 42 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.143647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103920 restraints weight = 19066.740| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.73 r_work: 0.3117 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16192 Z= 0.139 Angle : 0.531 8.944 21980 Z= 0.276 Chirality : 0.043 0.233 2340 Planarity : 0.004 0.061 2808 Dihedral : 12.116 60.776 2636 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.37 % Allowed : 21.09 % Favored : 75.54 % 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: 1.22 (0.21), residues: 696 sheet: -0.50 (0.25), residues: 428 loop : 0.30 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 120 TYR 0.019 0.001 TYR D 118 PHE 0.018 0.001 PHE D 88 TRP 0.015 0.001 TRP A 164 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00317 (16192) covalent geometry : angle 0.53128 (21980) hydrogen bonds : bond 0.03957 ( 678) hydrogen bonds : angle 5.30454 ( 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 277 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7547 (ttm170) REVERT: B 182 ARG cc_start: 0.7185 (ttp-110) cc_final: 0.6900 (ttt-90) REVERT: B 413 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.6840 (t80) REVERT: B 419 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8522 (pm20) REVERT: B 424 TYR cc_start: 0.5294 (OUTLIER) cc_final: 0.4579 (p90) REVERT: C 239 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: C 404 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8303 (ppp) REVERT: C 466 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8579 (m) REVERT: D 99 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7448 (mm-30) REVERT: D 133 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7275 (pm20) REVERT: D 297 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: D 413 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7311 (t80) outliers start: 56 outliers final: 22 residues processed: 259 average time/residue: 0.7411 time to fit residues: 209.5426 Evaluate side-chains 244 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 76 THR 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 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 239 GLU Chi-restraints excluded: chain C residue 291 VAL 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 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 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: 7.9990 chunk 22 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 148 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 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 = 0.3741 r_free = 0.3741 target = 0.141911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101795 restraints weight = 18972.119| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.74 r_work: 0.3092 rms_B_bonded: 2.20 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: 0.8693 moved from start: 0.1247 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= 0.221 Angle : 0.588 9.603 21980 Z= 0.305 Chirality : 0.045 0.153 2340 Planarity : 0.005 0.071 2808 Dihedral : 12.307 60.428 2636 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.21 % Allowed : 20.49 % Favored : 75.30 % 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: 0.48 (0.20), residues: 1884 helix: 1.13 (0.21), residues: 696 sheet: -0.52 (0.25), residues: 428 loop : 0.26 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 120 TYR 0.022 0.002 TYR D 118 PHE 0.020 0.002 PHE B 101 TRP 0.016 0.002 TRP A 164 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00523 (16192) covalent geometry : angle 0.58846 (21980) hydrogen bonds : bond 0.04550 ( 678) hydrogen bonds : angle 5.46264 ( 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 291 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 221 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7700 (mptm) REVERT: A 182 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7528 (ttm170) REVERT: A 413 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7648 (t80) REVERT: B 119 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7107 (mm-40) REVERT: B 133 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: B 178 GLN cc_start: 0.7315 (mp10) cc_final: 0.7107 (mp-120) REVERT: B 413 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.6839 (t80) REVERT: B 419 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8534 (pm20) REVERT: B 424 TYR cc_start: 0.5277 (OUTLIER) cc_final: 0.4554 (p90) REVERT: C 239 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: C 404 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8383 (ppp) REVERT: C 424 TYR cc_start: 0.3775 (OUTLIER) cc_final: 0.1920 (t80) REVERT: C 466 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8607 (m) REVERT: D 42 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6871 (p0) REVERT: D 99 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7320 (mm-30) REVERT: D 102 PHE cc_start: 0.8233 (m-80) cc_final: 0.8025 (m-80) REVERT: D 133 GLN cc_start: 0.7504 (pm20) cc_final: 0.7269 (pm20) REVERT: D 249 TYR cc_start: 0.7631 (t80) cc_final: 0.7422 (t80) REVERT: D 297 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: D 413 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7593 (t80) REVERT: D 421 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8186 (m-30) outliers start: 70 outliers final: 28 residues processed: 268 average time/residue: 0.7015 time to fit residues: 204.9833 Evaluate side-chains 256 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 252 GLU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 320 LYS 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 76 THR Chi-restraints excluded: chain B residue 133 GLN 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 42 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 50 optimal weight: 0.0980 chunk 118 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN ** 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 = 0.3758 r_free = 0.3758 target = 0.143270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103713 restraints weight = 18951.579| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.72 r_work: 0.3121 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1253 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= 0.131 Angle : 0.531 8.966 21980 Z= 0.276 Chirality : 0.043 0.144 2340 Planarity : 0.004 0.056 2808 Dihedral : 11.855 60.227 2636 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.91 % Allowed : 21.39 % 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: 0.49 (0.20), residues: 1884 helix: 1.20 (0.21), residues: 696 sheet: -0.58 (0.25), residues: 428 loop : 0.26 (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 D 118 PHE 0.025 0.001 PHE B 101 TRP 0.016 0.001 TRP A 164 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00296 (16192) covalent geometry : angle 0.53085 (21980) hydrogen bonds : bond 0.03887 ( 678) hydrogen bonds : angle 5.31392 ( 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 282 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: B 88 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6734 (t80) REVERT: B 119 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7047 (mm-40) REVERT: B 182 ARG cc_start: 0.7197 (ttp-110) cc_final: 0.6889 (ttt-90) REVERT: B 398 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: B 413 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.6788 (t80) REVERT: B 419 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: B 424 TYR cc_start: 0.5305 (OUTLIER) cc_final: 0.4578 (p90) REVERT: C 239 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: C 404 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8324 (ppp) REVERT: C 466 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8595 (m) REVERT: D 42 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6837 (p0) REVERT: D 99 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7347 (mm-30) REVERT: D 102 PHE cc_start: 0.8233 (m-80) cc_final: 0.7886 (m-80) REVERT: D 133 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: D 297 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: D 421 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8106 (m-30) outliers start: 65 outliers final: 30 residues processed: 261 average time/residue: 0.7455 time to fit residues: 211.7366 Evaluate side-chains 251 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR 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 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 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 239 GLU Chi-restraints excluded: chain C residue 291 VAL 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 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 282 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3766 r_free = 0.3766 target = 0.143904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104074 restraints weight = 18737.678| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.73 r_work: 0.3116 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1264 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= 0.136 Angle : 0.532 9.200 21980 Z= 0.277 Chirality : 0.043 0.246 2340 Planarity : 0.004 0.053 2808 Dihedral : 11.690 59.477 2636 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.43 % Allowed : 22.00 % Favored : 74.58 % 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: 0.48 (0.20), residues: 1884 helix: 1.18 (0.21), residues: 696 sheet: -0.59 (0.25), residues: 428 loop : 0.28 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 120 TYR 0.020 0.001 TYR B 118 PHE 0.028 0.001 PHE B 101 TRP 0.015 0.001 TRP A 164 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00313 (16192) covalent geometry : angle 0.53238 (21980) hydrogen bonds : bond 0.03809 ( 678) hydrogen bonds : angle 5.23809 ( 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 272 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7491 (ttm170) REVERT: A 246 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7180 (ptt-90) REVERT: B 119 GLN cc_start: 0.7700 (mm-40) cc_final: 0.6956 (mm-40) REVERT: B 398 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: B 413 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6785 (t80) REVERT: B 419 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: B 424 TYR cc_start: 0.5293 (OUTLIER) cc_final: 0.4549 (p90) REVERT: C 85 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7446 (mm-30) REVERT: C 239 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: C 404 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8262 (ppp) REVERT: C 466 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8555 (m) REVERT: D 42 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6808 (p0) REVERT: D 99 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7408 (mm-30) REVERT: D 133 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7231 (pm20) REVERT: D 297 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: D 413 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7790 (t80) REVERT: D 421 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: D 466 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8693 (m) outliers start: 57 outliers final: 28 residues processed: 252 average time/residue: 0.7157 time to fit residues: 197.1429 Evaluate side-chains 256 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR 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 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 262 ASN 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 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 239 GLU Chi-restraints excluded: chain C residue 291 VAL 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 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 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 466 THR 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: 4.9990 chunk 51 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3755 r_free = 0.3755 target = 0.142954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103087 restraints weight = 18921.572| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.74 r_work: 0.3110 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16192 Z= 0.167 Angle : 0.552 9.160 21980 Z= 0.286 Chirality : 0.044 0.157 2340 Planarity : 0.005 0.058 2808 Dihedral : 11.768 59.384 2636 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.85 % Allowed : 21.75 % Favored : 74.40 % 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: 1.13 (0.21), residues: 696 sheet: -0.58 (0.25), residues: 428 loop : 0.25 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 120 TYR 0.020 0.002 TYR B 118 PHE 0.033 0.001 PHE B 101 TRP 0.015 0.002 TRP A 164 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00392 (16192) covalent geometry : angle 0.55160 (21980) hydrogen bonds : bond 0.04056 ( 678) hydrogen bonds : angle 5.28528 ( 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 279 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 215 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7484 (ttm170) REVERT: A 246 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7192 (ptt-90) REVERT: A 419 GLU cc_start: 0.8550 (pm20) cc_final: 0.8278 (pt0) REVERT: B 119 GLN cc_start: 0.7744 (mm-40) cc_final: 0.6963 (mm-40) REVERT: B 182 ARG cc_start: 0.7173 (ttp-110) cc_final: 0.6873 (ttt-90) REVERT: B 413 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.6924 (t80) REVERT: B 419 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8462 (pm20) REVERT: B 424 TYR cc_start: 0.5320 (OUTLIER) cc_final: 0.4582 (p90) REVERT: C 85 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7425 (mm-30) REVERT: C 239 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: C 404 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8295 (ppp) REVERT: C 424 TYR cc_start: 0.3671 (OUTLIER) cc_final: 0.1834 (t80) REVERT: C 466 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8577 (m) REVERT: D 42 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6822 (p0) REVERT: D 249 TYR cc_start: 0.7556 (t80) cc_final: 0.7314 (t80) REVERT: D 297 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: D 413 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7924 (t80) REVERT: D 421 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8129 (m-30) outliers start: 64 outliers final: 30 residues processed: 260 average time/residue: 0.6571 time to fit residues: 186.9948 Evaluate side-chains 253 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR 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 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 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 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 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 506 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3762 r_free = 0.3762 target = 0.143612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103773 restraints weight = 18811.512| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.74 r_work: 0.3119 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1322 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= 0.143 Angle : 0.540 9.418 21980 Z= 0.280 Chirality : 0.043 0.246 2340 Planarity : 0.004 0.056 2808 Dihedral : 11.627 59.990 2636 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.94 % Allowed : 22.90 % 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: 0.44 (0.20), residues: 1884 helix: 1.13 (0.21), residues: 696 sheet: -0.59 (0.25), residues: 428 loop : 0.26 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 120 TYR 0.020 0.001 TYR B 118 PHE 0.041 0.001 PHE B 101 TRP 0.016 0.001 TRP A 53 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00329 (16192) covalent geometry : angle 0.54022 (21980) hydrogen bonds : bond 0.03858 ( 678) hydrogen bonds : angle 5.24321 ( 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 262 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7503 (ttm170) REVERT: A 246 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7229 (ptt-90) REVERT: A 419 GLU cc_start: 0.8551 (pm20) cc_final: 0.8255 (pt0) REVERT: B 119 GLN cc_start: 0.7759 (mm-40) cc_final: 0.6961 (mm-40) REVERT: B 182 ARG cc_start: 0.7129 (ttp-110) cc_final: 0.6828 (ttt-90) REVERT: B 260 MET cc_start: 0.9101 (ttm) cc_final: 0.8794 (mtt) REVERT: B 413 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6823 (t80) REVERT: B 419 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: B 424 TYR cc_start: 0.5322 (OUTLIER) cc_final: 0.4606 (p90) REVERT: C 85 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7441 (mm-30) REVERT: C 239 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: C 404 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8272 (ppp) REVERT: C 424 TYR cc_start: 0.3743 (OUTLIER) cc_final: 0.1893 (t80) REVERT: C 466 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8565 (m) REVERT: D 249 TYR cc_start: 0.7561 (t80) cc_final: 0.7345 (t80) REVERT: D 297 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: D 413 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7865 (t80) REVERT: D 421 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8113 (m-30) REVERT: D 466 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8715 (m) outliers start: 49 outliers final: 31 residues processed: 249 average time/residue: 0.6985 time to fit residues: 190.2872 Evaluate side-chains 255 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR 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 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 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 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 422 LEU 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: 4.9990 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 104 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3755 r_free = 0.3755 target = 0.143121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103082 restraints weight = 18774.246| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.75 r_work: 0.3111 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1344 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= 0.158 Angle : 0.549 10.066 21980 Z= 0.285 Chirality : 0.043 0.147 2340 Planarity : 0.004 0.053 2808 Dihedral : 11.653 59.715 2636 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.00 % Allowed : 22.66 % Favored : 74.34 % 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: 0.43 (0.20), residues: 1884 helix: 1.10 (0.21), residues: 696 sheet: -0.58 (0.25), residues: 428 loop : 0.24 (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 0.044 0.001 PHE B 101 TRP 0.019 0.002 TRP A 53 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00367 (16192) covalent geometry : angle 0.54935 (21980) hydrogen bonds : bond 0.03984 ( 678) hydrogen bonds : angle 5.27095 ( 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 261 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7490 (ttm170) REVERT: A 246 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7217 (ptt-90) REVERT: A 419 GLU cc_start: 0.8581 (pm20) cc_final: 0.8277 (pt0) REVERT: B 119 GLN cc_start: 0.7779 (mm-40) cc_final: 0.6976 (mm-40) REVERT: B 182 ARG cc_start: 0.7140 (ttp-110) cc_final: 0.6837 (ttt-90) REVERT: B 413 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6822 (t80) REVERT: B 419 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: B 424 TYR cc_start: 0.5307 (OUTLIER) cc_final: 0.4589 (p90) REVERT: C 85 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7496 (mm-30) REVERT: C 239 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: C 404 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8275 (ppp) REVERT: C 411 MET cc_start: 0.6088 (tpt) cc_final: 0.5882 (tpp) REVERT: C 424 TYR cc_start: 0.3733 (OUTLIER) cc_final: 0.1905 (t80) REVERT: C 466 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8574 (m) REVERT: D 249 TYR cc_start: 0.7578 (t80) cc_final: 0.7332 (t80) REVERT: D 297 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: D 413 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7946 (t80) REVERT: D 421 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: D 466 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8725 (m) outliers start: 50 outliers final: 32 residues processed: 247 average time/residue: 0.6859 time to fit residues: 185.1879 Evaluate side-chains 256 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 252 GLU Chi-restraints excluded: chain A residue 262 ASN 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 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 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 422 LEU 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: 8.9990 chunk 97 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3738 r_free = 0.3738 target = 0.141670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101649 restraints weight = 18827.378| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.73 r_work: 0.3090 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16192 Z= 0.221 Angle : 0.594 9.873 21980 Z= 0.309 Chirality : 0.046 0.255 2340 Planarity : 0.005 0.070 2808 Dihedral : 11.942 59.036 2636 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.06 % Allowed : 22.60 % Favored : 74.34 % 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: 0.32 (0.20), residues: 1884 helix: 0.98 (0.20), residues: 700 sheet: -0.57 (0.25), residues: 428 loop : 0.18 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 120 TYR 0.022 0.002 TYR B 118 PHE 0.044 0.002 PHE B 101 TRP 0.021 0.002 TRP A 53 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00523 (16192) covalent geometry : angle 0.59400 (21980) hydrogen bonds : bond 0.04492 ( 678) hydrogen bonds : angle 5.43533 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6411.44 seconds wall clock time: 109 minutes 40.79 seconds (6580.79 seconds total)