Starting phenix.real_space_refine on Wed Sep 17 20:58:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f5o_50195/09_2025/9f5o_50195.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f5o_50195/09_2025/9f5o_50195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f5o_50195/09_2025/9f5o_50195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f5o_50195/09_2025/9f5o_50195.map" model { file = "/net/cci-nas-00/data/ceres_data/9f5o_50195/09_2025/9f5o_50195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f5o_50195/09_2025/9f5o_50195.cif" } resolution = 4.16 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 7690 2.51 5 N 1945 2.21 5 O 1985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11630 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2326 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 298} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 8, 'GLN:plan1': 3, 'ARG:plan': 6, 'HIS:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 162 Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.15, per 1000 atoms: 0.18 Number of scatterers: 11630 At special positions: 0 Unit cell: (87.75, 86.45, 122.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 1985 8.00 N 1945 7.00 C 7690 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: 1.23 Conformation dependent library (CDL) restraints added in 646.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 42.9% alpha, 47.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 43 through 46 Processing helix chain 'A' and resid 61 through 72 Processing helix chain 'A' and resid 118 through 122 removed outlier: 4.015A pdb=" N LEU A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 223 through 247 Processing helix chain 'A' and resid 254 through 283 Processing helix chain 'A' and resid 285 through 315 removed outlier: 3.612A pdb=" N ALA A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'B' and resid 43 through 46 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 118 through 122 removed outlier: 4.016A pdb=" N LEU B 121 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 223 through 247 Processing helix chain 'B' and resid 254 through 283 Processing helix chain 'B' and resid 285 through 315 removed outlier: 3.613A pdb=" N ALA B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Proline residue: B 301 - end of helix Processing helix chain 'C' and resid 43 through 46 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 118 through 122 removed outlier: 4.016A pdb=" N LEU C 121 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 223 through 247 Processing helix chain 'C' and resid 254 through 283 Processing helix chain 'C' and resid 285 through 315 removed outlier: 3.613A pdb=" N ALA C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Proline residue: C 301 - end of helix Processing helix chain 'D' and resid 43 through 46 Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 118 through 122 removed outlier: 4.016A pdb=" N LEU D 121 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 202 Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 223 through 247 Processing helix chain 'D' and resid 254 through 283 Processing helix chain 'D' and resid 285 through 315 removed outlier: 3.612A pdb=" N ALA D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Proline residue: D 301 - end of helix Processing helix chain 'E' and resid 43 through 46 Processing helix chain 'E' and resid 61 through 72 Processing helix chain 'E' and resid 118 through 122 removed outlier: 4.015A pdb=" N LEU E 121 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 202 Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 223 through 247 Processing helix chain 'E' and resid 254 through 283 Processing helix chain 'E' and resid 285 through 315 removed outlier: 3.612A pdb=" N ALA E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Proline residue: E 301 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 60 removed outlier: 10.388A pdb=" N GLY A 85 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLN A 113 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET A 87 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR A 111 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE A 89 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 109 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN A 29 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE A 23 " --> pdb=" O ASN A 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER A 31 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER A 35 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE A 17 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG A 37 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU A 15 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP A 39 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE A 13 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ARG A 41 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL A 11 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 9 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLN A 145 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 11 " --> pdb=" O GLN A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 60 removed outlier: 10.388A pdb=" N GLY A 85 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLN A 113 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET A 87 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR A 111 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE A 89 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 109 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN A 29 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE A 23 " --> pdb=" O ASN A 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER A 31 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER A 35 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE A 17 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG A 37 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU A 15 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP A 39 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE A 13 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ARG A 41 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL A 11 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY A 152 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 15 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 80 removed outlier: 5.172A pdb=" N SER A 183 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU A 166 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU A 192 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL A 164 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 60 removed outlier: 10.388A pdb=" N GLY B 85 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLN B 113 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET B 87 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR B 111 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE B 89 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR B 109 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN B 29 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE B 23 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER B 31 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER B 35 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE B 17 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG B 37 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU B 15 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP B 39 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE B 13 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ARG B 41 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL B 11 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER B 9 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLN B 145 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 11 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 60 removed outlier: 10.388A pdb=" N GLY B 85 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLN B 113 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET B 87 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR B 111 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE B 89 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR B 109 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN B 29 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE B 23 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER B 31 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER B 35 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE B 17 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG B 37 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU B 15 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP B 39 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE B 13 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ARG B 41 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL B 11 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY B 152 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 15 " --> pdb=" O GLY B 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 80 removed outlier: 5.173A pdb=" N SER B 183 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 166 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU B 192 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL B 164 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 57 through 60 removed outlier: 10.388A pdb=" N GLY C 85 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N GLN C 113 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET C 87 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N THR C 111 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE C 89 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR C 109 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN C 29 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE C 23 " --> pdb=" O ASN C 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER C 31 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER C 35 " --> pdb=" O ILE C 17 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE C 17 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG C 37 " --> pdb=" O LEU C 15 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU C 15 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP C 39 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE C 13 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ARG C 41 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL C 11 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER C 9 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN C 145 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C 11 " --> pdb=" O GLN C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 57 through 60 removed outlier: 10.388A pdb=" N GLY C 85 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N GLN C 113 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET C 87 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N THR C 111 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE C 89 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR C 109 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN C 29 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE C 23 " --> pdb=" O ASN C 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER C 31 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER C 35 " --> pdb=" O ILE C 17 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE C 17 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG C 37 " --> pdb=" O LEU C 15 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU C 15 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP C 39 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE C 13 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ARG C 41 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL C 11 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY C 152 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 15 " --> pdb=" O GLY C 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 80 removed outlier: 5.173A pdb=" N SER C 183 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU C 166 " --> pdb=" O HIS C 190 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU C 192 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL C 164 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 60 removed outlier: 10.388A pdb=" N GLY D 85 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLN D 113 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET D 87 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR D 111 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE D 89 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 109 " --> pdb=" O PHE D 89 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN D 29 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE D 23 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER D 31 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER D 35 " --> pdb=" O ILE D 17 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE D 17 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG D 37 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU D 15 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP D 39 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE D 13 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ARG D 41 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL D 11 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER D 9 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLN D 145 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 11 " --> pdb=" O GLN D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 57 through 60 removed outlier: 10.388A pdb=" N GLY D 85 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLN D 113 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET D 87 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR D 111 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE D 89 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 109 " --> pdb=" O PHE D 89 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN D 29 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE D 23 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER D 31 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER D 35 " --> pdb=" O ILE D 17 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE D 17 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG D 37 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU D 15 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP D 39 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE D 13 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ARG D 41 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL D 11 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY D 152 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU D 15 " --> pdb=" O GLY D 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 78 through 80 removed outlier: 5.173A pdb=" N SER D 183 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU D 166 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU D 192 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL D 164 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 57 through 60 removed outlier: 10.388A pdb=" N GLY E 85 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLN E 113 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET E 87 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR E 111 " --> pdb=" O MET E 87 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE E 89 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR E 109 " --> pdb=" O PHE E 89 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN E 29 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE E 23 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER E 31 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER E 35 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE E 17 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG E 37 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU E 15 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP E 39 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE E 13 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ARG E 41 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL E 11 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER E 9 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLN E 145 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL E 11 " --> pdb=" O GLN E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 57 through 60 removed outlier: 10.388A pdb=" N GLY E 85 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLN E 113 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET E 87 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR E 111 " --> pdb=" O MET E 87 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE E 89 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR E 109 " --> pdb=" O PHE E 89 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN E 29 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE E 23 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER E 31 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER E 35 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE E 17 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG E 37 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU E 15 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP E 39 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE E 13 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ARG E 41 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL E 11 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY E 152 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU E 15 " --> pdb=" O GLY E 152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 78 through 80 removed outlier: 5.173A pdb=" N SER E 183 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU E 166 " --> pdb=" O HIS E 190 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU E 192 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL E 164 " --> pdb=" O GLU E 192 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 2355 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: 2.23 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3695 1.34 - 1.45: 2055 1.45 - 1.57: 6175 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 11945 Sorted by residual: bond pdb=" CA ASP C 88 " pdb=" CB ASP C 88 " ideal model delta sigma weight residual 1.531 1.492 0.039 3.28e-02 9.30e+02 1.41e+00 bond pdb=" CA ASN D 82 " pdb=" C ASN D 82 " ideal model delta sigma weight residual 1.524 1.507 0.018 1.48e-02 4.57e+03 1.40e+00 bond pdb=" CA ASN A 82 " pdb=" C ASN A 82 " ideal model delta sigma weight residual 1.524 1.507 0.018 1.48e-02 4.57e+03 1.40e+00 bond pdb=" CA ASN C 82 " pdb=" C ASN C 82 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.48e-02 4.57e+03 1.40e+00 bond pdb=" CG ARG A 86 " pdb=" CD ARG A 86 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.38e+00 ... (remaining 11940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 15740 1.63 - 3.27: 501 3.27 - 4.90: 73 4.90 - 6.53: 6 6.53 - 8.17: 5 Bond angle restraints: 16325 Sorted by residual: angle pdb=" C GLN D 84 " pdb=" N GLY D 85 " pdb=" CA GLY D 85 " ideal model delta sigma weight residual 120.36 112.19 8.17 2.89e+00 1.20e-01 7.98e+00 angle pdb=" C GLN E 84 " pdb=" N GLY E 85 " pdb=" CA GLY E 85 " ideal model delta sigma weight residual 120.36 112.20 8.16 2.89e+00 1.20e-01 7.98e+00 angle pdb=" C GLN C 84 " pdb=" N GLY C 85 " pdb=" CA GLY C 85 " ideal model delta sigma weight residual 120.36 112.22 8.14 2.89e+00 1.20e-01 7.94e+00 angle pdb=" C GLN A 84 " pdb=" N GLY A 85 " pdb=" CA GLY A 85 " ideal model delta sigma weight residual 120.36 112.26 8.10 2.89e+00 1.20e-01 7.85e+00 angle pdb=" C GLN B 84 " pdb=" N GLY B 85 " pdb=" CA GLY B 85 " ideal model delta sigma weight residual 120.36 112.28 8.08 2.89e+00 1.20e-01 7.81e+00 ... (remaining 16320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 6173 16.60 - 33.20: 474 33.20 - 49.80: 103 49.80 - 66.40: 35 66.40 - 83.01: 5 Dihedral angle restraints: 6790 sinusoidal: 2280 harmonic: 4510 Sorted by residual: dihedral pdb=" CA ALA D 116 " pdb=" C ALA D 116 " pdb=" N PHE D 117 " pdb=" CA PHE D 117 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ALA A 116 " pdb=" C ALA A 116 " pdb=" N PHE A 117 " pdb=" CA PHE A 117 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ALA B 116 " pdb=" C ALA B 116 " pdb=" N PHE B 117 " pdb=" CA PHE B 117 " ideal model delta harmonic sigma weight residual 180.00 155.84 24.16 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 6787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 955 0.028 - 0.055: 620 0.055 - 0.083: 194 0.083 - 0.111: 92 0.111 - 0.138: 39 Chirality restraints: 1900 Sorted by residual: chirality pdb=" CA ILE C 23 " pdb=" N ILE C 23 " pdb=" C ILE C 23 " pdb=" CB ILE C 23 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE A 23 " pdb=" N ILE A 23 " pdb=" C ILE A 23 " pdb=" CB ILE A 23 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL E 167 " pdb=" N VAL E 167 " pdb=" C VAL E 167 " pdb=" CB VAL E 167 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1897 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 197 " 0.019 2.00e-02 2.50e+03 1.46e-02 4.28e+00 pdb=" CG TYR A 197 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 197 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 197 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 197 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 197 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 197 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 197 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 197 " 0.019 2.00e-02 2.50e+03 1.45e-02 4.21e+00 pdb=" CG TYR B 197 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 197 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 197 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 197 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 197 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 197 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 197 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 197 " 0.019 2.00e-02 2.50e+03 1.45e-02 4.20e+00 pdb=" CG TYR C 197 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 197 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C 197 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 197 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 197 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 197 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 197 " 0.001 2.00e-02 2.50e+03 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2776 2.79 - 3.31: 11023 3.31 - 3.84: 18329 3.84 - 4.37: 19833 4.37 - 4.90: 35832 Nonbonded interactions: 87793 Sorted by model distance: nonbonded pdb=" NE2 GLN A 84 " pdb=" OG1 THR E 21 " model vdw 2.258 3.120 nonbonded pdb=" OG1 THR A 21 " pdb=" NE2 GLN B 84 " model vdw 2.290 3.120 nonbonded pdb=" OG1 THR D 21 " pdb=" NE2 GLN E 84 " model vdw 2.295 3.120 nonbonded pdb=" OG1 THR B 21 " pdb=" NE2 GLN C 84 " model vdw 2.312 3.120 nonbonded pdb=" OG1 THR C 21 " pdb=" NE2 GLN D 84 " model vdw 2.317 3.120 ... (remaining 87788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11945 Z= 0.239 Angle : 0.682 8.165 16325 Z= 0.366 Chirality : 0.043 0.138 1900 Planarity : 0.006 0.067 2080 Dihedral : 13.603 83.005 3870 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1540 helix: 1.83 (0.21), residues: 605 sheet: -1.03 (0.26), residues: 425 loop : -0.83 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 249 TYR 0.035 0.003 TYR A 197 PHE 0.020 0.002 PHE D 259 TRP 0.006 0.001 TRP A 40 HIS 0.004 0.001 HIS E 174 Details of bonding type rmsd covalent geometry : bond 0.00529 (11945) covalent geometry : angle 0.68211 (16325) hydrogen bonds : bond 0.10097 ( 690) hydrogen bonds : angle 5.81406 ( 2355) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: B 198 TYR cc_start: 0.8481 (m-80) cc_final: 0.7761 (m-10) REVERT: E 108 PHE cc_start: 0.9252 (p90) cc_final: 0.9047 (p90) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.0786 time to fit residues: 29.3974 Evaluate side-chains 197 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 91 ASN B 81 HIS B 91 ASN B 190 HIS C 81 HIS C 91 ASN D 81 HIS D 91 ASN E 81 HIS E 91 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.133481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.113995 restraints weight = 19835.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.116368 restraints weight = 12691.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.118077 restraints weight = 9227.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.119296 restraints weight = 7419.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.120007 restraints weight = 6328.282| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11945 Z= 0.157 Angle : 0.542 5.641 16325 Z= 0.288 Chirality : 0.042 0.156 1900 Planarity : 0.004 0.032 2080 Dihedral : 4.963 19.269 1645 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.22), residues: 1540 helix: 2.42 (0.20), residues: 600 sheet: -0.90 (0.26), residues: 425 loop : -0.77 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 86 TYR 0.011 0.002 TYR C 304 PHE 0.017 0.001 PHE E 236 TRP 0.004 0.001 TRP A 40 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00351 (11945) covalent geometry : angle 0.54201 (16325) hydrogen bonds : bond 0.03857 ( 690) hydrogen bonds : angle 4.41411 ( 2355) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 ASN cc_start: 0.8732 (t0) cc_final: 0.8442 (t0) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.0834 time to fit residues: 35.5806 Evaluate side-chains 217 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 57 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 127 GLN B 84 GLN B 127 GLN C 84 GLN C 127 GLN D 84 GLN D 127 GLN E 84 GLN E 127 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.137863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.118968 restraints weight = 19578.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.121535 restraints weight = 12232.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.123317 restraints weight = 8674.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.124501 restraints weight = 6790.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.125381 restraints weight = 5714.357| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11945 Z= 0.105 Angle : 0.497 5.473 16325 Z= 0.260 Chirality : 0.040 0.157 1900 Planarity : 0.003 0.027 2080 Dihedral : 4.629 19.754 1645 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.22), residues: 1540 helix: 2.69 (0.20), residues: 600 sheet: -0.81 (0.27), residues: 425 loop : -0.59 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 86 TYR 0.022 0.001 TYR D 197 PHE 0.013 0.001 PHE D 236 TRP 0.004 0.001 TRP E 40 HIS 0.002 0.001 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00224 (11945) covalent geometry : angle 0.49659 (16325) hydrogen bonds : bond 0.03341 ( 690) hydrogen bonds : angle 4.11151 ( 2355) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.8116 (ttp-170) cc_final: 0.7442 (ttm170) REVERT: C 87 MET cc_start: 0.8756 (tpt) cc_final: 0.7850 (tpt) REVERT: C 108 PHE cc_start: 0.9137 (p90) cc_final: 0.8849 (p90) REVERT: D 86 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7609 (ttp80) REVERT: D 87 MET cc_start: 0.8975 (tpt) cc_final: 0.8032 (tpt) REVERT: E 87 MET cc_start: 0.8425 (tpt) cc_final: 0.7853 (tpt) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.0853 time to fit residues: 36.6807 Evaluate side-chains 210 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 50 optimal weight: 0.0070 chunk 87 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.137851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.119596 restraints weight = 19815.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.120939 restraints weight = 14171.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.122816 restraints weight = 10022.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.123620 restraints weight = 7810.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.124564 restraints weight = 6579.568| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11945 Z= 0.156 Angle : 0.523 5.529 16325 Z= 0.277 Chirality : 0.041 0.150 1900 Planarity : 0.003 0.027 2080 Dihedral : 4.676 19.271 1645 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.22), residues: 1540 helix: 2.62 (0.20), residues: 605 sheet: -0.84 (0.26), residues: 425 loop : -0.50 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 86 TYR 0.009 0.001 TYR D 197 PHE 0.012 0.001 PHE E 236 TRP 0.005 0.001 TRP C 40 HIS 0.003 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00353 (11945) covalent geometry : angle 0.52335 (16325) hydrogen bonds : bond 0.03523 ( 690) hydrogen bonds : angle 4.11367 ( 2355) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7583 (ttp80) REVERT: D 87 MET cc_start: 0.8974 (tpt) cc_final: 0.7892 (tpt) REVERT: E 24 ASN cc_start: 0.8771 (t0) cc_final: 0.8412 (t0) REVERT: E 86 ARG cc_start: 0.7591 (ttp-110) cc_final: 0.7222 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.0821 time to fit residues: 35.3132 Evaluate side-chains 222 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 127 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 12 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN B 84 GLN C 84 GLN D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.140185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.121403 restraints weight = 19566.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.123780 restraints weight = 12430.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.125438 restraints weight = 9023.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.126567 restraints weight = 7207.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.127106 restraints weight = 6157.112| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11945 Z= 0.111 Angle : 0.482 5.439 16325 Z= 0.254 Chirality : 0.039 0.142 1900 Planarity : 0.003 0.027 2080 Dihedral : 4.531 19.615 1645 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.23), residues: 1540 helix: 2.74 (0.20), residues: 605 sheet: -0.86 (0.26), residues: 425 loop : -0.30 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 86 TYR 0.007 0.001 TYR C 104 PHE 0.012 0.001 PHE D 236 TRP 0.004 0.000 TRP C 75 HIS 0.007 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00245 (11945) covalent geometry : angle 0.48200 (16325) hydrogen bonds : bond 0.03198 ( 690) hydrogen bonds : angle 3.96790 ( 2355) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7474 (ttm110) REVERT: C 83 GLN cc_start: 0.8502 (tt0) cc_final: 0.8170 (tt0) REVERT: C 87 MET cc_start: 0.8725 (tpt) cc_final: 0.7360 (tpt) REVERT: D 72 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8373 (mm-40) REVERT: E 142 PHE cc_start: 0.8581 (m-10) cc_final: 0.8195 (m-10) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.0812 time to fit residues: 35.7871 Evaluate side-chains 221 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 153 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.131817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.112774 restraints weight = 20109.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.115077 restraints weight = 13010.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.116696 restraints weight = 9483.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.117727 restraints weight = 7596.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.118527 restraints weight = 6505.588| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11945 Z= 0.221 Angle : 0.596 5.850 16325 Z= 0.315 Chirality : 0.043 0.137 1900 Planarity : 0.004 0.033 2080 Dihedral : 4.982 19.025 1645 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.22), residues: 1540 helix: 2.45 (0.21), residues: 605 sheet: -0.99 (0.26), residues: 425 loop : -0.55 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 86 TYR 0.011 0.002 TYR C 198 PHE 0.027 0.002 PHE E 89 TRP 0.007 0.001 TRP A 40 HIS 0.004 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00508 (11945) covalent geometry : angle 0.59574 (16325) hydrogen bonds : bond 0.03986 ( 690) hydrogen bonds : angle 4.29031 ( 2355) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: C 83 GLN cc_start: 0.8938 (tt0) cc_final: 0.8730 (tt0) REVERT: C 87 MET cc_start: 0.8734 (tpt) cc_final: 0.8207 (tpp) REVERT: E 24 ASN cc_start: 0.8880 (t0) cc_final: 0.8678 (t0) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.0848 time to fit residues: 37.4115 Evaluate side-chains 224 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 36 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 135 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.132661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.114328 restraints weight = 20120.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.116526 restraints weight = 13147.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.118005 restraints weight = 9702.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.119021 restraints weight = 7848.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.119441 restraints weight = 6808.824| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11945 Z= 0.272 Angle : 0.646 7.137 16325 Z= 0.343 Chirality : 0.045 0.141 1900 Planarity : 0.004 0.052 2080 Dihedral : 5.334 19.947 1645 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1540 helix: 2.02 (0.20), residues: 605 sheet: -1.21 (0.25), residues: 425 loop : -0.76 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 86 TYR 0.012 0.002 TYR E 198 PHE 0.017 0.002 PHE A 259 TRP 0.007 0.001 TRP A 40 HIS 0.006 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00627 (11945) covalent geometry : angle 0.64566 (16325) hydrogen bonds : bond 0.04493 ( 690) hydrogen bonds : angle 4.49700 ( 2355) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: B 82 ASN cc_start: 0.8791 (t0) cc_final: 0.8411 (t0) REVERT: D 86 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7679 (ttp80) REVERT: D 87 MET cc_start: 0.8954 (tpt) cc_final: 0.7878 (tpt) REVERT: D 90 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8294 (tm-30) REVERT: E 24 ASN cc_start: 0.8955 (t0) cc_final: 0.8562 (t0) REVERT: E 87 MET cc_start: 0.8762 (tpt) cc_final: 0.7914 (tpt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.0801 time to fit residues: 33.1449 Evaluate side-chains 214 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 9 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 44 optimal weight: 0.0060 chunk 15 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.134933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.116413 restraints weight = 19702.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.118837 restraints weight = 12417.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.120404 restraints weight = 8921.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.121607 restraints weight = 7068.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.122256 restraints weight = 6007.069| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11945 Z= 0.155 Angle : 0.550 5.620 16325 Z= 0.289 Chirality : 0.041 0.137 1900 Planarity : 0.004 0.061 2080 Dihedral : 5.000 19.078 1645 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.22), residues: 1540 helix: 2.38 (0.20), residues: 600 sheet: -1.21 (0.25), residues: 425 loop : -0.56 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 86 TYR 0.010 0.001 TYR B 198 PHE 0.017 0.001 PHE D 142 TRP 0.005 0.001 TRP B 75 HIS 0.003 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00354 (11945) covalent geometry : angle 0.54982 (16325) hydrogen bonds : bond 0.03803 ( 690) hydrogen bonds : angle 4.23427 ( 2355) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7701 (mt-10) REVERT: B 82 ASN cc_start: 0.8811 (t0) cc_final: 0.8466 (t0) REVERT: C 87 MET cc_start: 0.8756 (tpt) cc_final: 0.7516 (tpt) REVERT: D 87 MET cc_start: 0.8783 (tpt) cc_final: 0.7954 (tpt) REVERT: E 87 MET cc_start: 0.8794 (tpt) cc_final: 0.8162 (tpt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.0790 time to fit residues: 33.0419 Evaluate side-chains 217 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 129 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.134473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.115812 restraints weight = 19525.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.118160 restraints weight = 12372.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.119821 restraints weight = 8943.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.120862 restraints weight = 7095.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.121696 restraints weight = 6055.548| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11945 Z= 0.172 Angle : 0.565 6.104 16325 Z= 0.296 Chirality : 0.042 0.142 1900 Planarity : 0.004 0.051 2080 Dihedral : 4.949 19.047 1645 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.23), residues: 1540 helix: 2.41 (0.20), residues: 600 sheet: -1.17 (0.25), residues: 425 loop : -0.44 (0.30), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 86 TYR 0.009 0.001 TYR B 198 PHE 0.016 0.001 PHE D 142 TRP 0.005 0.001 TRP A 40 HIS 0.003 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00397 (11945) covalent geometry : angle 0.56546 (16325) hydrogen bonds : bond 0.03776 ( 690) hydrogen bonds : angle 4.22623 ( 2355) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 82 ASN cc_start: 0.8827 (t0) cc_final: 0.8495 (t0) REVERT: C 87 MET cc_start: 0.8781 (tpt) cc_final: 0.7621 (tpt) REVERT: D 87 MET cc_start: 0.8769 (tpt) cc_final: 0.7936 (tpt) REVERT: E 87 MET cc_start: 0.8736 (tpt) cc_final: 0.8011 (tpt) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.0787 time to fit residues: 32.1326 Evaluate side-chains 214 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 49 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN C 83 GLN C 84 GLN D 83 GLN D 84 GLN D 90 GLN E 84 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.139920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.121568 restraints weight = 19539.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.124056 restraints weight = 12386.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.125723 restraints weight = 8875.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.126925 restraints weight = 7028.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.127608 restraints weight = 5934.206| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11945 Z= 0.109 Angle : 0.528 5.401 16325 Z= 0.271 Chirality : 0.040 0.139 1900 Planarity : 0.003 0.029 2080 Dihedral : 4.789 21.987 1645 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.23), residues: 1540 helix: 2.54 (0.20), residues: 605 sheet: -1.12 (0.26), residues: 425 loop : -0.18 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 86 TYR 0.010 0.001 TYR D 104 PHE 0.015 0.001 PHE D 142 TRP 0.005 0.001 TRP B 75 HIS 0.004 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00236 (11945) covalent geometry : angle 0.52776 (16325) hydrogen bonds : bond 0.03268 ( 690) hydrogen bonds : angle 4.04139 ( 2355) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8613 (mm-40) REVERT: B 82 ASN cc_start: 0.8751 (t0) cc_final: 0.8537 (t0) REVERT: D 72 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8311 (mm-40) REVERT: E 87 MET cc_start: 0.8421 (tpt) cc_final: 0.7757 (tpt) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.0754 time to fit residues: 32.8083 Evaluate side-chains 204 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 8 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 90 GLN E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.132405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.113390 restraints weight = 19900.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.115712 restraints weight = 12674.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.117477 restraints weight = 9160.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.118613 restraints weight = 7277.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.119148 restraints weight = 6193.659| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11945 Z= 0.202 Angle : 0.606 5.612 16325 Z= 0.318 Chirality : 0.043 0.138 1900 Planarity : 0.004 0.036 2080 Dihedral : 5.023 19.880 1645 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.23), residues: 1540 helix: 2.47 (0.20), residues: 600 sheet: -1.16 (0.26), residues: 425 loop : -0.34 (0.30), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 86 TYR 0.014 0.002 TYR A 197 PHE 0.025 0.002 PHE D 89 TRP 0.005 0.001 TRP C 162 HIS 0.004 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00467 (11945) covalent geometry : angle 0.60602 (16325) hydrogen bonds : bond 0.03831 ( 690) hydrogen bonds : angle 4.32332 ( 2355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1753.60 seconds wall clock time: 31 minutes 12.31 seconds (1872.31 seconds total)