Starting phenix.real_space_refine on Wed May 14 03:08:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f5o_50195/05_2025/9f5o_50195.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f5o_50195/05_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_50195/05_2025/9f5o_50195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f5o_50195/05_2025/9f5o_50195.map" model { file = "/net/cci-nas-00/data/ceres_data/9f5o_50195/05_2025/9f5o_50195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f5o_50195/05_2025/9f5o_50195.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 Restraints were copied for chains: C, B, E, D Time building chain proxies: 4.74, per 1000 atoms: 0.41 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: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.50 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: 3.63 Time building geometry restraints manager: 3.38 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.730 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (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 TRP 0.006 0.001 TRP A 40 HIS 0.004 0.001 HIS E 174 PHE 0.020 0.002 PHE D 259 TYR 0.035 0.003 TYR A 197 ARG 0.014 0.001 ARG E 249 Details of bonding type rmsd hydrogen bonds : bond 0.10097 ( 690) hydrogen bonds : angle 5.81406 ( 2355) covalent geometry : bond 0.00529 (11945) covalent geometry : angle 0.68211 (16325) *********************** 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 : 1.237 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: 0.1608 time to fit residues: 59.4833 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 : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 overall best weight: 5.3786 ------------------------------------------------------------------------------- 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 A 190 HIS B 81 HIS ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 190 HIS C 81 HIS ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN D 81 HIS D 91 ASN D 190 HIS E 81 HIS E 91 ASN E 190 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.129291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.109552 restraints weight = 19967.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.111878 restraints weight = 12808.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.113411 restraints weight = 9365.037| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11945 Z= 0.279 Angle : 0.660 7.371 16325 Z= 0.351 Chirality : 0.045 0.160 1900 Planarity : 0.005 0.048 2080 Dihedral : 5.436 18.654 1645 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1540 helix: 1.91 (0.20), residues: 605 sheet: -1.13 (0.26), residues: 430 loop : -1.00 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 40 HIS 0.004 0.001 HIS B 190 PHE 0.020 0.002 PHE D 236 TYR 0.013 0.002 TYR C 304 ARG 0.006 0.001 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 690) hydrogen bonds : angle 4.72277 ( 2355) covalent geometry : bond 0.00637 (11945) covalent geometry : angle 0.66037 (16325) *********************** 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 261 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: D 86 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7973 (ttm170) REVERT: E 24 ASN cc_start: 0.8820 (t0) cc_final: 0.8511 (t0) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1522 time to fit residues: 64.3283 Evaluate side-chains 209 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 153 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 84 GLN C 83 GLN C 84 GLN D 84 GLN E 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.137608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.120008 restraints weight = 19649.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.121107 restraints weight = 13963.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.122956 restraints weight = 9962.762| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11945 Z= 0.163 Angle : 0.556 5.621 16325 Z= 0.295 Chirality : 0.042 0.149 1900 Planarity : 0.004 0.040 2080 Dihedral : 5.047 18.998 1645 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1540 helix: 2.36 (0.20), residues: 600 sheet: -1.06 (0.26), residues: 425 loop : -0.92 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 40 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE D 236 TYR 0.010 0.002 TYR C 304 ARG 0.004 0.001 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 690) hydrogen bonds : angle 4.39954 ( 2355) covalent geometry : bond 0.00366 (11945) covalent geometry : angle 0.55586 (16325) *********************** 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 263 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8358 (tt0) cc_final: 0.7930 (tt0) REVERT: C 87 MET cc_start: 0.8849 (tpt) cc_final: 0.7723 (tpt) REVERT: D 87 MET cc_start: 0.9029 (tpt) cc_final: 0.7995 (tpt) REVERT: E 87 MET cc_start: 0.8923 (tpt) cc_final: 0.7818 (tpt) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1556 time to fit residues: 67.2452 Evaluate side-chains 220 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 48 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 141 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.131222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.111674 restraints weight = 19939.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.113970 restraints weight = 12890.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.115601 restraints weight = 9457.935| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11945 Z= 0.184 Angle : 0.557 5.614 16325 Z= 0.297 Chirality : 0.042 0.149 1900 Planarity : 0.004 0.027 2080 Dihedral : 4.996 19.101 1645 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1540 helix: 2.34 (0.20), residues: 605 sheet: -1.09 (0.25), residues: 425 loop : -0.79 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 40 HIS 0.003 0.001 HIS C 190 PHE 0.014 0.002 PHE B 130 TYR 0.009 0.002 TYR C 304 ARG 0.005 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 690) hydrogen bonds : angle 4.33268 ( 2355) covalent geometry : bond 0.00422 (11945) covalent geometry : angle 0.55658 (16325) *********************** 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 267 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.8806 (m-80) cc_final: 0.8600 (m-10) REVERT: C 27 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7813 (mt-10) REVERT: D 87 MET cc_start: 0.9034 (tpt) cc_final: 0.7854 (tpt) REVERT: E 87 MET cc_start: 0.9044 (tpt) cc_final: 0.8751 (tpt) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1583 time to fit residues: 69.3470 Evaluate side-chains 216 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 28 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 59 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 84 GLN E 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.133045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.114016 restraints weight = 19739.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.116393 restraints weight = 12731.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.117957 restraints weight = 9299.278| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11945 Z= 0.190 Angle : 0.562 5.609 16325 Z= 0.298 Chirality : 0.042 0.145 1900 Planarity : 0.004 0.033 2080 Dihedral : 5.013 18.962 1645 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1540 helix: 2.31 (0.20), residues: 605 sheet: -1.12 (0.25), residues: 425 loop : -0.79 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 214 HIS 0.003 0.001 HIS A 174 PHE 0.015 0.002 PHE D 89 TYR 0.009 0.002 TYR B 198 ARG 0.005 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 690) hydrogen bonds : angle 4.31489 ( 2355) covalent geometry : bond 0.00434 (11945) covalent geometry : angle 0.56216 (16325) *********************** 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 267 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.8909 (m-80) cc_final: 0.8650 (m-10) REVERT: C 87 MET cc_start: 0.8929 (tpt) cc_final: 0.7705 (tpt) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1542 time to fit residues: 67.1355 Evaluate side-chains 219 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 67 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.134280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.114805 restraints weight = 19824.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.117269 restraints weight = 12676.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.118955 restraints weight = 9194.515| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11945 Z= 0.133 Angle : 0.526 5.513 16325 Z= 0.277 Chirality : 0.041 0.156 1900 Planarity : 0.003 0.027 2080 Dihedral : 4.806 19.610 1645 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.22), residues: 1540 helix: 2.50 (0.20), residues: 605 sheet: -1.08 (0.25), residues: 425 loop : -0.60 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 214 HIS 0.003 0.001 HIS D 140 PHE 0.016 0.001 PHE D 142 TYR 0.008 0.001 TYR A 104 ARG 0.004 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 690) hydrogen bonds : angle 4.14463 ( 2355) covalent geometry : bond 0.00302 (11945) covalent geometry : angle 0.52594 (16325) *********************** 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 270 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.8908 (m-80) cc_final: 0.8652 (m-10) REVERT: B 87 MET cc_start: 0.8320 (tpt) cc_final: 0.7882 (tpt) REVERT: C 87 MET cc_start: 0.8815 (tpt) cc_final: 0.7581 (tpt) REVERT: D 87 MET cc_start: 0.8757 (tpt) cc_final: 0.7603 (tpt) REVERT: D 113 GLN cc_start: 0.8570 (tt0) cc_final: 0.8238 (tt0) REVERT: E 87 MET cc_start: 0.8822 (tpt) cc_final: 0.8521 (tpt) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1715 time to fit residues: 74.3650 Evaluate side-chains 216 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 13 optimal weight: 0.0050 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN C 84 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.135735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.116878 restraints weight = 19901.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.119333 restraints weight = 12514.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.121041 restraints weight = 8983.105| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11945 Z= 0.151 Angle : 0.539 5.518 16325 Z= 0.284 Chirality : 0.041 0.149 1900 Planarity : 0.003 0.035 2080 Dihedral : 4.814 19.361 1645 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1540 helix: 2.47 (0.20), residues: 605 sheet: -1.07 (0.25), residues: 425 loop : -0.55 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.003 0.001 HIS A 140 PHE 0.012 0.001 PHE C 142 TYR 0.016 0.001 TYR B 252 ARG 0.003 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 690) hydrogen bonds : angle 4.16457 ( 2355) covalent geometry : bond 0.00346 (11945) covalent geometry : angle 0.53948 (16325) *********************** 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 268 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.8942 (m-80) cc_final: 0.8685 (m-10) REVERT: C 87 MET cc_start: 0.8832 (tpt) cc_final: 0.7511 (tpt) REVERT: E 108 PHE cc_start: 0.9050 (p90) cc_final: 0.8702 (p90) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1646 time to fit residues: 71.6086 Evaluate side-chains 220 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 104 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN E 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.138829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.120453 restraints weight = 19650.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.122828 restraints weight = 12534.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.124441 restraints weight = 9076.442| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11945 Z= 0.124 Angle : 0.527 5.475 16325 Z= 0.276 Chirality : 0.040 0.152 1900 Planarity : 0.003 0.036 2080 Dihedral : 4.842 20.170 1645 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1540 helix: 2.52 (0.20), residues: 610 sheet: -1.05 (0.26), residues: 425 loop : -0.40 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 75 HIS 0.003 0.001 HIS D 140 PHE 0.014 0.001 PHE D 236 TYR 0.009 0.001 TYR C 104 ARG 0.004 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 690) hydrogen bonds : angle 4.05081 ( 2355) covalent geometry : bond 0.00278 (11945) covalent geometry : angle 0.52700 (16325) *********************** 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 263 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8161 (tt0) cc_final: 0.7917 (tt0) REVERT: A 142 PHE cc_start: 0.8916 (m-80) cc_final: 0.8667 (m-10) REVERT: C 83 GLN cc_start: 0.7301 (mt0) cc_final: 0.6764 (mt0) REVERT: C 87 MET cc_start: 0.8811 (tpt) cc_final: 0.7296 (tpt) REVERT: D 87 MET cc_start: 0.8880 (tpt) cc_final: 0.7552 (tpt) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1572 time to fit residues: 67.6596 Evaluate side-chains 218 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN C 84 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.139621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.121788 restraints weight = 19596.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.123290 restraints weight = 13651.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.124977 restraints weight = 10582.460| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11945 Z= 0.142 Angle : 0.549 5.532 16325 Z= 0.286 Chirality : 0.042 0.152 1900 Planarity : 0.003 0.032 2080 Dihedral : 4.843 19.525 1645 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1540 helix: 2.41 (0.20), residues: 610 sheet: -1.04 (0.26), residues: 425 loop : -0.38 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 75 HIS 0.003 0.001 HIS D 140 PHE 0.017 0.001 PHE B 89 TYR 0.016 0.001 TYR C 252 ARG 0.003 0.000 ARG A 120 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 690) hydrogen bonds : angle 4.13865 ( 2355) covalent geometry : bond 0.00323 (11945) covalent geometry : angle 0.54927 (16325) *********************** 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 260 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.8959 (m-80) cc_final: 0.8696 (m-10) REVERT: B 87 MET cc_start: 0.7940 (tpt) cc_final: 0.7726 (tpt) REVERT: C 87 MET cc_start: 0.8794 (tpt) cc_final: 0.7425 (tpt) REVERT: D 87 MET cc_start: 0.8887 (tpt) cc_final: 0.7636 (tpt) REVERT: E 87 MET cc_start: 0.8659 (tpt) cc_final: 0.8355 (tpt) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1694 time to fit residues: 69.6641 Evaluate side-chains 215 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.117593 restraints weight = 19801.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.119916 restraints weight = 12739.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.121483 restraints weight = 9280.781| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11945 Z= 0.171 Angle : 0.574 5.708 16325 Z= 0.302 Chirality : 0.042 0.148 1900 Planarity : 0.004 0.043 2080 Dihedral : 5.001 19.661 1645 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.23), residues: 1540 helix: 2.34 (0.20), residues: 610 sheet: -1.07 (0.26), residues: 425 loop : -0.40 (0.31), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 40 HIS 0.003 0.001 HIS A 81 PHE 0.014 0.002 PHE B 117 TYR 0.011 0.001 TYR C 252 ARG 0.007 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 690) hydrogen bonds : angle 4.23383 ( 2355) covalent geometry : bond 0.00393 (11945) covalent geometry : angle 0.57413 (16325) ********************** 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 255 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.8980 (m-80) cc_final: 0.8718 (m-10) REVERT: B 82 ASN cc_start: 0.8562 (t0) cc_final: 0.8287 (t0) REVERT: B 87 MET cc_start: 0.7883 (tpt) cc_final: 0.7680 (tpt) REVERT: D 87 MET cc_start: 0.8960 (tpt) cc_final: 0.7544 (tpt) REVERT: E 87 MET cc_start: 0.8846 (tpt) cc_final: 0.8237 (tpt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1522 time to fit residues: 63.8122 Evaluate side-chains 223 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 131 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** ** D 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 = 0.3434 r_free = 0.3434 target = 0.137102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.118361 restraints weight = 19532.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.120765 restraints weight = 12420.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.122429 restraints weight = 8949.793| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11945 Z= 0.129 Angle : 0.544 5.493 16325 Z= 0.283 Chirality : 0.041 0.151 1900 Planarity : 0.004 0.110 2080 Dihedral : 4.899 19.486 1645 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1540 helix: 2.51 (0.20), residues: 605 sheet: -1.04 (0.26), residues: 425 loop : -0.32 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 75 HIS 0.003 0.001 HIS A 140 PHE 0.015 0.001 PHE D 236 TYR 0.008 0.001 TYR B 104 ARG 0.005 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 690) hydrogen bonds : angle 4.12327 ( 2355) covalent geometry : bond 0.00291 (11945) covalent geometry : angle 0.54439 (16325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3136.54 seconds wall clock time: 55 minutes 36.51 seconds (3336.51 seconds total)