Starting phenix.real_space_refine on Tue Jun 10 04:18:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f5o_50195/06_2025/9f5o_50195.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f5o_50195/06_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_50195/06_2025/9f5o_50195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f5o_50195/06_2025/9f5o_50195.map" model { file = "/net/cci-nas-00/data/ceres_data/9f5o_50195/06_2025/9f5o_50195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f5o_50195/06_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-5710/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: 5.20, per 1000 atoms: 0.45 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: 3.23 Conformation dependent library (CDL) restraints added in 1.7 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: 1.52 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: 4.12 Time building geometry restraints manager: 3.81 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: 0.670 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.540 Find NCS groups from input model: 0.260 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.870 ------------------------------------------------------------------------------- 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 : 1.284 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: 0.1646 time to fit residues: 60.8023 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 : 1.337 ------------------------------------------------------------------------------- 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 = 0.109551 restraints weight = 19967.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.111870 restraints weight = 12810.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.113406 restraints weight = 9379.108| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 1.868 Fit side-chains revert: symmetry clash REVERT: D 86 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7973 (ttm170) REVERT: E 24 ASN cc_start: 0.8821 (t0) cc_final: 0.8510 (t0) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1599 time to fit residues: 68.0938 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 : 1.224 ------------------------------------------------------------------------------- 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: 0.2980 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 77 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.135549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.116577 restraints weight = 19705.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.119035 restraints weight = 12509.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.120767 restraints weight = 9024.678| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11945 Z= 0.113 Angle : 0.524 5.512 16325 Z= 0.276 Chirality : 0.041 0.155 1900 Planarity : 0.004 0.043 2080 Dihedral : 4.872 19.548 1645 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 0.60 (0.22), residues: 1540 helix: 2.46 (0.20), residues: 600 sheet: -1.00 (0.26), residues: 425 loop : -0.77 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 40 HIS 0.005 0.001 HIS B 174 PHE 0.013 0.001 PHE D 236 TYR 0.009 0.001 TYR C 304 ARG 0.005 0.001 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 690) hydrogen bonds : angle 4.24250 ( 2355) covalent geometry : bond 0.00237 (11945) covalent geometry : angle 0.52435 (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 268 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8270 (tt0) cc_final: 0.7895 (tt0) REVERT: C 83 GLN cc_start: 0.8004 (tt0) cc_final: 0.7187 (tt0) REVERT: C 87 MET cc_start: 0.8871 (tpt) cc_final: 0.7648 (tpt) REVERT: D 83 GLN cc_start: 0.7907 (tt0) cc_final: 0.7517 (tt0) REVERT: D 87 MET cc_start: 0.9044 (tpt) cc_final: 0.8016 (tpt) REVERT: E 87 MET cc_start: 0.8861 (tpt) cc_final: 0.7814 (tpt) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1624 time to fit residues: 71.0519 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 : 1.423 ------------------------------------------------------------------------------- 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: 9.9990 chunk 138 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 chunk 60 optimal weight: 0.0470 chunk 24 optimal weight: 0.0270 chunk 7 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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** A 127 GLN B 127 GLN C 84 GLN C 127 GLN C 194 HIS D 84 GLN D 127 GLN E 84 GLN E 127 GLN E 194 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.142627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.124949 restraints weight = 19394.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.126549 restraints weight = 13462.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.128799 restraints weight = 9281.239| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11945 Z= 0.097 Angle : 0.483 5.365 16325 Z= 0.252 Chirality : 0.040 0.160 1900 Planarity : 0.003 0.026 2080 Dihedral : 4.534 20.572 1645 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 0.96 (0.23), residues: 1540 helix: 2.74 (0.20), residues: 600 sheet: -0.90 (0.26), residues: 425 loop : -0.46 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 75 HIS 0.003 0.001 HIS B 81 PHE 0.013 0.001 PHE E 236 TYR 0.008 0.001 TYR A 104 ARG 0.002 0.000 ARG D 74 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 690) hydrogen bonds : angle 3.93528 ( 2355) covalent geometry : bond 0.00204 (11945) covalent geometry : angle 0.48270 (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 279 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8906 (mm) cc_final: 0.8596 (mt) REVERT: A 83 GLN cc_start: 0.8599 (tt0) cc_final: 0.8208 (pt0) REVERT: A 86 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7567 (ttm170) REVERT: C 83 GLN cc_start: 0.8196 (tt0) cc_final: 0.7641 (tt0) REVERT: C 86 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7715 (ttm110) REVERT: C 87 MET cc_start: 0.8654 (tpt) cc_final: 0.7621 (tpt) REVERT: D 83 GLN cc_start: 0.7952 (tt0) cc_final: 0.7505 (tt0) REVERT: D 87 MET cc_start: 0.8811 (tpt) cc_final: 0.7803 (tpt) REVERT: E 87 MET cc_start: 0.8904 (tpt) cc_final: 0.7905 (tpt) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1570 time to fit residues: 70.6457 Evaluate side-chains 211 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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: 20.0000 chunk 6 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 75 optimal weight: 0.0370 overall best weight: 1.8064 ------------------------------------------------------------------------------- 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 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 = 0.3468 r_free = 0.3468 target = 0.140268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.121524 restraints weight = 19318.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.123835 restraints weight = 12546.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.125492 restraints weight = 9201.736| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11945 Z= 0.122 Angle : 0.489 5.452 16325 Z= 0.257 Chirality : 0.039 0.131 1900 Planarity : 0.003 0.027 2080 Dihedral : 4.475 19.795 1645 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: 1.05 (0.23), residues: 1540 helix: 2.74 (0.20), residues: 605 sheet: -0.86 (0.26), residues: 425 loop : -0.32 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.002 0.001 HIS E 194 PHE 0.014 0.001 PHE A 236 TYR 0.009 0.001 TYR D 197 ARG 0.004 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 690) hydrogen bonds : angle 3.96304 ( 2355) covalent geometry : bond 0.00275 (11945) covalent geometry : angle 0.48875 (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 262 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: B 87 MET cc_start: 0.8568 (tpt) cc_final: 0.8070 (tpp) REVERT: C 87 MET cc_start: 0.8679 (tpt) cc_final: 0.8369 (tpt) REVERT: D 27 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7631 (mt-10) REVERT: D 83 GLN cc_start: 0.8104 (tt0) cc_final: 0.7343 (tt0) REVERT: D 87 MET cc_start: 0.8754 (tpt) cc_final: 0.7593 (tpt) REVERT: E 87 MET cc_start: 0.9001 (tpt) cc_final: 0.8753 (tpt) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1746 time to fit residues: 73.4794 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 : 1.322 ------------------------------------------------------------------------------- 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: 9.9990 chunk 75 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 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 B 84 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 194 HIS D 84 GLN E 84 GLN E 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.138259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.119047 restraints weight = 19772.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.121601 restraints weight = 12481.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.123364 restraints weight = 8871.026| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11945 Z= 0.100 Angle : 0.477 5.425 16325 Z= 0.249 Chirality : 0.039 0.137 1900 Planarity : 0.003 0.028 2080 Dihedral : 4.394 20.227 1645 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: 1.20 (0.23), residues: 1540 helix: 2.81 (0.20), residues: 605 sheet: -0.80 (0.26), residues: 425 loop : -0.15 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 75 HIS 0.004 0.001 HIS D 174 PHE 0.016 0.001 PHE D 236 TYR 0.008 0.001 TYR A 104 ARG 0.006 0.000 ARG C 184 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 690) hydrogen bonds : angle 3.85409 ( 2355) covalent geometry : bond 0.00221 (11945) covalent geometry : angle 0.47725 (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 261 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7786 (ttm170) cc_final: 0.7554 (ttm170) REVERT: B 87 MET cc_start: 0.8356 (tpt) cc_final: 0.8021 (tpt) REVERT: D 83 GLN cc_start: 0.7974 (tt0) cc_final: 0.7510 (tt0) REVERT: D 87 MET cc_start: 0.8589 (tpt) cc_final: 0.7534 (tpt) REVERT: E 142 PHE cc_start: 0.8517 (m-10) cc_final: 0.8115 (m-10) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1624 time to fit residues: 68.3900 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 : 1.247 ------------------------------------------------------------------------------- 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: 9.9990 chunk 74 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 13 optimal weight: 0.0060 overall best weight: 4.8004 ------------------------------------------------------------------------------- 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** B 84 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 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 = 0.3350 r_free = 0.3350 target = 0.130012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.110749 restraints weight = 20322.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.113090 restraints weight = 13016.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.114701 restraints weight = 9368.532| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11945 Z= 0.256 Angle : 0.637 5.990 16325 Z= 0.338 Chirality : 0.044 0.142 1900 Planarity : 0.004 0.033 2080 Dihedral : 5.029 18.301 1645 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 0.70 (0.22), residues: 1540 helix: 2.46 (0.20), residues: 605 sheet: -0.96 (0.26), residues: 425 loop : -0.62 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 40 HIS 0.007 0.001 HIS E 194 PHE 0.027 0.002 PHE D 89 TYR 0.012 0.002 TYR E 80 ARG 0.007 0.001 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 690) hydrogen bonds : angle 4.33420 ( 2355) covalent geometry : bond 0.00590 (11945) covalent geometry : angle 0.63655 (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 263 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 87 MET cc_start: 0.9008 (tpt) cc_final: 0.7908 (tpt) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1876 time to fit residues: 78.9088 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 : 1.431 ------------------------------------------------------------------------------- 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: 2.9990 chunk 48 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 84 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 = 0.3394 r_free = 0.3394 target = 0.133859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.115313 restraints weight = 19950.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.117716 restraints weight = 12588.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.119404 restraints weight = 9088.727| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11945 Z= 0.157 Angle : 0.549 5.582 16325 Z= 0.289 Chirality : 0.041 0.143 1900 Planarity : 0.004 0.052 2080 Dihedral : 4.917 19.073 1645 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 0.78 (0.23), residues: 1540 helix: 2.51 (0.20), residues: 605 sheet: -1.02 (0.26), residues: 425 loop : -0.44 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 75 HIS 0.004 0.001 HIS E 194 PHE 0.014 0.001 PHE C 108 TYR 0.009 0.001 TYR B 198 ARG 0.005 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 690) hydrogen bonds : angle 4.15834 ( 2355) covalent geometry : bond 0.00358 (11945) covalent geometry : angle 0.54882 (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 267 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 82 ASN cc_start: 0.8431 (t0) cc_final: 0.7973 (t0) REVERT: C 87 MET cc_start: 0.8833 (tpt) cc_final: 0.7630 (tpt) REVERT: D 87 MET cc_start: 0.8762 (tpt) cc_final: 0.7684 (tpt) REVERT: E 82 ASN cc_start: 0.8725 (t0) cc_final: 0.8308 (t0) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1615 time to fit residues: 70.3207 Evaluate side-chains 226 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 46 optimal weight: 0.0980 chunk 26 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 37 optimal weight: 0.0470 chunk 149 optimal weight: 6.9990 overall best weight: 4.6284 ------------------------------------------------------------------------------- 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** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN ** E 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 = 0.3351 r_free = 0.3351 target = 0.130400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.111512 restraints weight = 20168.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.113869 restraints weight = 12811.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.115457 restraints weight = 9265.712| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11945 Z= 0.244 Angle : 0.638 6.155 16325 Z= 0.337 Chirality : 0.045 0.142 1900 Planarity : 0.004 0.046 2080 Dihedral : 5.300 24.019 1645 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1540 helix: 2.18 (0.20), residues: 605 sheet: -1.15 (0.25), residues: 425 loop : -0.62 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 40 HIS 0.006 0.001 HIS E 194 PHE 0.019 0.002 PHE C 108 TYR 0.010 0.002 TYR D 222 ARG 0.010 0.001 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 690) hydrogen bonds : angle 4.43693 ( 2355) covalent geometry : bond 0.00564 (11945) covalent geometry : angle 0.63806 (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 247 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 ASN cc_start: 0.8683 (t0) cc_final: 0.8369 (t0) REVERT: D 87 MET cc_start: 0.8777 (tpt) cc_final: 0.7782 (tpt) REVERT: E 82 ASN cc_start: 0.8943 (t0) cc_final: 0.8548 (t0) REVERT: E 87 MET cc_start: 0.9037 (tpt) cc_final: 0.8163 (tpt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1744 time to fit residues: 71.1795 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 : 1.853 ------------------------------------------------------------------------------- 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: 7.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** B 90 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 = 0.3457 r_free = 0.3457 target = 0.139393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.121040 restraints weight = 19646.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.123533 restraints weight = 12267.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.125233 restraints weight = 8720.579| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11945 Z= 0.110 Angle : 0.533 5.434 16325 Z= 0.276 Chirality : 0.041 0.150 1900 Planarity : 0.003 0.029 2080 Dihedral : 4.926 21.838 1645 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 0.78 (0.23), residues: 1540 helix: 2.49 (0.20), residues: 605 sheet: -1.07 (0.26), residues: 425 loop : -0.35 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 75 HIS 0.003 0.001 HIS D 140 PHE 0.014 0.001 PHE B 117 TYR 0.010 0.001 TYR A 104 ARG 0.008 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 690) hydrogen bonds : angle 4.11269 ( 2355) covalent geometry : bond 0.00238 (11945) covalent geometry : angle 0.53338 (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 256 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ASN cc_start: 0.8450 (t0) cc_final: 0.8166 (t0) REVERT: C 87 MET cc_start: 0.8620 (tpt) cc_final: 0.8356 (tpt) REVERT: D 83 GLN cc_start: 0.8166 (tt0) cc_final: 0.7936 (tt0) REVERT: D 87 MET cc_start: 0.8575 (tpt) cc_final: 0.7652 (tpt) REVERT: E 82 ASN cc_start: 0.8844 (t0) cc_final: 0.8515 (t0) REVERT: E 87 MET cc_start: 0.8864 (tpt) cc_final: 0.8319 (tpt) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1544 time to fit residues: 64.9734 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 : 1.215 ------------------------------------------------------------------------------- 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: 0.2980 chunk 73 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 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 = 0.3410 r_free = 0.3410 target = 0.135505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.116832 restraints weight = 19680.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.119244 restraints weight = 12462.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.120944 restraints weight = 8981.709| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11945 Z= 0.151 Angle : 0.549 5.550 16325 Z= 0.286 Chirality : 0.041 0.145 1900 Planarity : 0.003 0.028 2080 Dihedral : 4.913 19.955 1645 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: 0.83 (0.23), residues: 1540 helix: 2.58 (0.20), residues: 605 sheet: -1.08 (0.26), residues: 425 loop : -0.37 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 162 HIS 0.003 0.001 HIS E 194 PHE 0.015 0.001 PHE B 236 TYR 0.007 0.001 TYR C 198 ARG 0.008 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 690) hydrogen bonds : angle 4.15118 ( 2355) covalent geometry : bond 0.00348 (11945) covalent geometry : angle 0.54870 (16325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3443.03 seconds wall clock time: 61 minutes 18.72 seconds (3678.72 seconds total)