Starting phenix.real_space_refine on Sat Mar 7 05:56:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rsm_54221/03_2026/9rsm_54221.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rsm_54221/03_2026/9rsm_54221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rsm_54221/03_2026/9rsm_54221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rsm_54221/03_2026/9rsm_54221.map" model { file = "/net/cci-nas-00/data/ceres_data/9rsm_54221/03_2026/9rsm_54221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rsm_54221/03_2026/9rsm_54221.cif" } resolution = 2.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 12213 2.51 5 N 3177 2.21 5 O 3807 1.98 5 H 18639 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37881 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4209 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 256} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I Time building chain proxies: 4.99, per 1000 atoms: 0.13 Number of scatterers: 37881 At special positions: 0 Unit cell: (124.1, 124.83, 89.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 O 3807 8.00 N 3177 7.00 C 12213 6.00 H 18639 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 979.0 milliseconds 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4500 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 45 sheets defined 6.0% alpha, 74.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 213 through 218 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 213 through 218 Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 213 through 218 Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 208 through 212 Processing helix chain 'H' and resid 213 through 218 Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 208 through 212 Processing helix chain 'I' and resid 213 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR A 55 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 102 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS A 229 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE A 100 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR A 55 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 72 removed outlier: 5.913A pdb=" N ASN A 78 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU A 252 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR A 80 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR A 250 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP A 248 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 161 removed outlier: 5.538A pdb=" N THR A 156 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 171 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN A 158 " --> pdb=" O ASN A 169 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN A 169 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 160 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER A 83 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN A 78 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU A 252 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR A 80 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR A 250 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP A 248 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A 289 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU A 277 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE A 287 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP A 279 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL A 285 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 125 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR B 55 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU B 102 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS B 229 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE B 100 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR B 55 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 72 removed outlier: 5.913A pdb=" N ASN B 78 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU B 252 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR B 80 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR B 250 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 248 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 154 through 161 removed outlier: 5.538A pdb=" N THR B 156 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 171 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLN B 158 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN B 169 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 160 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER B 83 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN B 78 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU B 252 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR B 80 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR B 250 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 248 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR B 289 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU B 277 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE B 287 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP B 279 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 285 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 125 through 129 Processing sheet with id=AB2, first strand: chain 'C' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR C 55 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 102 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS C 229 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE C 100 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR C 55 " --> pdb=" O ILE C 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 69 through 72 removed outlier: 5.913A pdb=" N ASN C 78 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU C 252 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR C 80 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR C 250 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP C 248 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 161 removed outlier: 5.539A pdb=" N THR C 156 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 171 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN C 158 " --> pdb=" O ASN C 169 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN C 169 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER C 160 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER C 83 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN C 78 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU C 252 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR C 80 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR C 250 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP C 248 " --> pdb=" O PRO C 82 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR C 289 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C 277 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE C 287 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP C 279 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL C 285 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 125 through 129 Processing sheet with id=AB7, first strand: chain 'D' and resid 24 through 34 removed outlier: 3.659A pdb=" N THR D 55 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU D 102 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS D 229 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE D 100 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 24 through 34 removed outlier: 3.659A pdb=" N THR D 55 " --> pdb=" O ILE D 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 69 through 72 removed outlier: 5.912A pdb=" N ASN D 78 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU D 252 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR D 80 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR D 250 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP D 248 " --> pdb=" O PRO D 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 154 through 161 removed outlier: 5.538A pdb=" N THR D 156 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 171 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLN D 158 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN D 169 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 160 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER D 83 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN D 78 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU D 252 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR D 80 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR D 250 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP D 248 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR D 289 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLU D 277 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE D 287 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP D 279 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL D 285 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 125 through 129 Processing sheet with id=AC3, first strand: chain 'E' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR E 55 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU E 102 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS E 229 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE E 100 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR E 55 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 69 through 72 removed outlier: 5.912A pdb=" N ASN E 78 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU E 252 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR E 80 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR E 250 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP E 248 " --> pdb=" O PRO E 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 154 through 161 removed outlier: 5.538A pdb=" N THR E 156 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL E 171 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN E 158 " --> pdb=" O ASN E 169 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN E 169 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER E 160 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER E 83 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN E 78 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU E 252 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR E 80 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR E 250 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP E 248 " --> pdb=" O PRO E 82 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR E 289 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU E 277 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE E 287 " --> pdb=" O GLU E 277 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP E 279 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL E 285 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 125 through 129 Processing sheet with id=AC8, first strand: chain 'F' and resid 24 through 34 removed outlier: 3.661A pdb=" N THR F 55 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU F 102 " --> pdb=" O ALA F 227 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS F 229 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE F 100 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 24 through 34 removed outlier: 3.661A pdb=" N THR F 55 " --> pdb=" O ILE F 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 69 through 72 removed outlier: 5.913A pdb=" N ASN F 78 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU F 252 " --> pdb=" O ASN F 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR F 80 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR F 250 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP F 248 " --> pdb=" O PRO F 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 154 through 161 removed outlier: 5.538A pdb=" N THR F 156 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL F 171 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLN F 158 " --> pdb=" O ASN F 169 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN F 169 " --> pdb=" O GLN F 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER F 160 " --> pdb=" O SER F 167 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER F 83 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN F 78 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU F 252 " --> pdb=" O ASN F 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR F 80 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR F 250 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP F 248 " --> pdb=" O PRO F 82 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR F 289 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLU F 277 " --> pdb=" O PHE F 287 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE F 287 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP F 279 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL F 285 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 125 through 129 Processing sheet with id=AD4, first strand: chain 'G' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR G 55 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU G 102 " --> pdb=" O ALA G 227 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS G 229 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE G 100 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR G 55 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 69 through 72 removed outlier: 5.912A pdb=" N ASN G 78 " --> pdb=" O LEU G 252 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU G 252 " --> pdb=" O ASN G 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR G 80 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR G 250 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP G 248 " --> pdb=" O PRO G 82 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 154 through 161 removed outlier: 5.538A pdb=" N THR G 156 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL G 171 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN G 158 " --> pdb=" O ASN G 169 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN G 169 " --> pdb=" O GLN G 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER G 160 " --> pdb=" O SER G 167 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER G 83 " --> pdb=" O PHE G 172 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN G 78 " --> pdb=" O LEU G 252 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU G 252 " --> pdb=" O ASN G 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR G 80 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR G 250 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP G 248 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR G 289 " --> pdb=" O THR G 275 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU G 277 " --> pdb=" O PHE G 287 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE G 287 " --> pdb=" O GLU G 277 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP G 279 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL G 285 " --> pdb=" O ASP G 279 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 125 through 129 Processing sheet with id=AD9, first strand: chain 'H' and resid 24 through 34 removed outlier: 3.661A pdb=" N THR H 55 " --> pdb=" O ILE H 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU H 102 " --> pdb=" O ALA H 227 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS H 229 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE H 100 " --> pdb=" O LYS H 229 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 24 through 34 removed outlier: 3.661A pdb=" N THR H 55 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 69 through 72 removed outlier: 5.913A pdb=" N ASN H 78 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU H 252 " --> pdb=" O ASN H 78 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR H 80 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR H 250 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP H 248 " --> pdb=" O PRO H 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 154 through 161 removed outlier: 5.539A pdb=" N THR H 156 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL H 171 " --> pdb=" O THR H 156 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLN H 158 " --> pdb=" O ASN H 169 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN H 169 " --> pdb=" O GLN H 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER H 160 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER H 83 " --> pdb=" O PHE H 172 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN H 78 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU H 252 " --> pdb=" O ASN H 78 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR H 80 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR H 250 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP H 248 " --> pdb=" O PRO H 82 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR H 289 " --> pdb=" O THR H 275 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU H 277 " --> pdb=" O PHE H 287 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE H 287 " --> pdb=" O GLU H 277 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP H 279 " --> pdb=" O VAL H 285 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL H 285 " --> pdb=" O ASP H 279 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 125 through 129 Processing sheet with id=AE5, first strand: chain 'I' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR I 55 " --> pdb=" O ILE I 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU I 102 " --> pdb=" O ALA I 227 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS I 229 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE I 100 " --> pdb=" O LYS I 229 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 24 through 34 removed outlier: 3.660A pdb=" N THR I 55 " --> pdb=" O ILE I 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 69 through 72 removed outlier: 5.912A pdb=" N ASN I 78 " --> pdb=" O LEU I 252 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU I 252 " --> pdb=" O ASN I 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR I 80 " --> pdb=" O TYR I 250 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR I 250 " --> pdb=" O TYR I 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP I 248 " --> pdb=" O PRO I 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 154 through 161 removed outlier: 5.538A pdb=" N THR I 156 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL I 171 " --> pdb=" O THR I 156 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN I 158 " --> pdb=" O ASN I 169 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN I 169 " --> pdb=" O GLN I 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER I 160 " --> pdb=" O SER I 167 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER I 83 " --> pdb=" O PHE I 172 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN I 78 " --> pdb=" O LEU I 252 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU I 252 " --> pdb=" O ASN I 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR I 80 " --> pdb=" O TYR I 250 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR I 250 " --> pdb=" O TYR I 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP I 248 " --> pdb=" O PRO I 82 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR I 289 " --> pdb=" O THR I 275 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU I 277 " --> pdb=" O PHE I 287 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE I 287 " --> pdb=" O GLU I 277 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP I 279 " --> pdb=" O VAL I 285 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL I 285 " --> pdb=" O ASP I 279 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 125 through 129 1116 hydrogen bonds defined for protein. 3024 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: 9.74 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18639 1.03 - 1.22: 0 1.22 - 1.42: 8533 1.42 - 1.61: 11060 1.61 - 1.80: 90 Bond restraints: 38322 Sorted by residual: bond pdb=" N GLY A 140 " pdb=" H GLY A 140 " ideal model delta sigma weight residual 0.860 0.906 -0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" N GLY E 140 " pdb=" H GLY E 140 " ideal model delta sigma weight residual 0.860 0.906 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" N GLY H 140 " pdb=" H GLY H 140 " ideal model delta sigma weight residual 0.860 0.906 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" N GLY G 140 " pdb=" H GLY G 140 " ideal model delta sigma weight residual 0.860 0.905 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" N GLY C 140 " pdb=" H GLY C 140 " ideal model delta sigma weight residual 0.860 0.905 -0.045 2.00e-02 2.50e+03 5.11e+00 ... (remaining 38317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 64299 0.96 - 1.93: 4271 1.93 - 2.89: 232 2.89 - 3.86: 132 3.86 - 4.82: 15 Bond angle restraints: 68949 Sorted by residual: angle pdb=" CA GLY B 140 " pdb=" C GLY B 140 " pdb=" O GLY B 140 " ideal model delta sigma weight residual 122.65 117.83 4.82 1.28e+00 6.10e-01 1.42e+01 angle pdb=" CA GLY F 140 " pdb=" C GLY F 140 " pdb=" O GLY F 140 " ideal model delta sigma weight residual 122.65 117.85 4.80 1.28e+00 6.10e-01 1.41e+01 angle pdb=" CA GLY D 140 " pdb=" C GLY D 140 " pdb=" O GLY D 140 " ideal model delta sigma weight residual 122.65 117.86 4.79 1.28e+00 6.10e-01 1.40e+01 angle pdb=" CA GLY H 140 " pdb=" C GLY H 140 " pdb=" O GLY H 140 " ideal model delta sigma weight residual 122.65 117.86 4.79 1.28e+00 6.10e-01 1.40e+01 angle pdb=" CA GLY E 140 " pdb=" C GLY E 140 " pdb=" O GLY E 140 " ideal model delta sigma weight residual 122.65 117.87 4.78 1.28e+00 6.10e-01 1.40e+01 ... (remaining 68944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.85: 16065 11.85 - 23.70: 1476 23.70 - 35.55: 378 35.55 - 47.40: 180 47.40 - 59.25: 99 Dihedral angle restraints: 18198 sinusoidal: 9729 harmonic: 8469 Sorted by residual: dihedral pdb=" CA TYR B 270 " pdb=" C TYR B 270 " pdb=" N TYR B 271 " pdb=" CA TYR B 271 " ideal model delta harmonic sigma weight residual -180.00 -163.40 -16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA TYR F 270 " pdb=" C TYR F 270 " pdb=" N TYR F 271 " pdb=" CA TYR F 271 " ideal model delta harmonic sigma weight residual -180.00 -163.40 -16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA TYR A 270 " pdb=" C TYR A 270 " pdb=" N TYR A 271 " pdb=" CA TYR A 271 " ideal model delta harmonic sigma weight residual -180.00 -163.42 -16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 18195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1571 0.027 - 0.053: 884 0.053 - 0.080: 174 0.080 - 0.107: 137 0.107 - 0.134: 105 Chirality restraints: 2871 Sorted by residual: chirality pdb=" CA ILE G 109 " pdb=" N ILE G 109 " pdb=" C ILE G 109 " pdb=" CB ILE G 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE E 109 " pdb=" N ILE E 109 " pdb=" C ILE E 109 " pdb=" CB ILE E 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE F 109 " pdb=" N ILE F 109 " pdb=" C ILE F 109 " pdb=" CB ILE F 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 2868 not shown) Planarity restraints: 5688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 138 " 0.188 2.00e-02 2.50e+03 2.08e-01 6.50e+02 pdb=" CG ASN F 138 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN F 138 " -0.181 2.00e-02 2.50e+03 pdb=" ND2 ASN F 138 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN F 138 " -0.306 2.00e-02 2.50e+03 pdb="HD22 ASN F 138 " 0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 138 " -0.188 2.00e-02 2.50e+03 2.08e-01 6.49e+02 pdb=" CG ASN H 138 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN H 138 " 0.181 2.00e-02 2.50e+03 pdb=" ND2 ASN H 138 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN H 138 " 0.306 2.00e-02 2.50e+03 pdb="HD22 ASN H 138 " -0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 138 " 0.188 2.00e-02 2.50e+03 2.08e-01 6.48e+02 pdb=" CG ASN B 138 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN B 138 " -0.181 2.00e-02 2.50e+03 pdb=" ND2 ASN B 138 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN B 138 " -0.305 2.00e-02 2.50e+03 pdb="HD22 ASN B 138 " 0.313 2.00e-02 2.50e+03 ... (remaining 5685 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 10615 2.32 - 2.89: 84970 2.89 - 3.46: 94445 3.46 - 4.03: 142890 4.03 - 4.60: 210718 Nonbonded interactions: 543638 Sorted by model distance: nonbonded pdb=" HE1 TYR I 179 " pdb="HE21 GLN I 191 " model vdw 1.752 2.100 nonbonded pdb=" HE1 TYR D 179 " pdb="HE21 GLN D 191 " model vdw 1.752 2.100 nonbonded pdb=" HE1 TYR F 179 " pdb="HE21 GLN F 191 " model vdw 1.752 2.100 nonbonded pdb=" HE1 TYR B 179 " pdb="HE21 GLN B 191 " model vdw 1.752 2.100 nonbonded pdb=" HE1 TYR G 179 " pdb="HE21 GLN G 191 " model vdw 1.753 2.100 ... (remaining 543633 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 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: 0.190 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.170 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 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 0.033 19683 Z= 0.208 Angle : 0.548 4.819 26667 Z= 0.313 Chirality : 0.042 0.134 2871 Planarity : 0.003 0.039 3393 Dihedral : 10.470 59.252 7209 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.42 % Allowed : 0.42 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2358 helix: -4.59 (0.13), residues: 54 sheet: -0.02 (0.14), residues: 1368 loop : -0.58 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 145 TYR 0.021 0.001 TYR D 255 PHE 0.009 0.001 PHE G 154 TRP 0.008 0.001 TRP H 254 HIS 0.001 0.000 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00458 (19683) covalent geometry : angle 0.54751 (26667) hydrogen bonds : bond 0.19137 ( 837) hydrogen bonds : angle 8.35552 ( 3024) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 250 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8138 (tt0) REVERT: B 113 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8517 (tpp80) REVERT: B 174 LYS cc_start: 0.8803 (pttp) cc_final: 0.8592 (ptpp) REVERT: B 286 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7787 (mm-30) REVERT: C 113 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8513 (tpp80) REVERT: C 174 LYS cc_start: 0.8823 (pttp) cc_final: 0.8608 (ptpp) REVERT: C 286 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7764 (mm-30) REVERT: D 113 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8531 (tpp80) REVERT: D 174 LYS cc_start: 0.8817 (pttp) cc_final: 0.8600 (ptpp) REVERT: D 256 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7938 (mtmt) REVERT: D 286 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7741 (mm-30) REVERT: E 113 ARG cc_start: 0.8741 (ttm110) cc_final: 0.8537 (tpp80) REVERT: E 148 GLN cc_start: 0.8784 (tt0) cc_final: 0.8195 (tm-30) REVERT: E 174 LYS cc_start: 0.8835 (pttp) cc_final: 0.8612 (ptpp) REVERT: E 286 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7747 (mm-30) REVERT: F 174 LYS cc_start: 0.8821 (pttp) cc_final: 0.8550 (ptpp) REVERT: F 286 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7847 (mm-30) REVERT: G 113 ARG cc_start: 0.8782 (ttm110) cc_final: 0.8561 (tpp80) REVERT: G 174 LYS cc_start: 0.8825 (pttp) cc_final: 0.8615 (ptpp) REVERT: G 286 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7761 (mm-30) REVERT: H 174 LYS cc_start: 0.8813 (pttp) cc_final: 0.8555 (ptpp) REVERT: H 286 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7805 (mm-30) REVERT: I 113 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8525 (tpp80) REVERT: I 148 GLN cc_start: 0.8738 (tt0) cc_final: 0.8142 (tm-30) REVERT: I 174 LYS cc_start: 0.8819 (pttp) cc_final: 0.8569 (ptpp) REVERT: I 286 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7819 (mm-30) outliers start: 9 outliers final: 0 residues processed: 259 average time/residue: 2.0208 time to fit residues: 568.5162 Evaluate side-chains 173 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 144 GLN B 86 ASN C 86 ASN D 86 ASN E 86 ASN E 144 GLN F 144 GLN G 86 ASN G 144 GLN H 86 ASN H 144 GLN I 86 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.067049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.052299 restraints weight = 96158.512| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 2.31 r_work: 0.2390 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2285 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 19683 Z= 0.214 Angle : 0.530 4.518 26667 Z= 0.287 Chirality : 0.045 0.152 2871 Planarity : 0.004 0.035 3393 Dihedral : 4.622 15.167 2601 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.14 % Allowed : 4.11 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2358 helix: -4.30 (0.19), residues: 54 sheet: 0.16 (0.14), residues: 1368 loop : -0.39 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 113 TYR 0.012 0.001 TYR D 255 PHE 0.011 0.001 PHE A 154 TRP 0.009 0.001 TRP E 254 HIS 0.002 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00475 (19683) covalent geometry : angle 0.53027 (26667) hydrogen bonds : bond 0.04179 ( 837) hydrogen bonds : angle 5.46853 ( 3024) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7982 (mtmt) REVERT: B 113 ARG cc_start: 0.8826 (ttm110) cc_final: 0.8592 (tpp80) REVERT: C 113 ARG cc_start: 0.8714 (ttm110) cc_final: 0.8472 (tpp80) REVERT: C 286 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8162 (mt-10) REVERT: D 113 ARG cc_start: 0.8783 (ttm110) cc_final: 0.8478 (tpp80) REVERT: D 174 LYS cc_start: 0.8818 (pttp) cc_final: 0.8479 (ptpp) REVERT: E 113 ARG cc_start: 0.8766 (ttm110) cc_final: 0.8559 (tpp80) REVERT: E 148 GLN cc_start: 0.8760 (tt0) cc_final: 0.8181 (tm-30) REVERT: E 174 LYS cc_start: 0.8834 (pttp) cc_final: 0.8476 (ptpp) REVERT: E 286 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8033 (mt-10) REVERT: F 174 LYS cc_start: 0.8758 (pttp) cc_final: 0.8364 (ptpp) REVERT: F 286 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8082 (mt-10) REVERT: G 113 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8526 (tpp80) REVERT: G 174 LYS cc_start: 0.8777 (pttp) cc_final: 0.8427 (ptpp) REVERT: G 286 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7900 (tt0) REVERT: H 148 GLN cc_start: 0.8925 (tt0) cc_final: 0.7885 (tm-30) REVERT: H 174 LYS cc_start: 0.8837 (pttp) cc_final: 0.8456 (ptpp) REVERT: H 286 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7988 (mt-10) REVERT: I 113 ARG cc_start: 0.8708 (ttm110) cc_final: 0.8495 (tpp80) REVERT: I 148 GLN cc_start: 0.8794 (tt0) cc_final: 0.8072 (tm-30) REVERT: I 174 LYS cc_start: 0.8811 (pttp) cc_final: 0.8435 (ptpp) REVERT: I 286 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8175 (mt-10) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 2.2323 time to fit residues: 460.9270 Evaluate side-chains 167 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 133 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN E 144 GLN F 86 ASN G 144 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.067024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.052047 restraints weight = 95670.563| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 2.33 r_work: 0.2378 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2273 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 19683 Z= 0.173 Angle : 0.481 4.305 26667 Z= 0.263 Chirality : 0.044 0.149 2871 Planarity : 0.003 0.031 3393 Dihedral : 4.531 16.037 2601 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.23 % Allowed : 4.86 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2358 helix: -3.81 (0.31), residues: 54 sheet: 0.35 (0.13), residues: 1368 loop : -0.50 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.009 0.001 TYR B 149 PHE 0.009 0.001 PHE C 154 TRP 0.009 0.001 TRP A 254 HIS 0.001 0.000 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00386 (19683) covalent geometry : angle 0.48090 (26667) hydrogen bonds : bond 0.03590 ( 837) hydrogen bonds : angle 4.96651 ( 3024) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ARG cc_start: 0.8851 (ttm110) cc_final: 0.8548 (tpp80) REVERT: C 113 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8507 (tpp80) REVERT: D 113 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8552 (tpp80) REVERT: E 113 ARG cc_start: 0.8798 (ttm110) cc_final: 0.8573 (tpp80) REVERT: G 113 ARG cc_start: 0.8858 (ttm110) cc_final: 0.8614 (tpp80) REVERT: G 264 ARG cc_start: 0.8106 (ttp-170) cc_final: 0.7902 (ttp-170) REVERT: H 148 GLN cc_start: 0.8929 (tt0) cc_final: 0.7858 (tm-30) REVERT: I 113 ARG cc_start: 0.8741 (ttm110) cc_final: 0.8498 (tpp80) REVERT: I 174 LYS cc_start: 0.8765 (pttp) cc_final: 0.8331 (ptpp) REVERT: I 286 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8226 (mt-10) outliers start: 5 outliers final: 0 residues processed: 184 average time/residue: 2.3393 time to fit residues: 463.5193 Evaluate side-chains 165 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 139 optimal weight: 6.9990 chunk 50 optimal weight: 0.3980 chunk 123 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN D 144 GLN F 144 GLN H 144 GLN I 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.066872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.051906 restraints weight = 95332.244| |-----------------------------------------------------------------------------| r_work (start): 0.2486 rms_B_bonded: 2.34 r_work: 0.2373 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2269 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19683 Z= 0.162 Angle : 0.472 3.861 26667 Z= 0.257 Chirality : 0.044 0.142 2871 Planarity : 0.003 0.045 3393 Dihedral : 4.526 15.991 2601 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.37 % Allowed : 4.90 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2358 helix: -3.51 (0.39), residues: 54 sheet: 0.41 (0.13), residues: 1368 loop : -0.51 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 113 TYR 0.008 0.001 TYR F 149 PHE 0.008 0.001 PHE C 154 TRP 0.008 0.001 TRP A 254 HIS 0.001 0.000 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00360 (19683) covalent geometry : angle 0.47185 (26667) hydrogen bonds : bond 0.03273 ( 837) hydrogen bonds : angle 4.81041 ( 3024) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ARG cc_start: 0.8880 (ttm110) cc_final: 0.8573 (tpp80) REVERT: C 113 ARG cc_start: 0.8765 (ttm110) cc_final: 0.8505 (tpp80) REVERT: D 113 ARG cc_start: 0.8795 (ttm110) cc_final: 0.8488 (tpp80) REVERT: E 113 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8568 (tpp80) REVERT: G 113 ARG cc_start: 0.8849 (ttm110) cc_final: 0.8534 (tpp80) REVERT: G 264 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7912 (ttp-170) REVERT: H 148 GLN cc_start: 0.8922 (tt0) cc_final: 0.7895 (tm-30) REVERT: I 113 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8499 (tpp80) REVERT: I 144 GLN cc_start: 0.9040 (tt0) cc_final: 0.8833 (tt0) REVERT: I 148 GLN cc_start: 0.8874 (tt0) cc_final: 0.7877 (tm-30) outliers start: 8 outliers final: 0 residues processed: 172 average time/residue: 2.5642 time to fit residues: 473.6358 Evaluate side-chains 163 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 174 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 144 GLN D 144 GLN E 144 GLN F 144 GLN H 144 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.068883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.053921 restraints weight = 94722.124| |-----------------------------------------------------------------------------| r_work (start): 0.2531 rms_B_bonded: 2.33 r_work: 0.2419 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2315 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 19683 Z= 0.097 Angle : 0.438 3.728 26667 Z= 0.238 Chirality : 0.043 0.142 2871 Planarity : 0.003 0.030 3393 Dihedral : 4.271 15.890 2601 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.23 % Allowed : 5.04 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2358 helix: -3.10 (0.49), residues: 54 sheet: 0.49 (0.13), residues: 1368 loop : -0.42 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 113 TYR 0.007 0.001 TYR G 246 PHE 0.006 0.001 PHE G 45 TRP 0.006 0.001 TRP H 254 HIS 0.000 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00211 (19683) covalent geometry : angle 0.43769 (26667) hydrogen bonds : bond 0.02866 ( 837) hydrogen bonds : angle 4.49202 ( 3024) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ARG cc_start: 0.8841 (ttm110) cc_final: 0.8551 (tpp80) REVERT: C 113 ARG cc_start: 0.8748 (ttm110) cc_final: 0.8519 (tpp80) REVERT: D 113 ARG cc_start: 0.8798 (ttm110) cc_final: 0.8507 (tpp80) REVERT: E 113 ARG cc_start: 0.8806 (ttm110) cc_final: 0.8562 (tpp80) REVERT: G 113 ARG cc_start: 0.8859 (ttm110) cc_final: 0.8546 (tpp80) REVERT: G 264 ARG cc_start: 0.8115 (ttp-170) cc_final: 0.7804 (ttp-170) REVERT: H 148 GLN cc_start: 0.8892 (tt0) cc_final: 0.7864 (tm-30) REVERT: I 22 GLN cc_start: 0.8111 (tt0) cc_final: 0.7865 (tm-30) REVERT: I 113 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8496 (tpp80) REVERT: I 148 GLN cc_start: 0.8843 (tt0) cc_final: 0.7873 (tm-30) outliers start: 5 outliers final: 0 residues processed: 171 average time/residue: 2.5238 time to fit residues: 462.7421 Evaluate side-chains 166 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 42 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 144 GLN C 191 GLN D 144 GLN F 144 GLN I 144 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.067145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.052184 restraints weight = 95464.739| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 2.34 r_work: 0.2380 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 19683 Z= 0.159 Angle : 0.465 3.798 26667 Z= 0.253 Chirality : 0.043 0.142 2871 Planarity : 0.003 0.030 3393 Dihedral : 4.424 15.784 2601 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.23 % Allowed : 5.09 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2358 helix: -3.23 (0.46), residues: 54 sheet: 0.48 (0.13), residues: 1368 loop : -0.49 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.008 0.001 TYR B 149 PHE 0.008 0.001 PHE C 45 TRP 0.007 0.001 TRP I 254 HIS 0.001 0.000 HIS I 185 Details of bonding type rmsd covalent geometry : bond 0.00358 (19683) covalent geometry : angle 0.46452 (26667) hydrogen bonds : bond 0.03160 ( 837) hydrogen bonds : angle 4.64149 ( 3024) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.9138 (tt0) cc_final: 0.8935 (tt0) REVERT: B 113 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8536 (tpp80) REVERT: B 264 ARG cc_start: 0.8114 (ttp-170) cc_final: 0.7825 (ttp-170) REVERT: C 113 ARG cc_start: 0.8766 (ttm110) cc_final: 0.8533 (tpp80) REVERT: D 113 ARG cc_start: 0.8802 (ttm110) cc_final: 0.8486 (tpp80) REVERT: E 113 ARG cc_start: 0.8813 (ttm110) cc_final: 0.8573 (tpp80) REVERT: G 113 ARG cc_start: 0.8853 (ttm110) cc_final: 0.8542 (tpp80) REVERT: G 264 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7916 (ttp-170) REVERT: H 22 GLN cc_start: 0.7994 (tt0) cc_final: 0.7741 (tm-30) REVERT: H 148 GLN cc_start: 0.8907 (tt0) cc_final: 0.7914 (tm-30) REVERT: I 113 ARG cc_start: 0.8747 (ttm110) cc_final: 0.8519 (ttm170) REVERT: I 144 GLN cc_start: 0.9083 (tt0) cc_final: 0.8867 (tt0) REVERT: I 148 GLN cc_start: 0.8836 (tt0) cc_final: 0.7860 (tm-30) outliers start: 5 outliers final: 0 residues processed: 174 average time/residue: 2.5327 time to fit residues: 473.1321 Evaluate side-chains 168 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 27 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN C 144 GLN D 144 GLN E 144 GLN F 144 GLN H 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.065398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.050382 restraints weight = 96088.317| |-----------------------------------------------------------------------------| r_work (start): 0.2454 rms_B_bonded: 2.33 r_work: 0.2341 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2235 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 19683 Z= 0.251 Angle : 0.515 3.936 26667 Z= 0.281 Chirality : 0.045 0.149 2871 Planarity : 0.003 0.030 3393 Dihedral : 4.710 15.818 2601 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.42 % Allowed : 5.00 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2358 helix: -3.48 (0.40), residues: 54 sheet: 0.41 (0.13), residues: 1368 loop : -0.57 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.010 0.001 TYR B 149 PHE 0.010 0.001 PHE I 45 TRP 0.008 0.001 TRP H 254 HIS 0.002 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00575 (19683) covalent geometry : angle 0.51459 (26667) hydrogen bonds : bond 0.03632 ( 837) hydrogen bonds : angle 4.93609 ( 3024) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ARG cc_start: 0.8858 (ttm110) cc_final: 0.8586 (tpp80) REVERT: C 138 ASN cc_start: 0.5951 (OUTLIER) cc_final: 0.5709 (m-40) REVERT: D 113 ARG cc_start: 0.8795 (ttm110) cc_final: 0.8518 (tpp80) REVERT: D 256 LYS cc_start: 0.8457 (mppt) cc_final: 0.8238 (mmtm) REVERT: E 113 ARG cc_start: 0.8805 (ttm110) cc_final: 0.8553 (tpp80) REVERT: G 113 ARG cc_start: 0.8836 (ttm110) cc_final: 0.8578 (tpp80) REVERT: G 264 ARG cc_start: 0.8102 (ttp-170) cc_final: 0.7892 (ttp-170) REVERT: H 22 GLN cc_start: 0.8030 (tt0) cc_final: 0.7781 (tm-30) REVERT: I 113 ARG cc_start: 0.8785 (ttm110) cc_final: 0.8559 (ttm170) outliers start: 9 outliers final: 0 residues processed: 179 average time/residue: 2.4090 time to fit residues: 464.1162 Evaluate side-chains 168 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 161 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 144 GLN D 144 GLN F 144 GLN G 144 GLN I 144 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.066269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.051250 restraints weight = 95322.453| |-----------------------------------------------------------------------------| r_work (start): 0.2474 rms_B_bonded: 2.34 r_work: 0.2361 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2255 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 19683 Z= 0.176 Angle : 0.480 3.870 26667 Z= 0.261 Chirality : 0.044 0.144 2871 Planarity : 0.003 0.030 3393 Dihedral : 4.585 15.991 2601 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.14 % Allowed : 5.37 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2358 helix: -3.35 (0.42), residues: 54 sheet: 0.43 (0.13), residues: 1368 loop : -0.56 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.008 0.001 TYR A 149 PHE 0.009 0.001 PHE C 45 TRP 0.008 0.001 TRP H 254 HIS 0.001 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00395 (19683) covalent geometry : angle 0.47960 (26667) hydrogen bonds : bond 0.03309 ( 837) hydrogen bonds : angle 4.77852 ( 3024) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ARG cc_start: 0.8840 (ttm110) cc_final: 0.8512 (tpp80) REVERT: D 113 ARG cc_start: 0.8788 (ttm110) cc_final: 0.8515 (tpp80) REVERT: D 256 LYS cc_start: 0.8508 (mppt) cc_final: 0.8282 (mmtm) REVERT: E 113 ARG cc_start: 0.8793 (ttm110) cc_final: 0.8538 (tpp80) REVERT: G 113 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8564 (tpp80) REVERT: H 22 GLN cc_start: 0.7993 (tt0) cc_final: 0.7745 (tm-30) REVERT: I 113 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8540 (ttm170) outliers start: 3 outliers final: 0 residues processed: 173 average time/residue: 2.4863 time to fit residues: 461.5512 Evaluate side-chains 169 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 181 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 144 GLN D 144 GLN E 144 GLN F 144 GLN H 144 GLN I 144 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.065583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.050534 restraints weight = 96516.918| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 2.35 r_work: 0.2345 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2240 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 19683 Z= 0.218 Angle : 0.499 3.911 26667 Z= 0.272 Chirality : 0.044 0.145 2871 Planarity : 0.003 0.030 3393 Dihedral : 4.681 15.994 2601 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.28 % Allowed : 5.28 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2358 helix: -3.43 (0.41), residues: 54 sheet: 0.40 (0.13), residues: 1368 loop : -0.60 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.010 0.001 TYR B 149 PHE 0.009 0.001 PHE I 45 TRP 0.008 0.001 TRP H 254 HIS 0.002 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00493 (19683) covalent geometry : angle 0.49884 (26667) hydrogen bonds : bond 0.03490 ( 837) hydrogen bonds : angle 4.87086 ( 3024) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ARG cc_start: 0.8829 (ttm110) cc_final: 0.8561 (tpp80) REVERT: D 113 ARG cc_start: 0.8793 (ttm110) cc_final: 0.8511 (tpp80) REVERT: D 256 LYS cc_start: 0.8513 (mppt) cc_final: 0.8285 (mmtm) REVERT: E 113 ARG cc_start: 0.8784 (ttm110) cc_final: 0.8526 (tpp80) REVERT: G 113 ARG cc_start: 0.8809 (ttm110) cc_final: 0.8556 (tpp80) REVERT: H 22 GLN cc_start: 0.7989 (tt0) cc_final: 0.7738 (tm-30) REVERT: I 113 ARG cc_start: 0.8772 (ttm110) cc_final: 0.8528 (ttm170) outliers start: 6 outliers final: 1 residues processed: 175 average time/residue: 2.5486 time to fit residues: 478.0744 Evaluate side-chains 172 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 144 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 187 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 144 GLN D 144 GLN F 144 GLN G 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.067216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.052590 restraints weight = 95578.071| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 2.29 r_work: 0.2392 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2288 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19683 Z= 0.102 Angle : 0.453 4.336 26667 Z= 0.246 Chirality : 0.044 0.146 2871 Planarity : 0.003 0.035 3393 Dihedral : 4.433 16.268 2601 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2358 helix: -3.11 (0.49), residues: 54 sheet: 0.48 (0.13), residues: 1368 loop : -0.48 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 145 TYR 0.007 0.001 TYR G 246 PHE 0.008 0.001 PHE I 45 TRP 0.008 0.001 TRP E 254 HIS 0.001 0.000 HIS E 283 Details of bonding type rmsd covalent geometry : bond 0.00222 (19683) covalent geometry : angle 0.45334 (26667) hydrogen bonds : bond 0.02979 ( 837) hydrogen bonds : angle 4.60053 ( 3024) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ARG cc_start: 0.8817 (ttm110) cc_final: 0.8504 (tpp80) REVERT: C 113 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8499 (tpp80) REVERT: D 113 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8506 (tpp80) REVERT: D 256 LYS cc_start: 0.8492 (mppt) cc_final: 0.8258 (mmtm) REVERT: E 113 ARG cc_start: 0.8764 (ttm110) cc_final: 0.8517 (tpp80) REVERT: G 113 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8483 (tpp80) REVERT: H 22 GLN cc_start: 0.7935 (tt0) cc_final: 0.7682 (tm-30) REVERT: I 113 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8519 (ttm170) outliers start: 2 outliers final: 0 residues processed: 171 average time/residue: 2.6182 time to fit residues: 479.5907 Evaluate side-chains 169 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 170 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 174 optimal weight: 0.4980 chunk 187 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 144 GLN D 144 GLN E 144 GLN F 144 GLN H 144 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.065921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.051332 restraints weight = 96389.210| |-----------------------------------------------------------------------------| r_work (start): 0.2480 rms_B_bonded: 2.30 r_work: 0.2368 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2263 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 19683 Z= 0.170 Angle : 0.473 4.193 26667 Z= 0.257 Chirality : 0.044 0.143 2871 Planarity : 0.003 0.030 3393 Dihedral : 4.523 15.940 2601 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.23 % Allowed : 5.42 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2358 helix: -3.18 (0.48), residues: 54 sheet: 0.46 (0.13), residues: 1368 loop : -0.55 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.008 0.001 TYR B 149 PHE 0.009 0.001 PHE I 45 TRP 0.008 0.001 TRP H 254 HIS 0.001 0.000 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00382 (19683) covalent geometry : angle 0.47308 (26667) hydrogen bonds : bond 0.03210 ( 837) hydrogen bonds : angle 4.68414 ( 3024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13970.91 seconds wall clock time: 237 minutes 10.81 seconds (14230.81 seconds total)