Starting phenix.real_space_refine on Thu Jul 31 08:29:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmr_40231/07_2025/8gmr_40231_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmr_40231/07_2025/8gmr_40231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gmr_40231/07_2025/8gmr_40231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmr_40231/07_2025/8gmr_40231.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmr_40231/07_2025/8gmr_40231_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmr_40231/07_2025/8gmr_40231_trim.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.010 sd= 0.445 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 96 5.16 5 C 8176 2.51 5 N 2048 2.21 5 O 2144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12472 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 5.08, per 1000 atoms: 0.41 Number of scatterers: 12472 At special positions: 0 Unit cell: (127.544, 127.544, 97.584, 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 96 16.00 P 8 15.00 O 2144 8.00 N 2048 7.00 C 8176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 127 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 0 sheets defined 69.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'B' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.567A pdb=" N ALA B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 127' Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR B 131 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 133 " --> pdb=" O CYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 179 through 197 Processing helix chain 'B' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL B 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B 242 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE B 251 " --> pdb=" O GLN B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'A' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE A 56 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Proline residue: A 60 - end of helix Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.566A pdb=" N ALA A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 127' Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR A 131 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 133 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL A 201 " --> pdb=" O LEU A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE A 242 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 removed outlier: 3.639A pdb=" N PHE A 251 " --> pdb=" O GLN A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'C' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE C 56 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 57 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Proline residue: C 60 - end of helix Processing helix chain 'C' and resid 75 through 81 removed outlier: 3.567A pdb=" N ALA C 79 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 122 " --> pdb=" O THR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 127' Processing helix chain 'C' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR C 131 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL C 133 " --> pdb=" O CYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 179 through 197 Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL C 201 " --> pdb=" O LEU C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 242 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE C 251 " --> pdb=" O GLN C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 251' Processing helix chain 'D' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA D 37 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE D 56 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Proline residue: D 60 - end of helix Processing helix chain 'D' and resid 75 through 81 removed outlier: 3.568A pdb=" N ALA D 79 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU D 126 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 127' Processing helix chain 'D' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR D 131 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL D 133 " --> pdb=" O CYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 179 through 197 Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL D 201 " --> pdb=" O LEU D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 213 through 219 Processing helix chain 'D' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE D 251 " --> pdb=" O GLN D 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 248 through 251' Processing helix chain 'E' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA E 37 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE E 56 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Proline residue: E 60 - end of helix Processing helix chain 'E' and resid 75 through 81 removed outlier: 3.567A pdb=" N ALA E 79 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 100 through 107 Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU E 119 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU E 126 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 127' Processing helix chain 'E' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR E 131 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL E 133 " --> pdb=" O CYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 179 through 197 Processing helix chain 'E' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL E 201 " --> pdb=" O LEU E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 213 through 219 Processing helix chain 'E' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 241 " --> pdb=" O GLU E 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE E 242 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE E 251 " --> pdb=" O GLN E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 248 through 251' Processing helix chain 'F' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA F 37 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE F 56 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 57 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Proline residue: F 60 - end of helix Processing helix chain 'F' and resid 75 through 81 removed outlier: 3.567A pdb=" N ALA F 79 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 115 Processing helix chain 'F' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU F 126 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 122 through 127' Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR F 131 " --> pdb=" O ALA F 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL F 133 " --> pdb=" O CYS F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 179 through 197 Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL F 201 " --> pdb=" O LEU F 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 198 through 201' Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS F 240 " --> pdb=" O THR F 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE F 242 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 251 removed outlier: 3.639A pdb=" N PHE F 251 " --> pdb=" O GLN F 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 248 through 251' Processing helix chain 'G' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA G 37 " --> pdb=" O GLN G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE G 56 " --> pdb=" O TYR G 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 57 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Proline residue: G 60 - end of helix Processing helix chain 'G' and resid 75 through 81 removed outlier: 3.568A pdb=" N ALA G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 100 through 107 Processing helix chain 'G' and resid 109 through 115 Processing helix chain 'G' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU G 119 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU G 126 " --> pdb=" O GLY G 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 127' Processing helix chain 'G' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR G 131 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL G 133 " --> pdb=" O CYS G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 157 Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 179 through 197 Processing helix chain 'G' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 201' Processing helix chain 'G' and resid 213 through 219 Processing helix chain 'G' and resid 222 through 247 removed outlier: 4.003A pdb=" N GLU G 233 " --> pdb=" O LYS G 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS G 240 " --> pdb=" O THR G 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA G 241 " --> pdb=" O GLU G 237 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE G 242 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE G 251 " --> pdb=" O GLN G 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 248 through 251' Processing helix chain 'H' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA H 37 " --> pdb=" O GLN H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE H 56 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Proline residue: H 60 - end of helix Processing helix chain 'H' and resid 75 through 81 removed outlier: 3.568A pdb=" N ALA H 79 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 100 through 107 Processing helix chain 'H' and resid 109 through 115 Processing helix chain 'H' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU H 119 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU H 126 " --> pdb=" O GLY H 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS H 127 " --> pdb=" O LYS H 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 122 through 127' Processing helix chain 'H' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR H 131 " --> pdb=" O ALA H 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL H 133 " --> pdb=" O CYS H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 157 Processing helix chain 'H' and resid 172 through 177 Processing helix chain 'H' and resid 179 through 197 Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL H 201 " --> pdb=" O LEU H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 213 through 219 Processing helix chain 'H' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 241 " --> pdb=" O GLU H 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE H 242 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS H 244 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE H 251 " --> pdb=" O GLN H 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 248 through 251' 520 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1904 1.31 - 1.44: 3312 1.44 - 1.56: 7376 1.56 - 1.69: 24 1.69 - 1.81: 120 Bond restraints: 12736 Sorted by residual: bond pdb=" C21 POV A 401 " pdb=" O21 POV A 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV H 401 " pdb=" O21 POV H 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV F 401 " pdb=" O21 POV F 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV B 401 " pdb=" O21 POV B 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C21 POV G 401 " pdb=" O21 POV G 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 12731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 17144 3.87 - 7.75: 208 7.75 - 11.62: 32 11.62 - 15.50: 16 15.50 - 19.37: 8 Bond angle restraints: 17408 Sorted by residual: angle pdb=" C13 POV H 401 " pdb=" N POV H 401 " pdb=" C14 POV H 401 " ideal model delta sigma weight residual 108.80 128.17 -19.37 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV A 401 " pdb=" N POV A 401 " pdb=" C14 POV A 401 " ideal model delta sigma weight residual 108.80 128.17 -19.37 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV D 401 " pdb=" N POV D 401 " pdb=" C14 POV D 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV E 401 " pdb=" N POV E 401 " pdb=" C14 POV E 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.16e+01 angle pdb=" C13 POV G 401 " pdb=" N POV G 401 " pdb=" C14 POV G 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.16e+01 ... (remaining 17403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 7049 22.84 - 45.68: 473 45.68 - 68.52: 81 68.52 - 91.36: 24 91.36 - 114.20: 8 Dihedral angle restraints: 7635 sinusoidal: 2595 harmonic: 5040 Sorted by residual: dihedral pdb=" CA VAL D 159 " pdb=" C VAL D 159 " pdb=" N PRO D 160 " pdb=" CA PRO D 160 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL E 159 " pdb=" C VAL E 159 " pdb=" N PRO E 160 " pdb=" CA PRO E 160 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL C 159 " pdb=" C VAL C 159 " pdb=" N PRO C 160 " pdb=" CA PRO C 160 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 7632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1265 0.034 - 0.068: 593 0.068 - 0.102: 175 0.102 - 0.136: 43 0.136 - 0.170: 12 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CB THR D 236 " pdb=" CA THR D 236 " pdb=" OG1 THR D 236 " pdb=" CG2 THR D 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CB THR C 236 " pdb=" CA THR C 236 " pdb=" OG1 THR C 236 " pdb=" CG2 THR C 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB THR E 236 " pdb=" CA THR E 236 " pdb=" OG1 THR E 236 " pdb=" CG2 THR E 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 2085 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 161 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO F 162 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO F 162 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 162 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS H 161 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO H 162 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO H 162 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 162 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 161 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO A 162 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " 0.032 5.00e-02 4.00e+02 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 15 2.24 - 2.90: 5066 2.90 - 3.57: 17275 3.57 - 4.23: 24176 4.23 - 4.90: 39367 Nonbonded interactions: 85899 Sorted by model distance: nonbonded pdb=" CB ASN F 255 " pdb=" CE2 TYR H 219 " model vdw 1.574 3.740 nonbonded pdb=" CB ASN E 255 " pdb=" CE2 TYR G 219 " model vdw 1.574 3.740 nonbonded pdb=" CB ASN D 255 " pdb=" CE2 TYR F 219 " model vdw 1.575 3.740 nonbonded pdb=" CB ASN B 255 " pdb=" CE2 TYR C 219 " model vdw 1.575 3.740 nonbonded pdb=" CB ASN C 255 " pdb=" CE2 TYR E 219 " model vdw 1.575 3.740 ... (remaining 85894 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.290 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.006 0.090 12737 Z= 0.310 Angle : 1.181 19.371 17410 Z= 0.527 Chirality : 0.043 0.170 2088 Planarity : 0.006 0.058 2176 Dihedral : 17.020 114.197 4336 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.56 % Favored : 86.96 % Rotamer: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.54 (0.17), residues: 1664 helix: -3.40 (0.12), residues: 912 sheet: None (None), residues: 0 loop : -4.03 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 220 HIS 0.005 0.003 HIS D 222 PHE 0.008 0.001 PHE A 40 TYR 0.013 0.001 TYR H 219 ARG 0.002 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.33712 ( 520) hydrogen bonds : angle 10.51303 ( 1536) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.97568 ( 2) covalent geometry : bond 0.00647 (12736) covalent geometry : angle 1.18117 (17408) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.288 Fit side-chains REVERT: B 158 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7855 (mtm180) REVERT: C 158 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7855 (mtm180) REVERT: E 158 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7854 (mtm180) REVERT: G 158 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7855 (mtm180) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2731 time to fit residues: 85.1723 Evaluate side-chains 208 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112350 restraints weight = 26354.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114607 restraints weight = 16362.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116172 restraints weight = 11822.502| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12737 Z= 0.187 Angle : 0.853 11.103 17410 Z= 0.410 Chirality : 0.046 0.168 2088 Planarity : 0.006 0.045 2176 Dihedral : 13.653 110.504 2160 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 1.29 % Allowed : 18.75 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.20), residues: 1664 helix: -1.81 (0.15), residues: 1024 sheet: None (None), residues: 0 loop : -3.68 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 189 HIS 0.005 0.003 HIS E 222 PHE 0.016 0.002 PHE G 38 TYR 0.010 0.002 TYR D 219 ARG 0.002 0.000 ARG G 106 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 520) hydrogen bonds : angle 5.67319 ( 1536) SS BOND : bond 0.00333 ( 1) SS BOND : angle 0.77031 ( 2) covalent geometry : bond 0.00456 (12736) covalent geometry : angle 0.85287 (17408) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 1.232 Fit side-chains REVERT: B 158 ARG cc_start: 0.8333 (mtt180) cc_final: 0.8001 (mtm180) REVERT: C 158 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7976 (mtm180) REVERT: E 108 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8571 (tt) REVERT: E 158 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7983 (mtm180) REVERT: G 108 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8575 (tt) REVERT: G 158 ARG cc_start: 0.8297 (mtt180) cc_final: 0.7979 (mtm180) REVERT: H 106 ARG cc_start: 0.8690 (ttp80) cc_final: 0.8464 (ttp80) outliers start: 14 outliers final: 4 residues processed: 218 average time/residue: 0.2429 time to fit residues: 76.6777 Evaluate side-chains 190 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 184 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 103 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 ASN E 105 GLN F 105 GLN H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115113 restraints weight = 26643.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117496 restraints weight = 16424.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119098 restraints weight = 11768.020| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12737 Z= 0.135 Angle : 0.768 10.549 17410 Z= 0.363 Chirality : 0.042 0.129 2088 Planarity : 0.005 0.048 2176 Dihedral : 12.510 108.120 2160 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 2.21 % Allowed : 25.83 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.21), residues: 1664 helix: -1.07 (0.16), residues: 1016 sheet: None (None), residues: 0 loop : -3.20 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 189 HIS 0.002 0.001 HIS B 222 PHE 0.009 0.001 PHE C 209 TYR 0.010 0.001 TYR B 223 ARG 0.002 0.000 ARG F 106 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 520) hydrogen bonds : angle 4.60714 ( 1536) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.51814 ( 2) covalent geometry : bond 0.00316 (12736) covalent geometry : angle 0.76786 (17408) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 1.300 Fit side-chains REVERT: B 158 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7897 (mtm180) REVERT: C 158 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7852 (mtm180) REVERT: E 108 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8672 (tt) REVERT: E 158 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7858 (mtm180) REVERT: F 66 LEU cc_start: 0.8791 (pp) cc_final: 0.8582 (tp) REVERT: G 108 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8666 (tt) REVERT: G 158 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7857 (mtm180) REVERT: H 66 LEU cc_start: 0.8801 (pp) cc_final: 0.8596 (tp) REVERT: H 106 ARG cc_start: 0.8621 (ttp80) cc_final: 0.8287 (ttp-110) outliers start: 24 outliers final: 12 residues processed: 248 average time/residue: 0.2370 time to fit residues: 84.3926 Evaluate side-chains 215 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 156 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 42 optimal weight: 10.0000 chunk 47 optimal weight: 0.0770 chunk 159 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.0570 chunk 48 optimal weight: 4.9990 chunk 110 optimal weight: 0.3980 chunk 129 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN A 105 GLN C 105 GLN D 105 GLN G 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.147877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119635 restraints weight = 26836.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122096 restraints weight = 16608.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123776 restraints weight = 11865.850| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12737 Z= 0.120 Angle : 0.761 10.712 17410 Z= 0.346 Chirality : 0.041 0.130 2088 Planarity : 0.005 0.048 2176 Dihedral : 11.275 106.027 2160 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 3.40 % Allowed : 27.02 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.22), residues: 1664 helix: -0.54 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -2.91 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 169 HIS 0.001 0.001 HIS E 222 PHE 0.025 0.001 PHE F 38 TYR 0.007 0.001 TYR F 35 ARG 0.005 0.000 ARG C 106 Details of bonding type rmsd hydrogen bonds : bond 0.02455 ( 520) hydrogen bonds : angle 3.86177 ( 1536) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.14456 ( 2) covalent geometry : bond 0.00260 (12736) covalent geometry : angle 0.76126 (17408) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 1.479 Fit side-chains REVERT: C 106 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7561 (ttp80) REVERT: F 34 MET cc_start: 0.5709 (tpt) cc_final: 0.4749 (ttm) outliers start: 37 outliers final: 8 residues processed: 248 average time/residue: 0.2455 time to fit residues: 89.1833 Evaluate side-chains 201 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 131 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 125 optimal weight: 0.0670 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.147524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119162 restraints weight = 26706.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121605 restraints weight = 16597.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122930 restraints weight = 11901.809| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12737 Z= 0.116 Angle : 0.727 10.656 17410 Z= 0.337 Chirality : 0.040 0.130 2088 Planarity : 0.005 0.045 2176 Dihedral : 10.770 106.648 2160 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 1.84 % Allowed : 27.94 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.22), residues: 1664 helix: -0.14 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.98 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 169 HIS 0.001 0.000 HIS A 222 PHE 0.015 0.001 PHE F 38 TYR 0.005 0.001 TYR F 165 ARG 0.002 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02323 ( 520) hydrogen bonds : angle 3.72322 ( 1536) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.20713 ( 2) covalent geometry : bond 0.00258 (12736) covalent geometry : angle 0.72671 (17408) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 1.103 Fit side-chains REVERT: A 108 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8528 (tt) REVERT: D 108 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8506 (tt) REVERT: F 34 MET cc_start: 0.5621 (tpt) cc_final: 0.4760 (ttm) REVERT: F 108 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8564 (tt) REVERT: H 108 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8523 (tt) outliers start: 20 outliers final: 12 residues processed: 223 average time/residue: 0.2212 time to fit residues: 75.2308 Evaluate side-chains 220 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 41 optimal weight: 0.0670 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 155 optimal weight: 0.0010 chunk 33 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.147091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122490 restraints weight = 25956.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124730 restraints weight = 15924.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125978 restraints weight = 11347.046| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12737 Z= 0.121 Angle : 0.728 11.014 17410 Z= 0.337 Chirality : 0.041 0.131 2088 Planarity : 0.005 0.042 2176 Dihedral : 10.726 107.417 2160 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 4.14 % Allowed : 26.10 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1664 helix: 0.15 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.86 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 169 HIS 0.001 0.000 HIS H 222 PHE 0.010 0.001 PHE D 38 TYR 0.022 0.001 TYR A 165 ARG 0.002 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02428 ( 520) hydrogen bonds : angle 3.76091 ( 1536) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.33368 ( 2) covalent geometry : bond 0.00284 (12736) covalent geometry : angle 0.72787 (17408) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.310 Fit side-chains REVERT: B 158 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7734 (mtm180) REVERT: B 198 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8422 (mp) REVERT: A 108 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8525 (tt) REVERT: C 71 MET cc_start: 0.8586 (mtt) cc_final: 0.8287 (tpp) REVERT: C 198 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8443 (mp) REVERT: D 108 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8515 (tt) REVERT: E 108 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8694 (tt) REVERT: E 198 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8437 (tt) REVERT: F 108 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8535 (tt) REVERT: G 108 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8685 (tt) REVERT: G 198 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8447 (mp) REVERT: H 108 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8524 (tt) outliers start: 45 outliers final: 11 residues processed: 242 average time/residue: 0.2312 time to fit residues: 84.7579 Evaluate side-chains 222 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 107 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 154 optimal weight: 0.0670 chunk 121 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 28 optimal weight: 0.0170 chunk 97 optimal weight: 7.9990 overall best weight: 2.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.144432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118852 restraints weight = 25713.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121081 restraints weight = 15991.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122420 restraints weight = 11490.736| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12737 Z= 0.170 Angle : 0.780 11.338 17410 Z= 0.367 Chirality : 0.043 0.129 2088 Planarity : 0.005 0.041 2176 Dihedral : 11.560 110.099 2160 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer: Outliers : 3.31 % Allowed : 25.46 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1664 helix: 0.19 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -2.90 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 169 HIS 0.002 0.001 HIS A 222 PHE 0.011 0.001 PHE C 209 TYR 0.010 0.002 TYR F 179 ARG 0.002 0.000 ARG C 178 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 520) hydrogen bonds : angle 4.11300 ( 1536) SS BOND : bond 0.00324 ( 1) SS BOND : angle 0.63788 ( 2) covalent geometry : bond 0.00409 (12736) covalent geometry : angle 0.77990 (17408) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 1.231 Fit side-chains REVERT: B 158 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7975 (mtm180) REVERT: A 108 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8527 (tt) REVERT: C 158 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7948 (mtm180) REVERT: D 108 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8542 (tt) REVERT: E 108 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8568 (tt) REVERT: E 158 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7956 (mtm180) REVERT: F 108 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8557 (tt) REVERT: G 108 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8556 (tt) REVERT: G 158 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7968 (mtm180) REVERT: H 108 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8546 (tt) outliers start: 36 outliers final: 17 residues processed: 237 average time/residue: 0.2982 time to fit residues: 110.7899 Evaluate side-chains 221 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 131 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 109 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN G 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.144768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119661 restraints weight = 25872.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121925 restraints weight = 15879.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123483 restraints weight = 11278.415| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12737 Z= 0.140 Angle : 0.762 11.282 17410 Z= 0.355 Chirality : 0.042 0.132 2088 Planarity : 0.005 0.040 2176 Dihedral : 11.452 109.122 2160 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 2.76 % Allowed : 28.03 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.23), residues: 1664 helix: 0.29 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -2.72 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 169 HIS 0.002 0.001 HIS H 222 PHE 0.009 0.001 PHE B 209 TYR 0.008 0.001 TYR H 179 ARG 0.001 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02629 ( 520) hydrogen bonds : angle 3.93756 ( 1536) SS BOND : bond 0.00243 ( 1) SS BOND : angle 0.44742 ( 2) covalent geometry : bond 0.00336 (12736) covalent geometry : angle 0.76230 (17408) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.540 Fit side-chains REVERT: B 158 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7907 (mtm180) REVERT: A 108 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8695 (tt) REVERT: C 158 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7822 (mtm180) REVERT: D 108 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8689 (tt) REVERT: E 108 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8616 (tt) REVERT: E 158 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7809 (mtm180) REVERT: F 108 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8706 (tt) REVERT: G 108 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8610 (tt) REVERT: G 158 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7813 (mtm180) REVERT: H 108 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8687 (tt) outliers start: 30 outliers final: 19 residues processed: 227 average time/residue: 0.2917 time to fit residues: 99.8950 Evaluate side-chains 223 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 131 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 7.9990 chunk 148 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.147713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123293 restraints weight = 25526.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125512 restraints weight = 15680.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.126928 restraints weight = 11182.727| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12737 Z= 0.117 Angle : 0.733 10.715 17410 Z= 0.341 Chirality : 0.040 0.129 2088 Planarity : 0.005 0.044 2176 Dihedral : 10.961 107.829 2160 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.21 % Allowed : 28.40 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1664 helix: 0.50 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -2.61 (0.28), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.001 0.001 HIS D 222 PHE 0.014 0.001 PHE H 38 TYR 0.005 0.001 TYR C 223 ARG 0.002 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02340 ( 520) hydrogen bonds : angle 3.68950 ( 1536) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.29997 ( 2) covalent geometry : bond 0.00265 (12736) covalent geometry : angle 0.73311 (17408) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 3.361 Fit side-chains REVERT: B 158 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7812 (mtm180) REVERT: A 108 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8687 (tt) REVERT: C 71 MET cc_start: 0.8560 (mmm) cc_final: 0.8335 (tpp) REVERT: C 158 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7757 (mtm180) REVERT: D 108 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8680 (tt) REVERT: E 108 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8617 (tt) REVERT: E 158 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7761 (mtm180) REVERT: F 108 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8685 (tt) REVERT: G 108 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8614 (tt) REVERT: G 158 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7771 (mtm180) REVERT: H 108 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8687 (tt) outliers start: 24 outliers final: 13 residues processed: 226 average time/residue: 0.2495 time to fit residues: 85.4466 Evaluate side-chains 226 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 0.0170 chunk 84 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 overall best weight: 1.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN G 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119388 restraints weight = 25334.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121427 restraints weight = 16648.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122683 restraints weight = 12404.270| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12737 Z= 0.133 Angle : 0.743 11.056 17410 Z= 0.346 Chirality : 0.041 0.130 2088 Planarity : 0.005 0.043 2176 Dihedral : 11.102 109.190 2160 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 1.84 % Allowed : 28.77 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1664 helix: 0.63 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -2.58 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 169 HIS 0.002 0.001 HIS D 222 PHE 0.016 0.001 PHE F 38 TYR 0.007 0.001 TYR D 179 ARG 0.001 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02533 ( 520) hydrogen bonds : angle 3.78786 ( 1536) SS BOND : bond 0.00226 ( 1) SS BOND : angle 0.47430 ( 2) covalent geometry : bond 0.00317 (12736) covalent geometry : angle 0.74271 (17408) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 1.351 Fit side-chains REVERT: B 158 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7881 (mtm180) REVERT: A 108 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8706 (tt) REVERT: C 71 MET cc_start: 0.8566 (mmm) cc_final: 0.8348 (mmm) REVERT: C 158 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7875 (mtm180) REVERT: D 108 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8694 (tt) REVERT: E 71 MET cc_start: 0.8622 (mmm) cc_final: 0.8401 (mmm) REVERT: E 108 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8645 (tt) REVERT: E 158 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7854 (mtm180) REVERT: F 108 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8707 (tt) REVERT: G 108 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8633 (tt) REVERT: G 158 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7852 (mtm180) REVERT: H 108 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8707 (tt) outliers start: 20 outliers final: 14 residues processed: 221 average time/residue: 0.2164 time to fit residues: 71.2762 Evaluate side-chains 225 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 101 optimal weight: 0.0370 chunk 111 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 114 optimal weight: 0.0570 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN G 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119077 restraints weight = 25456.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121092 restraints weight = 16453.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122390 restraints weight = 12245.342| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12737 Z= 0.138 Angle : 0.747 11.148 17410 Z= 0.347 Chirality : 0.041 0.129 2088 Planarity : 0.005 0.042 2176 Dihedral : 11.176 109.263 2160 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 2.21 % Allowed : 29.14 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1664 helix: 0.67 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -2.56 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 169 HIS 0.001 0.000 HIS A 222 PHE 0.016 0.001 PHE F 38 TYR 0.007 0.001 TYR F 179 ARG 0.001 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02542 ( 520) hydrogen bonds : angle 3.83800 ( 1536) SS BOND : bond 0.00241 ( 1) SS BOND : angle 0.44261 ( 2) covalent geometry : bond 0.00332 (12736) covalent geometry : angle 0.74677 (17408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4062.48 seconds wall clock time: 75 minutes 6.41 seconds (4506.41 seconds total)