Starting phenix.real_space_refine on Sat Aug 23 16:26:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmr_40231/08_2025/8gmr_40231_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmr_40231/08_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_40231/08_2025/8gmr_40231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmr_40231/08_2025/8gmr_40231.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmr_40231/08_2025/8gmr_40231_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmr_40231/08_2025/8gmr_40231_trim.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.010 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12472 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" 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: {'ASN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 6, 'TRP:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 108 Chain: "B" 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: A, C, D, E, F, G, H Time building chain proxies: 1.61, per 1000 atoms: 0.13 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=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 127 " distance=2.03 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 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: 1.11 Conformation dependent library (CDL) restraints added in 546.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.39 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: 1.71 Time building geometry restraints manager: 1.36 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: 7056 22.84 - 45.68: 487 45.68 - 68.52: 81 68.52 - 91.36: 24 91.36 - 114.20: 8 Dihedral angle restraints: 7656 sinusoidal: 2616 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 7653 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: 8 2.24 - 2.90: 5066 2.90 - 3.57: 17261 3.57 - 4.23: 24176 4.23 - 4.90: 39367 Nonbonded interactions: 85878 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 85873 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: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- 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 12744 Z= 0.310 Angle : 1.181 19.371 17424 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG H 106 TYR 0.013 0.001 TYR H 219 PHE 0.008 0.001 PHE A 40 TRP 0.008 0.001 TRP F 220 HIS 0.005 0.003 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00647 (12736) covalent geometry : angle 1.18117 (17408) SS BOND : bond 0.00113 ( 8) SS BOND : angle 0.97721 ( 16) hydrogen bonds : bond 0.33712 ( 520) hydrogen bonds : angle 10.51303 ( 1536) *********************** 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 : 0.373 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: 0.1071 time to fit residues: 33.3277 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 : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.142374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113833 restraints weight = 26455.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116079 restraints weight = 16424.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117551 restraints weight = 11862.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118651 restraints weight = 9573.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119368 restraints weight = 8272.839| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12744 Z= 0.167 Angle : 0.824 10.821 17424 Z= 0.395 Chirality : 0.045 0.169 2088 Planarity : 0.006 0.044 2176 Dihedral : 13.326 109.505 2160 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 1.29 % Allowed : 18.57 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.70 (0.20), residues: 1664 helix: -1.72 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -3.63 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 106 TYR 0.008 0.002 TYR D 179 PHE 0.015 0.001 PHE G 38 TRP 0.010 0.001 TRP B 189 HIS 0.005 0.003 HIS E 222 Details of bonding type rmsd covalent geometry : bond 0.00398 (12736) covalent geometry : angle 0.82392 (17408) SS BOND : bond 0.00259 ( 8) SS BOND : angle 0.64806 ( 16) hydrogen bonds : bond 0.04366 ( 520) hydrogen bonds : angle 5.53641 ( 1536) *********************** 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 228 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 0.353 Fit side-chains REVERT: B 158 ARG cc_start: 0.8262 (mtt180) cc_final: 0.7940 (mtm180) REVERT: C 158 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7937 (mtm180) REVERT: E 108 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8587 (tt) REVERT: E 158 ARG cc_start: 0.8262 (mtt180) cc_final: 0.7946 (mtm180) REVERT: G 108 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8585 (tt) REVERT: G 158 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7941 (mtm180) REVERT: H 106 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8404 (ttp80) outliers start: 14 outliers final: 4 residues processed: 216 average time/residue: 0.0997 time to fit residues: 30.8953 Evaluate side-chains 194 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 96 optimal weight: 3.9990 chunk 164 optimal weight: 0.0070 chunk 120 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 121 optimal weight: 0.0270 chunk 105 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- 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 E 105 GLN F 105 GLN G 105 GLN H 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116914 restraints weight = 26804.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119289 restraints weight = 16618.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120853 restraints weight = 11973.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122046 restraints weight = 9643.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122578 restraints weight = 8297.363| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12744 Z= 0.124 Angle : 0.755 10.380 17424 Z= 0.352 Chirality : 0.041 0.129 2088 Planarity : 0.005 0.045 2176 Dihedral : 11.992 106.897 2160 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 2.21 % Allowed : 25.46 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.21), residues: 1664 helix: -0.96 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -3.14 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 106 TYR 0.008 0.001 TYR G 223 PHE 0.017 0.001 PHE F 214 TRP 0.010 0.001 TRP D 169 HIS 0.002 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00284 (12736) covalent geometry : angle 0.75504 (17408) SS BOND : bond 0.00175 ( 8) SS BOND : angle 0.36529 ( 16) hydrogen bonds : bond 0.03002 ( 520) hydrogen bonds : angle 4.41932 ( 1536) *********************** 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 244 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.421 Fit side-chains REVERT: B 158 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7689 (mtm180) REVERT: A 108 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8575 (tt) REVERT: C 158 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7691 (mtm180) REVERT: D 108 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8580 (tt) REVERT: E 108 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8686 (tt) REVERT: E 158 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7690 (mtm180) REVERT: F 108 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8563 (tt) REVERT: G 108 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8686 (tt) REVERT: G 158 ARG cc_start: 0.8065 (mtt180) cc_final: 0.7689 (mtm180) REVERT: H 106 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8114 (ttp-110) REVERT: H 108 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8575 (tt) outliers start: 24 outliers final: 12 residues processed: 236 average time/residue: 0.1033 time to fit residues: 34.9980 Evaluate side-chains 214 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 108 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 108 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 108 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 76 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN C 72 ASN E 72 ASN G 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111644 restraints weight = 26788.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113937 restraints weight = 16604.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115397 restraints weight = 11972.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116544 restraints weight = 9685.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117279 restraints weight = 8362.325| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12744 Z= 0.222 Angle : 0.866 12.036 17424 Z= 0.404 Chirality : 0.045 0.154 2088 Planarity : 0.006 0.045 2176 Dihedral : 12.721 111.637 2160 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 4.60 % Allowed : 27.11 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.21), residues: 1664 helix: -0.97 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -3.24 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 178 TYR 0.013 0.002 TYR H 223 PHE 0.023 0.002 PHE F 38 TRP 0.007 0.001 TRP C 189 HIS 0.001 0.000 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00533 (12736) covalent geometry : angle 0.86627 (17408) SS BOND : bond 0.00406 ( 8) SS BOND : angle 0.76022 ( 16) hydrogen bonds : bond 0.03582 ( 520) hydrogen bonds : angle 4.69849 ( 1536) *********************** 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 230 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.458 Fit side-chains REVERT: B 158 ARG cc_start: 0.8337 (mtt180) cc_final: 0.8063 (mtm180) REVERT: C 158 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8061 (mtm180) REVERT: E 108 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8598 (tt) REVERT: E 158 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8064 (mtm180) REVERT: G 108 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8595 (tt) REVERT: G 158 ARG cc_start: 0.8329 (mtt180) cc_final: 0.8061 (mtm180) outliers start: 50 outliers final: 17 residues processed: 220 average time/residue: 0.1060 time to fit residues: 33.2835 Evaluate side-chains 190 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 ASN 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 131 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 72 ASN 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 72 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 159 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 104 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.143232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114718 restraints weight = 26959.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117036 restraints weight = 16672.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118673 restraints weight = 11991.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119489 restraints weight = 9583.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120054 restraints weight = 8421.340| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12744 Z= 0.136 Angle : 0.781 11.094 17424 Z= 0.365 Chirality : 0.042 0.142 2088 Planarity : 0.005 0.047 2176 Dihedral : 12.098 109.126 2160 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 2.48 % Allowed : 27.21 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.22), residues: 1664 helix: -0.63 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -3.14 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 206 TYR 0.009 0.001 TYR D 223 PHE 0.016 0.001 PHE H 38 TRP 0.005 0.001 TRP H 169 HIS 0.001 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00324 (12736) covalent geometry : angle 0.78138 (17408) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.55141 ( 16) hydrogen bonds : bond 0.02881 ( 520) hydrogen bonds : angle 4.26043 ( 1536) *********************** 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 229 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.345 Fit side-chains REVERT: B 158 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7941 (mtm180) REVERT: C 158 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7941 (mtm180) REVERT: E 108 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8691 (tt) REVERT: E 158 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7942 (mtm180) REVERT: G 108 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8657 (tt) REVERT: G 158 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7946 (mtm180) outliers start: 27 outliers final: 12 residues processed: 221 average time/residue: 0.0805 time to fit residues: 26.8023 Evaluate side-chains 188 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 56 ILE 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 56 ILE 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 56 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN A 72 ASN C 72 ASN D 72 ASN E 72 ASN F 72 ASN G 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110682 restraints weight = 26801.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112909 restraints weight = 16648.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114470 restraints weight = 12061.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115221 restraints weight = 9708.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115982 restraints weight = 8585.095| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12744 Z= 0.241 Angle : 0.889 12.123 17424 Z= 0.421 Chirality : 0.046 0.162 2088 Planarity : 0.006 0.047 2176 Dihedral : 13.462 113.183 2160 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 3.58 % Allowed : 28.31 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.21), residues: 1664 helix: -0.79 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -3.36 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.015 0.003 TYR H 223 PHE 0.017 0.002 PHE F 209 TRP 0.010 0.002 TRP G 169 HIS 0.001 0.000 HIS F 222 Details of bonding type rmsd covalent geometry : bond 0.00581 (12736) covalent geometry : angle 0.88875 (17408) SS BOND : bond 0.00471 ( 8) SS BOND : angle 0.93765 ( 16) hydrogen bonds : bond 0.03645 ( 520) hydrogen bonds : angle 4.72514 ( 1536) *********************** 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 205 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.310 Fit side-chains REVERT: E 108 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8543 (tt) REVERT: G 108 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8539 (tt) outliers start: 39 outliers final: 20 residues processed: 195 average time/residue: 0.0921 time to fit residues: 26.4289 Evaluate side-chains 176 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain A residue 72 ASN 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 72 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 156 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 156 LEU Chi-restraints excluded: chain H residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 91 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.144214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115997 restraints weight = 26607.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118356 restraints weight = 16487.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119931 restraints weight = 11792.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120996 restraints weight = 9481.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121702 restraints weight = 8155.122| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12744 Z= 0.125 Angle : 0.794 10.830 17424 Z= 0.367 Chirality : 0.042 0.145 2088 Planarity : 0.005 0.050 2176 Dihedral : 12.472 109.109 2160 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 2.30 % Allowed : 29.96 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.22), residues: 1664 helix: -0.45 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -3.07 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 106 TYR 0.007 0.001 TYR H 223 PHE 0.010 0.001 PHE H 214 TRP 0.014 0.001 TRP D 169 HIS 0.001 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00287 (12736) covalent geometry : angle 0.79448 (17408) SS BOND : bond 0.00184 ( 8) SS BOND : angle 0.47103 ( 16) hydrogen bonds : bond 0.02654 ( 520) hydrogen bonds : angle 4.06693 ( 1536) *********************** 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 199 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.462 Fit side-chains REVERT: A 187 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8689 (tt) REVERT: D 187 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8689 (tt) REVERT: E 108 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8662 (tt) REVERT: F 187 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8681 (tt) REVERT: G 108 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8660 (tt) REVERT: H 187 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8676 (tt) outliers start: 25 outliers final: 8 residues processed: 195 average time/residue: 0.0898 time to fit residues: 26.8601 Evaluate side-chains 182 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 187 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 187 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 187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 41 optimal weight: 30.0000 chunk 154 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN A 72 ASN C 72 ASN D 72 ASN E 72 ASN F 72 ASN G 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115272 restraints weight = 26670.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117595 restraints weight = 16559.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119135 restraints weight = 11936.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120309 restraints weight = 9588.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120896 restraints weight = 8226.000| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12744 Z= 0.135 Angle : 0.797 11.427 17424 Z= 0.367 Chirality : 0.042 0.147 2088 Planarity : 0.005 0.051 2176 Dihedral : 12.326 110.336 2160 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 2.76 % Allowed : 31.25 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.22), residues: 1664 helix: -0.22 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -2.76 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 106 TYR 0.008 0.001 TYR H 223 PHE 0.008 0.001 PHE D 209 TRP 0.011 0.001 TRP F 169 HIS 0.001 0.000 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00324 (12736) covalent geometry : angle 0.79691 (17408) SS BOND : bond 0.00236 ( 8) SS BOND : angle 0.52828 ( 16) hydrogen bonds : bond 0.02704 ( 520) hydrogen bonds : angle 4.05095 ( 1536) *********************** 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 197 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.317 Fit side-chains REVERT: B 108 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8668 (tt) REVERT: A 187 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8729 (tt) REVERT: D 187 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8729 (tt) REVERT: F 187 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8736 (tt) REVERT: H 187 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8740 (tt) outliers start: 30 outliers final: 23 residues processed: 193 average time/residue: 0.0862 time to fit residues: 25.1840 Evaluate side-chains 188 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 187 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 C residue 177 VAL Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 187 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 57 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 125 optimal weight: 30.0000 chunk 101 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN A 72 ASN C 72 ASN D 72 ASN E 72 ASN F 72 ASN G 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.143241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114956 restraints weight = 26841.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117307 restraints weight = 16592.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118817 restraints weight = 11896.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119944 restraints weight = 9561.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120332 restraints weight = 8237.191| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12744 Z= 0.151 Angle : 0.807 11.183 17424 Z= 0.372 Chirality : 0.043 0.141 2088 Planarity : 0.005 0.050 2176 Dihedral : 12.415 110.423 2160 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 3.22 % Allowed : 31.07 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.22), residues: 1664 helix: -0.20 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 106 TYR 0.008 0.001 TYR D 223 PHE 0.010 0.001 PHE B 209 TRP 0.011 0.001 TRP F 169 HIS 0.000 0.000 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00366 (12736) covalent geometry : angle 0.80756 (17408) SS BOND : bond 0.00268 ( 8) SS BOND : angle 0.55516 ( 16) hydrogen bonds : bond 0.02789 ( 520) hydrogen bonds : angle 4.11297 ( 1536) *********************** 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 200 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.361 Fit side-chains REVERT: B 108 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8674 (tt) REVERT: A 187 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8749 (tt) REVERT: D 187 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8750 (tt) REVERT: F 187 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8757 (tt) REVERT: H 187 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8753 (tt) outliers start: 35 outliers final: 28 residues processed: 196 average time/residue: 0.0844 time to fit residues: 25.4422 Evaluate side-chains 194 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 56 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 72 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN A 72 ASN C 72 ASN D 72 ASN E 72 ASN F 72 ASN G 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114225 restraints weight = 26762.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116506 restraints weight = 16565.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118095 restraints weight = 11926.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118980 restraints weight = 9531.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119755 restraints weight = 8306.486| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12744 Z= 0.173 Angle : 0.826 11.364 17424 Z= 0.382 Chirality : 0.043 0.137 2088 Planarity : 0.005 0.047 2176 Dihedral : 12.639 111.070 2160 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 3.49 % Allowed : 31.07 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.22), residues: 1664 helix: -0.16 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -2.83 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 158 TYR 0.010 0.002 TYR H 179 PHE 0.011 0.001 PHE B 209 TRP 0.008 0.001 TRP F 169 HIS 0.001 0.000 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00419 (12736) covalent geometry : angle 0.82609 (17408) SS BOND : bond 0.00328 ( 8) SS BOND : angle 0.65150 ( 16) hydrogen bonds : bond 0.02981 ( 520) hydrogen bonds : angle 4.21970 ( 1536) ********************** 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 202 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.288 Fit side-chains REVERT: B 108 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8682 (tt) REVERT: A 187 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8765 (tt) REVERT: D 187 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8758 (tt) REVERT: F 187 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8769 (tt) REVERT: H 187 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8768 (tt) outliers start: 38 outliers final: 25 residues processed: 198 average time/residue: 0.0849 time to fit residues: 25.3507 Evaluate side-chains 193 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 91 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 148 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 0.0570 chunk 132 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 112 optimal weight: 0.0870 chunk 4 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.147066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119239 restraints weight = 26368.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121560 restraints weight = 16492.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123240 restraints weight = 11911.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124091 restraints weight = 9498.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124663 restraints weight = 8293.514| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12744 Z= 0.124 Angle : 0.785 10.826 17424 Z= 0.357 Chirality : 0.041 0.144 2088 Planarity : 0.005 0.050 2176 Dihedral : 11.800 108.604 2160 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.21 % Allowed : 31.43 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.23), residues: 1664 helix: 0.15 (0.18), residues: 1016 sheet: None (None), residues: 0 loop : -2.53 (0.28), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 154 TYR 0.004 0.001 TYR A 165 PHE 0.006 0.001 PHE C 191 TRP 0.019 0.001 TRP H 169 HIS 0.001 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00275 (12736) covalent geometry : angle 0.78546 (17408) SS BOND : bond 0.00069 ( 8) SS BOND : angle 0.26923 ( 16) hydrogen bonds : bond 0.02367 ( 520) hydrogen bonds : angle 3.79173 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.46 seconds wall clock time: 29 minutes 3.02 seconds (1743.02 seconds total)