Starting phenix.real_space_refine on Sun Nov 17 08:30:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/11_2024/8gmr_40231_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/11_2024/8gmr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/11_2024/8gmr_40231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/11_2024/8gmr_40231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/11_2024/8gmr_40231_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/11_2024/8gmr_40231_trim.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.010 sd= 0.445 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 96 5.16 5 C 8176 2.51 5 N 2048 2.21 5 O 2144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12472 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 4.66, per 1000 atoms: 0.37 Number of scatterers: 12472 At special positions: 0 Unit cell: (127.544, 127.544, 97.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 8 15.00 O 2144 8.00 N 2048 7.00 C 8176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 127 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.7 seconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 0 sheets defined 69.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'B' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.567A pdb=" N ALA B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 127' Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR B 131 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 133 " --> pdb=" O CYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 179 through 197 Processing helix chain 'B' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL B 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B 242 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE B 251 " --> pdb=" O GLN B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'A' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE A 56 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Proline residue: A 60 - end of helix Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.566A pdb=" N ALA A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 127' Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR A 131 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 133 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL A 201 " --> pdb=" O LEU A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE A 242 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 removed outlier: 3.639A pdb=" N PHE A 251 " --> pdb=" O GLN A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'C' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE C 56 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 57 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Proline residue: C 60 - end of helix Processing helix chain 'C' and resid 75 through 81 removed outlier: 3.567A pdb=" N ALA C 79 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 122 " --> pdb=" O THR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 127' Processing helix chain 'C' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR C 131 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL C 133 " --> pdb=" O CYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 179 through 197 Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL C 201 " --> pdb=" O LEU C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 242 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE C 251 " --> pdb=" O GLN C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 251' Processing helix chain 'D' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA D 37 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE D 56 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Proline residue: D 60 - end of helix Processing helix chain 'D' and resid 75 through 81 removed outlier: 3.568A pdb=" N ALA D 79 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU D 126 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 127' Processing helix chain 'D' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR D 131 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL D 133 " --> pdb=" O CYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 179 through 197 Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL D 201 " --> pdb=" O LEU D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 213 through 219 Processing helix chain 'D' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE D 251 " --> pdb=" O GLN D 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 248 through 251' Processing helix chain 'E' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA E 37 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE E 56 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Proline residue: E 60 - end of helix Processing helix chain 'E' and resid 75 through 81 removed outlier: 3.567A pdb=" N ALA E 79 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 100 through 107 Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU E 119 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU E 126 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 127' Processing helix chain 'E' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR E 131 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL E 133 " --> pdb=" O CYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 179 through 197 Processing helix chain 'E' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL E 201 " --> pdb=" O LEU E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 213 through 219 Processing helix chain 'E' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 241 " --> pdb=" O GLU E 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE E 242 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE E 251 " --> pdb=" O GLN E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 248 through 251' Processing helix chain 'F' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA F 37 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE F 56 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 57 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Proline residue: F 60 - end of helix Processing helix chain 'F' and resid 75 through 81 removed outlier: 3.567A pdb=" N ALA F 79 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 115 Processing helix chain 'F' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU F 126 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 122 through 127' Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR F 131 " --> pdb=" O ALA F 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL F 133 " --> pdb=" O CYS F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 179 through 197 Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL F 201 " --> pdb=" O LEU F 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 198 through 201' Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS F 240 " --> pdb=" O THR F 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE F 242 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 251 removed outlier: 3.639A pdb=" N PHE F 251 " --> pdb=" O GLN F 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 248 through 251' Processing helix chain 'G' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA G 37 " --> pdb=" O GLN G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE G 56 " --> pdb=" O TYR G 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 57 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Proline residue: G 60 - end of helix Processing helix chain 'G' and resid 75 through 81 removed outlier: 3.568A pdb=" N ALA G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 100 through 107 Processing helix chain 'G' and resid 109 through 115 Processing helix chain 'G' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU G 119 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU G 126 " --> pdb=" O GLY G 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 127' Processing helix chain 'G' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR G 131 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL G 133 " --> pdb=" O CYS G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 157 Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 179 through 197 Processing helix chain 'G' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 201' Processing helix chain 'G' and resid 213 through 219 Processing helix chain 'G' and resid 222 through 247 removed outlier: 4.003A pdb=" N GLU G 233 " --> pdb=" O LYS G 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS G 240 " --> pdb=" O THR G 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA G 241 " --> pdb=" O GLU G 237 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE G 242 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE G 251 " --> pdb=" O GLN G 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 248 through 251' Processing helix chain 'H' and resid 33 through 38 removed outlier: 4.248A pdb=" N ALA H 37 " --> pdb=" O GLN H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 69 removed outlier: 3.556A pdb=" N ILE H 56 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Proline residue: H 60 - end of helix Processing helix chain 'H' and resid 75 through 81 removed outlier: 3.568A pdb=" N ALA H 79 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 100 through 107 Processing helix chain 'H' and resid 109 through 115 Processing helix chain 'H' and resid 115 through 122 removed outlier: 3.927A pdb=" N LEU H 119 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 127 removed outlier: 3.580A pdb=" N LEU H 126 " --> pdb=" O GLY H 122 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS H 127 " --> pdb=" O LYS H 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 122 through 127' Processing helix chain 'H' and resid 128 through 133 removed outlier: 4.312A pdb=" N THR H 131 " --> pdb=" O ALA H 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL H 133 " --> pdb=" O CYS H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 157 Processing helix chain 'H' and resid 172 through 177 Processing helix chain 'H' and resid 179 through 197 Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.681A pdb=" N VAL H 201 " --> pdb=" O LEU H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 213 through 219 Processing helix chain 'H' and resid 222 through 247 removed outlier: 4.002A pdb=" N GLU H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 241 " --> pdb=" O GLU H 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE H 242 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS H 244 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 251 removed outlier: 3.638A pdb=" N PHE H 251 " --> pdb=" O GLN H 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 248 through 251' 520 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1904 1.31 - 1.44: 3312 1.44 - 1.56: 7376 1.56 - 1.69: 24 1.69 - 1.81: 120 Bond restraints: 12736 Sorted by residual: bond pdb=" C21 POV A 401 " pdb=" O21 POV A 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV H 401 " pdb=" O21 POV H 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV F 401 " pdb=" O21 POV F 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV B 401 " pdb=" O21 POV B 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C21 POV G 401 " pdb=" O21 POV G 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 12731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 17144 3.87 - 7.75: 208 7.75 - 11.62: 32 11.62 - 15.50: 16 15.50 - 19.37: 8 Bond angle restraints: 17408 Sorted by residual: angle pdb=" C13 POV H 401 " pdb=" N POV H 401 " pdb=" C14 POV H 401 " ideal model delta sigma weight residual 108.80 128.17 -19.37 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV A 401 " pdb=" N POV A 401 " pdb=" C14 POV A 401 " ideal model delta sigma weight residual 108.80 128.17 -19.37 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV D 401 " pdb=" N POV D 401 " pdb=" C14 POV D 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV E 401 " pdb=" N POV E 401 " pdb=" C14 POV E 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.16e+01 angle pdb=" C13 POV G 401 " pdb=" N POV G 401 " pdb=" C14 POV G 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.16e+01 ... (remaining 17403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 7049 22.84 - 45.68: 473 45.68 - 68.52: 81 68.52 - 91.36: 24 91.36 - 114.20: 8 Dihedral angle restraints: 7635 sinusoidal: 2595 harmonic: 5040 Sorted by residual: dihedral pdb=" CA VAL D 159 " pdb=" C VAL D 159 " pdb=" N PRO D 160 " pdb=" CA PRO D 160 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL E 159 " pdb=" C VAL E 159 " pdb=" N PRO E 160 " pdb=" CA PRO E 160 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL C 159 " pdb=" C VAL C 159 " pdb=" N PRO C 160 " pdb=" CA PRO C 160 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 7632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1265 0.034 - 0.068: 593 0.068 - 0.102: 175 0.102 - 0.136: 43 0.136 - 0.170: 12 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CB THR D 236 " pdb=" CA THR D 236 " pdb=" OG1 THR D 236 " pdb=" CG2 THR D 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CB THR C 236 " pdb=" CA THR C 236 " pdb=" OG1 THR C 236 " pdb=" CG2 THR C 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB THR E 236 " pdb=" CA THR E 236 " pdb=" OG1 THR E 236 " pdb=" CG2 THR E 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 2085 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 161 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO F 162 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO F 162 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 162 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS H 161 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO H 162 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO H 162 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 162 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 161 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO A 162 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " 0.032 5.00e-02 4.00e+02 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 15 2.24 - 2.90: 5066 2.90 - 3.57: 17275 3.57 - 4.23: 24176 4.23 - 4.90: 39367 Nonbonded interactions: 85899 Sorted by model distance: nonbonded pdb=" CB ASN F 255 " pdb=" CE2 TYR H 219 " model vdw 1.574 3.740 nonbonded pdb=" CB ASN E 255 " pdb=" CE2 TYR G 219 " model vdw 1.574 3.740 nonbonded pdb=" CB ASN D 255 " pdb=" CE2 TYR F 219 " model vdw 1.575 3.740 nonbonded pdb=" CB ASN B 255 " pdb=" CE2 TYR C 219 " model vdw 1.575 3.740 nonbonded pdb=" CB ASN C 255 " pdb=" CE2 TYR E 219 " model vdw 1.575 3.740 ... (remaining 85894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 25.520 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.530 ------------------------------------------------------------------------------- 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 12736 Z= 0.428 Angle : 1.181 19.371 17408 Z= 0.527 Chirality : 0.043 0.170 2088 Planarity : 0.006 0.058 2176 Dihedral : 17.020 114.197 4336 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.56 % Favored : 86.96 % Rotamer: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.54 (0.17), residues: 1664 helix: -3.40 (0.12), residues: 912 sheet: None (None), residues: 0 loop : -4.03 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 220 HIS 0.005 0.003 HIS D 222 PHE 0.008 0.001 PHE A 40 TYR 0.013 0.001 TYR H 219 ARG 0.002 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.276 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: 0.2826 time to fit residues: 87.8560 Evaluate side-chains 208 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12736 Z= 0.307 Angle : 0.853 11.103 17408 Z= 0.410 Chirality : 0.046 0.168 2088 Planarity : 0.006 0.045 2176 Dihedral : 13.652 110.504 2160 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 1.29 % Allowed : 18.75 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.20), residues: 1664 helix: -1.81 (0.15), residues: 1024 sheet: None (None), residues: 0 loop : -3.68 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 189 HIS 0.005 0.003 HIS E 222 PHE 0.016 0.002 PHE G 38 TYR 0.010 0.002 TYR D 219 ARG 0.002 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 1.336 Fit side-chains REVERT: B 158 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7888 (mtm180) REVERT: C 158 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7868 (mtm180) REVERT: E 108 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8550 (tt) REVERT: E 158 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7867 (mtm180) REVERT: G 108 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8561 (tt) REVERT: G 158 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7868 (mtm180) REVERT: H 106 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8438 (ttp80) outliers start: 14 outliers final: 4 residues processed: 218 average time/residue: 0.2568 time to fit residues: 81.1237 Evaluate side-chains 190 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 184 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.0030 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 122 optimal weight: 0.0060 overall best weight: 3.8010 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12736 Z= 0.343 Angle : 0.856 11.448 17408 Z= 0.410 Chirality : 0.045 0.132 2088 Planarity : 0.006 0.049 2176 Dihedral : 13.447 110.986 2160 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 2.39 % Allowed : 28.58 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.21), residues: 1664 helix: -1.33 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -3.60 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 189 HIS 0.001 0.001 HIS C 222 PHE 0.017 0.001 PHE C 209 TYR 0.014 0.002 TYR G 223 ARG 0.002 0.000 ARG G 178 *********************** 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 235 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.351 Fit side-chains REVERT: A 108 LEU cc_start: 0.9127 (tp) cc_final: 0.8925 (tt) REVERT: E 108 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8615 (tt) REVERT: G 108 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8611 (tt) REVERT: H 108 LEU cc_start: 0.9117 (tp) cc_final: 0.8917 (tt) outliers start: 26 outliers final: 15 residues processed: 231 average time/residue: 0.2440 time to fit residues: 81.7299 Evaluate side-chains 200 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 72 ASN Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 156 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12736 Z= 0.328 Angle : 0.837 11.571 17408 Z= 0.398 Chirality : 0.045 0.143 2088 Planarity : 0.006 0.049 2176 Dihedral : 13.216 111.880 2160 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 4.04 % Allowed : 28.12 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.21), residues: 1664 helix: -1.18 (0.16), residues: 1016 sheet: None (None), residues: 0 loop : -3.49 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 189 HIS 0.000 0.000 HIS D 222 PHE 0.024 0.002 PHE H 38 TYR 0.012 0.002 TYR H 223 ARG 0.002 0.000 ARG B 158 *********************** 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 245 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 1.422 Fit side-chains REVERT: A 108 LEU cc_start: 0.9132 (tp) cc_final: 0.8884 (tt) REVERT: E 108 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8593 (tt) REVERT: G 108 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8593 (tt) REVERT: H 108 LEU cc_start: 0.9125 (tp) cc_final: 0.8874 (tt) outliers start: 44 outliers final: 8 residues processed: 238 average time/residue: 0.2650 time to fit residues: 90.2668 Evaluate side-chains 198 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 156 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.0370 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12736 Z= 0.274 Angle : 0.814 11.344 17408 Z= 0.383 Chirality : 0.043 0.128 2088 Planarity : 0.006 0.052 2176 Dihedral : 12.918 111.252 2160 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 4.14 % Allowed : 28.49 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.21), residues: 1664 helix: -0.89 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -3.43 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 189 HIS 0.001 0.000 HIS A 222 PHE 0.015 0.001 PHE A 38 TYR 0.011 0.002 TYR H 223 ARG 0.003 0.000 ARG E 206 *********************** 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 249 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 1.321 Fit side-chains REVERT: B 108 LEU cc_start: 0.9096 (tp) cc_final: 0.8865 (tt) REVERT: A 108 LEU cc_start: 0.9128 (tp) cc_final: 0.8836 (tt) REVERT: A 119 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8742 (mm) REVERT: A 187 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8693 (tt) REVERT: C 108 LEU cc_start: 0.9082 (tp) cc_final: 0.8851 (tt) REVERT: D 108 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8740 (tt) REVERT: D 119 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8741 (mm) REVERT: D 187 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8688 (tt) REVERT: E 108 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8545 (tt) REVERT: F 108 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8760 (tt) REVERT: F 119 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8741 (mm) REVERT: F 187 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8692 (tt) REVERT: G 108 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8548 (tt) REVERT: H 71 MET cc_start: 0.8768 (mtt) cc_final: 0.8518 (mmm) REVERT: H 108 LEU cc_start: 0.9109 (tp) cc_final: 0.8839 (tt) REVERT: H 119 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8747 (mm) REVERT: H 187 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8690 (tt) outliers start: 45 outliers final: 24 residues processed: 245 average time/residue: 0.2107 time to fit residues: 77.6047 Evaluate side-chains 212 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 161 CYS Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 161 CYS Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 206 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.3980 chunk 146 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 0.0870 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12736 Z= 0.181 Angle : 0.775 10.960 17408 Z= 0.352 Chirality : 0.041 0.149 2088 Planarity : 0.005 0.053 2176 Dihedral : 11.812 107.672 2160 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 2.02 % Allowed : 31.99 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.22), residues: 1664 helix: -0.45 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -3.11 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.000 0.000 HIS B 222 PHE 0.010 0.001 PHE C 214 TYR 0.005 0.001 TYR C 219 ARG 0.001 0.000 ARG C 154 *********************** 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 235 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 1.390 Fit side-chains REVERT: A 108 LEU cc_start: 0.9072 (tp) cc_final: 0.8760 (tt) REVERT: D 108 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8716 (tt) REVERT: F 108 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8740 (tt) REVERT: H 108 LEU cc_start: 0.9058 (tp) cc_final: 0.8780 (tt) outliers start: 22 outliers final: 17 residues processed: 231 average time/residue: 0.2084 time to fit residues: 72.4942 Evaluate side-chains 215 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 206 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 92 optimal weight: 0.0670 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12736 Z= 0.195 Angle : 0.764 10.985 17408 Z= 0.355 Chirality : 0.041 0.146 2088 Planarity : 0.005 0.053 2176 Dihedral : 11.616 109.034 2160 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 3.86 % Allowed : 30.15 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.22), residues: 1664 helix: -0.15 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -2.94 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 169 HIS 0.000 0.000 HIS B 222 PHE 0.014 0.001 PHE G 38 TYR 0.006 0.001 TYR A 223 ARG 0.001 0.000 ARG E 154 *********************** 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 244 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 1.211 Fit side-chains REVERT: A 108 LEU cc_start: 0.9067 (tp) cc_final: 0.8761 (tt) REVERT: A 187 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8657 (tt) REVERT: D 108 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8717 (tt) REVERT: D 187 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8665 (tt) REVERT: F 108 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8730 (tt) REVERT: F 187 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8669 (tt) REVERT: H 108 LEU cc_start: 0.9039 (tp) cc_final: 0.8740 (tt) REVERT: H 187 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8667 (tt) outliers start: 42 outliers final: 28 residues processed: 240 average time/residue: 0.2028 time to fit residues: 73.3755 Evaluate side-chains 234 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 206 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 147 optimal weight: 0.0770 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 0.035 12736 Z= 0.181 Angle : 0.763 11.328 17408 Z= 0.353 Chirality : 0.041 0.143 2088 Planarity : 0.005 0.050 2176 Dihedral : 11.096 107.733 2160 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 4.41 % Allowed : 32.17 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1664 helix: 0.25 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -2.76 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 169 HIS 0.004 0.002 HIS E 222 PHE 0.010 0.001 PHE C 38 TYR 0.005 0.001 TYR F 223 ARG 0.001 0.000 ARG B 158 *********************** 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 254 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 1.339 Fit side-chains REVERT: B 187 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8420 (tt) REVERT: A 108 LEU cc_start: 0.9029 (tp) cc_final: 0.8715 (tt) REVERT: A 187 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8630 (tt) REVERT: C 187 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8428 (tt) REVERT: D 108 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8698 (tt) REVERT: D 187 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8633 (tt) REVERT: E 187 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8426 (tt) REVERT: F 108 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8709 (tt) REVERT: F 187 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8638 (tt) REVERT: G 187 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8429 (tt) REVERT: H 108 LEU cc_start: 0.9010 (tp) cc_final: 0.8719 (tt) REVERT: H 187 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8637 (tt) outliers start: 48 outliers final: 20 residues processed: 249 average time/residue: 0.2226 time to fit residues: 84.4716 Evaluate side-chains 237 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 206 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 118 optimal weight: 7.9990 chunk 46 optimal weight: 0.0010 chunk 136 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12736 Z= 0.182 Angle : 0.744 11.232 17408 Z= 0.349 Chirality : 0.041 0.155 2088 Planarity : 0.005 0.051 2176 Dihedral : 10.730 107.961 2160 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 2.48 % Allowed : 33.09 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.23), residues: 1664 helix: 0.59 (0.18), residues: 1016 sheet: None (None), residues: 0 loop : -2.68 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 169 HIS 0.001 0.001 HIS E 222 PHE 0.010 0.001 PHE C 38 TYR 0.004 0.001 TYR F 165 ARG 0.002 0.000 ARG E 158 *********************** 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 243 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 1.437 Fit side-chains REVERT: B 71 MET cc_start: 0.8567 (mmm) cc_final: 0.8339 (mmm) REVERT: B 187 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8441 (tt) REVERT: A 71 MET cc_start: 0.8654 (mmm) cc_final: 0.8405 (tpp) REVERT: A 108 LEU cc_start: 0.9006 (tp) cc_final: 0.8720 (tt) REVERT: A 187 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8674 (tt) REVERT: C 71 MET cc_start: 0.8554 (mmm) cc_final: 0.8339 (mmm) REVERT: C 187 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8438 (tt) REVERT: D 71 MET cc_start: 0.8656 (mmm) cc_final: 0.8407 (tpp) REVERT: D 108 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8693 (tt) REVERT: E 71 MET cc_start: 0.8533 (mmm) cc_final: 0.8312 (mmm) REVERT: E 187 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8440 (tt) REVERT: F 108 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8691 (tt) REVERT: G 71 MET cc_start: 0.8535 (mmm) cc_final: 0.8317 (mmm) REVERT: G 187 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8443 (tt) REVERT: H 108 LEU cc_start: 0.9002 (tp) cc_final: 0.8707 (tt) outliers start: 27 outliers final: 18 residues processed: 242 average time/residue: 0.2088 time to fit residues: 75.8921 Evaluate side-chains 241 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 206 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.0980 chunk 75 optimal weight: 0.0060 chunk 110 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 154 optimal weight: 0.0070 chunk 133 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12736 Z= 0.178 Angle : 0.752 11.151 17408 Z= 0.350 Chirality : 0.041 0.141 2088 Planarity : 0.005 0.047 2176 Dihedral : 10.350 107.130 2160 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.67 % Allowed : 34.01 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1664 helix: 0.77 (0.18), residues: 1016 sheet: None (None), residues: 0 loop : -2.51 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.001 0.000 HIS B 222 PHE 0.009 0.001 PHE C 38 TYR 0.018 0.001 TYR A 165 ARG 0.001 0.000 ARG B 158 ********************** 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 259 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 1.423 Fit side-chains REVERT: B 71 MET cc_start: 0.8557 (mmm) cc_final: 0.8343 (tpp) REVERT: B 187 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8396 (tt) REVERT: A 71 MET cc_start: 0.8626 (mmm) cc_final: 0.8409 (tpp) REVERT: A 108 LEU cc_start: 0.8947 (tp) cc_final: 0.8667 (tt) REVERT: A 187 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8616 (tt) REVERT: C 42 CYS cc_start: 0.7791 (t) cc_final: 0.7511 (p) REVERT: C 71 MET cc_start: 0.8550 (mmm) cc_final: 0.8338 (tpp) REVERT: C 187 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8404 (tt) REVERT: D 71 MET cc_start: 0.8634 (mmm) cc_final: 0.8416 (tpp) REVERT: D 108 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8675 (tt) REVERT: D 187 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8642 (tt) REVERT: E 42 CYS cc_start: 0.7823 (t) cc_final: 0.7507 (p) REVERT: E 71 MET cc_start: 0.8509 (mmm) cc_final: 0.8297 (tpp) REVERT: E 187 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8399 (tt) REVERT: F 71 MET cc_start: 0.8633 (mmm) cc_final: 0.8422 (tpp) REVERT: F 108 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8684 (tt) REVERT: F 187 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8641 (tt) REVERT: G 42 CYS cc_start: 0.7838 (t) cc_final: 0.7514 (p) REVERT: G 71 MET cc_start: 0.8509 (mmm) cc_final: 0.8299 (tpp) REVERT: G 187 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8419 (tt) REVERT: H 108 LEU cc_start: 0.8920 (tp) cc_final: 0.8655 (tt) REVERT: H 187 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8634 (tt) outliers start: 29 outliers final: 18 residues processed: 258 average time/residue: 0.2075 time to fit residues: 80.3941 Evaluate side-chains 248 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 206 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.146994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118464 restraints weight = 26440.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120825 restraints weight = 16587.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122449 restraints weight = 11964.556| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12736 Z= 0.194 Angle : 0.741 11.288 17408 Z= 0.348 Chirality : 0.041 0.137 2088 Planarity : 0.005 0.052 2176 Dihedral : 10.504 108.304 2160 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 2.85 % Allowed : 34.47 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1664 helix: 0.85 (0.18), residues: 1016 sheet: None (None), residues: 0 loop : -2.49 (0.28), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 169 HIS 0.001 0.000 HIS G 222 PHE 0.009 0.001 PHE C 38 TYR 0.025 0.001 TYR F 165 ARG 0.002 0.000 ARG E 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2426.56 seconds wall clock time: 45 minutes 0.00 seconds (2700.00 seconds total)