Starting phenix.real_space_refine on Wed Mar 4 15:52:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tcp_25816/03_2026/7tcp_25816.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tcp_25816/03_2026/7tcp_25816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tcp_25816/03_2026/7tcp_25816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tcp_25816/03_2026/7tcp_25816.map" model { file = "/net/cci-nas-00/data/ceres_data/7tcp_25816/03_2026/7tcp_25816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tcp_25816/03_2026/7tcp_25816.cif" } resolution = 3.84 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= 0.008 sd= 0.017 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 Ca 12 9.91 5 S 68 5.16 5 C 9724 2.51 5 N 2572 2.21 5 O 2616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14992 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2711 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1034 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: E, G, C, F, H, D Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA F 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 residue: pdb="CA CA D 202 " occ=0.83 Time building chain proxies: 2.37, per 1000 atoms: 0.16 Number of scatterers: 14992 At special positions: 0 Unit cell: (102.93, 102.93, 122.64, 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) Ca 12 19.99 S 68 16.00 O 2616 8.00 N 2572 7.00 C 9724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 567.3 milliseconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 81.0% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 110 through 135 removed outlier: 3.763A pdb=" N ILE A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 168 removed outlier: 4.216A pdb=" N THR A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.688A pdb=" N ARG A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.561A pdb=" N ASP A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG A 233 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 234' Processing helix chain 'A' and resid 235 through 248 removed outlier: 3.836A pdb=" N LEU A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.583A pdb=" N ILE A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 274 removed outlier: 4.117A pdb=" N PHE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.793A pdb=" N VAL A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 325 " --> pdb=" O CYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 349 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 353 through 356 Processing helix chain 'A' and resid 357 through 375 removed outlier: 3.777A pdb=" N GLU A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 523 removed outlier: 3.796A pdb=" N ALA A 502 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 556 Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.662A pdb=" N GLU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 66 through 75 removed outlier: 3.605A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.801A pdb=" N GLU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 110 through 135 removed outlier: 3.764A pdb=" N ILE E 135 " --> pdb=" O VAL E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 168 removed outlier: 4.218A pdb=" N THR E 143 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 175 through 185 removed outlier: 3.756A pdb=" N ARG E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 205 Processing helix chain 'E' and resid 219 through 228 Processing helix chain 'E' and resid 229 through 234 removed outlier: 3.562A pdb=" N ASP E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG E 233 " --> pdb=" O HIS E 230 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN E 234 " --> pdb=" O VAL E 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 229 through 234' Processing helix chain 'E' and resid 235 through 248 removed outlier: 3.837A pdb=" N LEU E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.553A pdb=" N ILE E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 274 removed outlier: 4.123A pdb=" N PHE E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 300 Processing helix chain 'E' and resid 312 through 327 removed outlier: 3.795A pdb=" N VAL E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE E 325 " --> pdb=" O CYS E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 349 Proline residue: E 333 - end of helix Processing helix chain 'E' and resid 353 through 356 Processing helix chain 'E' and resid 357 through 375 removed outlier: 3.778A pdb=" N GLU E 375 " --> pdb=" O CYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 523 removed outlier: 3.796A pdb=" N ALA E 502 " --> pdb=" O HIS E 498 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL E 505 " --> pdb=" O ALA E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 556 Processing helix chain 'F' and resid 11 through 22 removed outlier: 3.657A pdb=" N GLU F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.606A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 94 removed outlier: 3.801A pdb=" N GLU F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 110 through 135 removed outlier: 3.763A pdb=" N ILE G 135 " --> pdb=" O VAL G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 168 removed outlier: 4.218A pdb=" N THR G 143 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 175 through 185 removed outlier: 3.737A pdb=" N ARG G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 205 Processing helix chain 'G' and resid 219 through 228 Processing helix chain 'G' and resid 229 through 234 removed outlier: 3.561A pdb=" N ASP G 232 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG G 233 " --> pdb=" O HIS G 230 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN G 234 " --> pdb=" O VAL G 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 234' Processing helix chain 'G' and resid 235 through 248 removed outlier: 3.837A pdb=" N LEU G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.579A pdb=" N ILE G 253 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 274 removed outlier: 4.121A pdb=" N PHE G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 300 Processing helix chain 'G' and resid 312 through 327 removed outlier: 3.793A pdb=" N VAL G 324 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE G 325 " --> pdb=" O CYS G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 349 Proline residue: G 333 - end of helix Processing helix chain 'G' and resid 353 through 356 Processing helix chain 'G' and resid 357 through 375 removed outlier: 3.779A pdb=" N GLU G 375 " --> pdb=" O CYS G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 523 removed outlier: 3.800A pdb=" N ALA G 502 " --> pdb=" O HIS G 498 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL G 505 " --> pdb=" O ALA G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 556 Processing helix chain 'H' and resid 11 through 22 removed outlier: 3.659A pdb=" N GLU H 15 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.603A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 94 removed outlier: 3.806A pdb=" N GLU H 85 " --> pdb=" O ASP H 81 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 139 through 146 Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 110 through 135 removed outlier: 3.764A pdb=" N ILE C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 168 removed outlier: 4.216A pdb=" N THR C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.688A pdb=" N ARG C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 205 Processing helix chain 'C' and resid 219 through 228 Processing helix chain 'C' and resid 229 through 234 removed outlier: 3.562A pdb=" N ASP C 232 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG C 233 " --> pdb=" O HIS C 230 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN C 234 " --> pdb=" O VAL C 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 234' Processing helix chain 'C' and resid 235 through 248 removed outlier: 3.836A pdb=" N LEU C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.553A pdb=" N ILE C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 274 removed outlier: 4.119A pdb=" N PHE C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 300 Processing helix chain 'C' and resid 312 through 327 removed outlier: 3.796A pdb=" N VAL C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE C 325 " --> pdb=" O CYS C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 349 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 353 through 356 Processing helix chain 'C' and resid 357 through 375 removed outlier: 3.778A pdb=" N GLU C 375 " --> pdb=" O CYS C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 523 removed outlier: 3.796A pdb=" N ALA C 502 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 556 Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.659A pdb=" N GLU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.605A pdb=" N ARG D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 94 removed outlier: 3.801A pdb=" N GLU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 139 through 146 Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.502A pdb=" N ILE B 64 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 27 through 28 removed outlier: 3.500A pdb=" N ILE F 64 " --> pdb=" O ILE F 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'H' and resid 27 through 28 removed outlier: 3.502A pdb=" N ILE H 64 " --> pdb=" O ILE H 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'D' and resid 100 through 102 1066 hydrogen bonds defined for protein. 3183 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: 2.36 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4804 1.34 - 1.46: 3672 1.46 - 1.58: 6712 1.58 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 15304 Sorted by residual: bond pdb=" CA VAL G 300 " pdb=" C VAL G 300 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.26e-02 6.30e+03 6.72e-01 bond pdb=" CA VAL A 300 " pdb=" C VAL A 300 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.26e-02 6.30e+03 6.30e-01 bond pdb=" CA VAL E 300 " pdb=" C VAL E 300 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.26e-02 6.30e+03 6.24e-01 bond pdb=" CA VAL C 300 " pdb=" C VAL C 300 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.26e-02 6.30e+03 5.68e-01 bond pdb=" CA VAL C 300 " pdb=" CB VAL C 300 " ideal model delta sigma weight residual 1.542 1.534 0.008 1.28e-02 6.10e+03 4.08e-01 ... (remaining 15299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 20388 1.21 - 2.42: 264 2.42 - 3.62: 48 3.62 - 4.83: 12 4.83 - 6.04: 8 Bond angle restraints: 20720 Sorted by residual: angle pdb=" C GLU A 105 " pdb=" N ARG A 106 " pdb=" CA ARG A 106 " ideal model delta sigma weight residual 121.80 126.68 -4.88 2.44e+00 1.68e-01 4.00e+00 angle pdb=" C GLU G 105 " pdb=" N ARG G 106 " pdb=" CA ARG G 106 " ideal model delta sigma weight residual 121.80 126.67 -4.87 2.44e+00 1.68e-01 3.98e+00 angle pdb=" C GLU E 105 " pdb=" N ARG E 106 " pdb=" CA ARG E 106 " ideal model delta sigma weight residual 121.80 126.66 -4.86 2.44e+00 1.68e-01 3.97e+00 angle pdb=" C GLU C 105 " pdb=" N ARG C 106 " pdb=" CA ARG C 106 " ideal model delta sigma weight residual 121.80 126.65 -4.85 2.44e+00 1.68e-01 3.95e+00 angle pdb=" CA ARG G 106 " pdb=" CB ARG G 106 " pdb=" CG ARG G 106 " ideal model delta sigma weight residual 114.10 117.69 -3.59 2.00e+00 2.50e-01 3.23e+00 ... (remaining 20715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 8463 15.61 - 31.23: 384 31.23 - 46.84: 63 46.84 - 62.46: 18 62.46 - 78.07: 4 Dihedral angle restraints: 8932 sinusoidal: 3408 harmonic: 5524 Sorted by residual: dihedral pdb=" N PHE A 322 " pdb=" CA PHE A 322 " pdb=" CB PHE A 322 " pdb=" CG PHE A 322 " ideal model delta sinusoidal sigma weight residual 60.00 109.70 -49.70 3 1.50e+01 4.44e-03 8.81e+00 dihedral pdb=" N PHE G 322 " pdb=" CA PHE G 322 " pdb=" CB PHE G 322 " pdb=" CG PHE G 322 " ideal model delta sinusoidal sigma weight residual 60.00 109.67 -49.67 3 1.50e+01 4.44e-03 8.81e+00 dihedral pdb=" N PHE C 322 " pdb=" CA PHE C 322 " pdb=" CB PHE C 322 " pdb=" CG PHE C 322 " ideal model delta sinusoidal sigma weight residual 60.00 109.66 -49.66 3 1.50e+01 4.44e-03 8.80e+00 ... (remaining 8929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 1388 0.023 - 0.047: 530 0.047 - 0.070: 304 0.070 - 0.093: 67 0.093 - 0.117: 51 Chirality restraints: 2340 Sorted by residual: chirality pdb=" CA ILE D 101 " pdb=" N ILE D 101 " pdb=" C ILE D 101 " pdb=" CB ILE D 101 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA ILE B 101 " pdb=" N ILE B 101 " pdb=" C ILE B 101 " pdb=" CB ILE B 101 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA ILE H 101 " pdb=" N ILE H 101 " pdb=" C ILE H 101 " pdb=" CB ILE H 101 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 2337 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 298 " -0.005 2.00e-02 2.50e+03 9.44e-03 8.91e-01 pdb=" C VAL E 298 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL E 298 " -0.006 2.00e-02 2.50e+03 pdb=" N THR E 299 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 298 " -0.005 2.00e-02 2.50e+03 9.22e-03 8.50e-01 pdb=" C VAL G 298 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL G 298 " -0.006 2.00e-02 2.50e+03 pdb=" N THR G 299 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 298 " -0.005 2.00e-02 2.50e+03 9.16e-03 8.39e-01 pdb=" C VAL C 298 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL C 298 " -0.006 2.00e-02 2.50e+03 pdb=" N THR C 299 " -0.005 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5011 2.84 - 3.36: 15741 3.36 - 3.87: 24497 3.87 - 4.39: 26433 4.39 - 4.90: 46762 Nonbonded interactions: 118444 Sorted by model distance: nonbonded pdb=" OG1 THR A 299 " pdb=" OH TYR G 305 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR A 305 " pdb=" OG1 THR C 299 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR E 305 " pdb=" OG1 THR G 299 " model vdw 2.329 3.040 nonbonded pdb=" OG1 THR E 299 " pdb=" OH TYR C 305 " model vdw 2.335 3.040 nonbonded pdb=" O VAL A 297 " pdb=" OG1 THR A 301 " model vdw 2.343 3.040 ... (remaining 118439 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'G' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'H' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.83 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: 3.610 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.400 Find NCS groups from input model: 0.120 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.002 0.018 15304 Z= 0.092 Angle : 0.375 6.039 20720 Z= 0.202 Chirality : 0.035 0.117 2340 Planarity : 0.002 0.023 2604 Dihedral : 9.569 78.072 5372 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.26 % Allowed : 3.32 % Favored : 95.41 % 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 are not related in a simple way. whole: 2.66 (0.20), residues: 1880 helix: 2.57 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -0.80 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 227 TYR 0.011 0.001 TYR E 534 PHE 0.005 0.001 PHE B 17 TRP 0.006 0.001 TRP G 369 HIS 0.001 0.000 HIS G 353 Details of bonding type rmsd covalent geometry : bond 0.00177 (15304) covalent geometry : angle 0.37473 (20720) hydrogen bonds : bond 0.13649 ( 1066) hydrogen bonds : angle 4.73910 ( 3183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.427 Fit side-chains REVERT: B 118 THR cc_start: 0.8536 (p) cc_final: 0.8299 (m) REVERT: F 118 THR cc_start: 0.8559 (p) cc_final: 0.8292 (m) REVERT: H 118 THR cc_start: 0.8541 (p) cc_final: 0.8290 (m) REVERT: D 118 THR cc_start: 0.8541 (p) cc_final: 0.8291 (m) outliers start: 19 outliers final: 15 residues processed: 153 average time/residue: 0.1006 time to fit residues: 24.5032 Evaluate side-chains 113 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.126188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116300 restraints weight = 275078.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116756 restraints weight = 189311.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.116167 restraints weight = 173220.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116219 restraints weight = 181142.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116139 restraints weight = 164021.415| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15304 Z= 0.211 Angle : 0.540 7.275 20720 Z= 0.289 Chirality : 0.040 0.130 2340 Planarity : 0.003 0.021 2604 Dihedral : 4.783 55.371 2099 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.66 % Allowed : 6.72 % Favored : 90.62 % 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 are not related in a simple way. whole: 1.88 (0.20), residues: 1880 helix: 2.03 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.49 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 127 TYR 0.018 0.002 TYR C 534 PHE 0.023 0.002 PHE F 93 TRP 0.008 0.001 TRP E 369 HIS 0.005 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00505 (15304) covalent geometry : angle 0.53983 (20720) hydrogen bonds : bond 0.04250 ( 1066) hydrogen bonds : angle 4.16575 ( 3183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.407 Fit side-chains outliers start: 40 outliers final: 34 residues processed: 128 average time/residue: 0.0832 time to fit residues: 18.3944 Evaluate side-chains 126 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 55 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.121795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.116881 restraints weight = 27058.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116393 restraints weight = 40245.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.116141 restraints weight = 34608.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115781 restraints weight = 35726.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.115673 restraints weight = 35978.420| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15304 Z= 0.197 Angle : 0.511 7.228 20720 Z= 0.273 Chirality : 0.039 0.125 2340 Planarity : 0.003 0.019 2604 Dihedral : 4.686 55.845 2097 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.59 % Allowed : 7.31 % Favored : 89.10 % 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 are not related in a simple way. whole: 1.70 (0.19), residues: 1880 helix: 1.93 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.66 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 227 TYR 0.017 0.002 TYR C 534 PHE 0.022 0.002 PHE H 93 TRP 0.009 0.001 TRP G 369 HIS 0.004 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00475 (15304) covalent geometry : angle 0.51141 (20720) hydrogen bonds : bond 0.04079 ( 1066) hydrogen bonds : angle 4.12730 ( 3183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 100 time to evaluate : 0.601 Fit side-chains outliers start: 54 outliers final: 36 residues processed: 128 average time/residue: 0.0864 time to fit residues: 19.1265 Evaluate side-chains 128 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 123 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 184 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.125913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122417 restraints weight = 27167.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.117645 restraints weight = 50620.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.117389 restraints weight = 44499.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.116832 restraints weight = 48550.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.116829 restraints weight = 42191.574| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15304 Z= 0.124 Angle : 0.447 6.809 20720 Z= 0.238 Chirality : 0.036 0.116 2340 Planarity : 0.002 0.019 2604 Dihedral : 4.538 55.658 2097 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.12 % Allowed : 8.24 % Favored : 88.63 % 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 are not related in a simple way. whole: 1.92 (0.19), residues: 1880 helix: 2.08 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.60 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 107 TYR 0.015 0.001 TYR G 534 PHE 0.025 0.001 PHE F 93 TRP 0.009 0.001 TRP E 369 HIS 0.004 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00278 (15304) covalent geometry : angle 0.44682 (20720) hydrogen bonds : bond 0.03596 ( 1066) hydrogen bonds : angle 3.90321 ( 3183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 96 time to evaluate : 0.571 Fit side-chains outliers start: 47 outliers final: 35 residues processed: 120 average time/residue: 0.0855 time to fit residues: 17.9135 Evaluate side-chains 128 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 137 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 129 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.125436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115665 restraints weight = 275690.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.116112 restraints weight = 189349.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115552 restraints weight = 178403.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115699 restraints weight = 179369.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115618 restraints weight = 166970.115| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15304 Z= 0.163 Angle : 0.479 7.017 20720 Z= 0.254 Chirality : 0.038 0.120 2340 Planarity : 0.003 0.018 2604 Dihedral : 4.589 56.139 2097 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.46 % Allowed : 8.84 % Favored : 87.70 % 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 are not related in a simple way. whole: 1.81 (0.19), residues: 1880 helix: 2.03 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.75 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 75 TYR 0.017 0.001 TYR C 534 PHE 0.025 0.001 PHE F 93 TRP 0.008 0.001 TRP E 369 HIS 0.003 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00388 (15304) covalent geometry : angle 0.47913 (20720) hydrogen bonds : bond 0.03732 ( 1066) hydrogen bonds : angle 3.95279 ( 3183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 0.609 Fit side-chains outliers start: 52 outliers final: 40 residues processed: 121 average time/residue: 0.0878 time to fit residues: 18.4048 Evaluate side-chains 132 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 55 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 175 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 0.0030 chunk 184 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 overall best weight: 0.8392 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.127633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.125260 restraints weight = 26850.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.124325 restraints weight = 41177.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123578 restraints weight = 53513.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.123343 restraints weight = 52082.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.122765 restraints weight = 40005.890| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15304 Z= 0.098 Angle : 0.420 6.105 20720 Z= 0.222 Chirality : 0.036 0.120 2340 Planarity : 0.002 0.020 2604 Dihedral : 4.377 55.258 2097 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.59 % Allowed : 9.77 % Favored : 87.63 % 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 are not related in a simple way. whole: 2.28 (0.20), residues: 1880 helix: 2.28 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.27 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 233 TYR 0.012 0.001 TYR C 534 PHE 0.011 0.001 PHE F 93 TRP 0.008 0.001 TRP C 295 HIS 0.002 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00203 (15304) covalent geometry : angle 0.42028 (20720) hydrogen bonds : bond 0.03223 ( 1066) hydrogen bonds : angle 3.67059 ( 3183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.533 Fit side-chains REVERT: A 509 MET cc_start: 0.8571 (mtt) cc_final: 0.8087 (mtt) outliers start: 39 outliers final: 31 residues processed: 121 average time/residue: 0.0847 time to fit residues: 17.5284 Evaluate side-chains 135 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 49 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.126497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.123038 restraints weight = 26922.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.122231 restraints weight = 44561.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.122040 restraints weight = 44796.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.121196 restraints weight = 46037.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120882 restraints weight = 52808.066| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15304 Z= 0.114 Angle : 0.440 6.316 20720 Z= 0.231 Chirality : 0.036 0.116 2340 Planarity : 0.002 0.020 2604 Dihedral : 4.295 55.821 2094 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.93 % Allowed : 9.24 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.20), residues: 1880 helix: 2.29 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.32 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 75 TYR 0.014 0.001 TYR C 534 PHE 0.012 0.001 PHE F 93 TRP 0.007 0.001 TRP E 369 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00253 (15304) covalent geometry : angle 0.44024 (20720) hydrogen bonds : bond 0.03328 ( 1066) hydrogen bonds : angle 3.69442 ( 3183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.473 Fit side-chains REVERT: A 509 MET cc_start: 0.8624 (mtt) cc_final: 0.8245 (mtt) REVERT: E 509 MET cc_start: 0.8622 (mtt) cc_final: 0.8303 (mtt) REVERT: G 509 MET cc_start: 0.8595 (mtt) cc_final: 0.8233 (mtt) REVERT: C 509 MET cc_start: 0.8599 (mtt) cc_final: 0.8204 (mtt) outliers start: 44 outliers final: 36 residues processed: 117 average time/residue: 0.0876 time to fit residues: 17.6322 Evaluate side-chains 134 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 56 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.0370 chunk 75 optimal weight: 0.0970 chunk 133 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.129010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.125754 restraints weight = 26762.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124760 restraints weight = 44019.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124819 restraints weight = 47641.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.124593 restraints weight = 42539.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.124380 restraints weight = 47108.173| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15304 Z= 0.092 Angle : 0.423 7.938 20720 Z= 0.220 Chirality : 0.035 0.117 2340 Planarity : 0.002 0.021 2604 Dihedral : 4.215 55.196 2094 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.06 % Allowed : 10.24 % Favored : 87.70 % 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 are not related in a simple way. whole: 2.49 (0.20), residues: 1880 helix: 2.44 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 233 TYR 0.011 0.001 TYR C 534 PHE 0.013 0.001 PHE B 93 TRP 0.007 0.001 TRP E 369 HIS 0.003 0.001 HIS E 498 Details of bonding type rmsd covalent geometry : bond 0.00183 (15304) covalent geometry : angle 0.42289 (20720) hydrogen bonds : bond 0.03061 ( 1066) hydrogen bonds : angle 3.53102 ( 3183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.601 Fit side-chains REVERT: A 509 MET cc_start: 0.8593 (mtt) cc_final: 0.8268 (mtt) REVERT: E 509 MET cc_start: 0.8587 (mtt) cc_final: 0.8279 (mtt) REVERT: G 509 MET cc_start: 0.8574 (mtt) cc_final: 0.8283 (mtt) REVERT: C 509 MET cc_start: 0.8549 (mtt) cc_final: 0.8106 (mtt) outliers start: 31 outliers final: 31 residues processed: 120 average time/residue: 0.0856 time to fit residues: 17.5662 Evaluate side-chains 138 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 13 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 171 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 165 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 = 0.3831 r_free = 0.3831 target = 0.129124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119609 restraints weight = 275258.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.120335 restraints weight = 188053.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.119832 restraints weight = 168651.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119982 restraints weight = 175641.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119909 restraints weight = 159406.157| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15304 Z= 0.102 Angle : 0.433 8.715 20720 Z= 0.224 Chirality : 0.036 0.117 2340 Planarity : 0.002 0.020 2604 Dihedral : 4.229 55.756 2094 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.99 % Allowed : 10.51 % Favored : 87.50 % 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 are not related in a simple way. whole: 2.54 (0.20), residues: 1880 helix: 2.48 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.21 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 233 TYR 0.013 0.001 TYR C 534 PHE 0.016 0.001 PHE F 93 TRP 0.007 0.001 TRP G 369 HIS 0.001 0.000 HIS G 230 Details of bonding type rmsd covalent geometry : bond 0.00222 (15304) covalent geometry : angle 0.43307 (20720) hydrogen bonds : bond 0.03134 ( 1066) hydrogen bonds : angle 3.53881 ( 3183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.583 Fit side-chains REVERT: A 322 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7988 (t80) REVERT: G 322 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7924 (t80) REVERT: C 509 MET cc_start: 0.8764 (mtt) cc_final: 0.8435 (mtt) outliers start: 30 outliers final: 28 residues processed: 109 average time/residue: 0.0871 time to fit residues: 16.4702 Evaluate side-chains 131 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 187 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.126679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.123080 restraints weight = 26712.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.122419 restraints weight = 48557.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122355 restraints weight = 48653.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.121936 restraints weight = 43609.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119364 restraints weight = 40531.050| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15304 Z= 0.121 Angle : 0.455 9.604 20720 Z= 0.235 Chirality : 0.036 0.117 2340 Planarity : 0.002 0.019 2604 Dihedral : 4.268 55.975 2094 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.06 % Allowed : 10.70 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.20), residues: 1880 helix: 2.47 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.25 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 544 TYR 0.014 0.001 TYR A 534 PHE 0.017 0.001 PHE F 93 TRP 0.007 0.001 TRP E 369 HIS 0.002 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00277 (15304) covalent geometry : angle 0.45470 (20720) hydrogen bonds : bond 0.03260 ( 1066) hydrogen bonds : angle 3.59467 ( 3183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.643 Fit side-chains REVERT: A 509 MET cc_start: 0.8722 (mtt) cc_final: 0.8505 (mtt) REVERT: E 509 MET cc_start: 0.8719 (mtt) cc_final: 0.8488 (mtt) REVERT: G 509 MET cc_start: 0.8648 (mtt) cc_final: 0.8380 (mtt) outliers start: 31 outliers final: 31 residues processed: 110 average time/residue: 0.0908 time to fit residues: 17.2234 Evaluate side-chains 132 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 0.3980 chunk 82 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.124076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.120270 restraints weight = 27202.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119257 restraints weight = 45860.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119209 restraints weight = 51098.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.118707 restraints weight = 51007.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.118520 restraints weight = 50218.898| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15304 Z= 0.168 Angle : 0.495 9.284 20720 Z= 0.259 Chirality : 0.038 0.119 2340 Planarity : 0.003 0.019 2604 Dihedral : 4.390 56.309 2094 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.66 % Allowed : 10.11 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.20), residues: 1880 helix: 2.33 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.27 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 75 TYR 0.017 0.002 TYR G 534 PHE 0.022 0.001 PHE F 93 TRP 0.008 0.001 TRP A 369 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00401 (15304) covalent geometry : angle 0.49506 (20720) hydrogen bonds : bond 0.03632 ( 1066) hydrogen bonds : angle 3.77934 ( 3183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1766.79 seconds wall clock time: 31 minutes 33.21 seconds (1893.21 seconds total)