Starting phenix.real_space_refine on Sun Nov 17 21:24:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/11_2024/7tcp_25816.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/11_2024/7tcp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/11_2024/7tcp_25816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/11_2024/7tcp_25816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/11_2024/7tcp_25816.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/11_2024/7tcp_25816.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} 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: D, F, H, C, E, G 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: 7.94, per 1000 atoms: 0.53 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: 3.99 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.49 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: 4.47 Time building geometry restraints manager: 4.53 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 33.650 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.840 ------------------------------------------------------------------------------- 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= 0.114 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 : 4.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (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 TRP 0.006 0.001 TRP G 369 HIS 0.001 0.000 HIS G 353 PHE 0.005 0.001 PHE B 17 TYR 0.011 0.001 TYR E 534 ARG 0.002 0.000 ARG C 227 *********************** 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 : 1.623 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: 0.8293 (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: 0.2462 time to fit residues: 59.7629 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 : 1.707 ------------------------------------------------------------------------------- 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 158 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15304 Z= 0.207 Angle : 0.462 6.486 20720 Z= 0.247 Chirality : 0.037 0.122 2340 Planarity : 0.003 0.018 2604 Dihedral : 4.605 54.164 2099 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.59 % Allowed : 5.85 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.20), residues: 1880 helix: 2.31 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.30 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 369 HIS 0.006 0.001 HIS D 108 PHE 0.019 0.001 PHE F 93 TYR 0.014 0.001 TYR G 534 ARG 0.003 0.000 ARG D 127 *********************** 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 155 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 1.810 Fit side-chains REVERT: B 118 THR cc_start: 0.8538 (p) cc_final: 0.8294 (m) REVERT: F 118 THR cc_start: 0.8554 (p) cc_final: 0.8297 (m) REVERT: H 118 THR cc_start: 0.8546 (p) cc_final: 0.8302 (m) REVERT: D 118 THR cc_start: 0.8545 (p) cc_final: 0.8293 (m) outliers start: 39 outliers final: 31 residues processed: 136 average time/residue: 0.1953 time to fit residues: 45.6453 Evaluate side-chains 127 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 152 optimal weight: 0.0970 chunk 169 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 137 optimal weight: 8.9990 overall best weight: 3.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15304 Z= 0.364 Angle : 0.549 7.456 20720 Z= 0.294 Chirality : 0.040 0.130 2340 Planarity : 0.003 0.024 2604 Dihedral : 4.804 56.021 2099 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.46 % Allowed : 7.11 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 1880 helix: 1.94 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.62 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 369 HIS 0.004 0.001 HIS D 108 PHE 0.028 0.002 PHE H 93 TYR 0.019 0.002 TYR C 534 ARG 0.003 0.001 ARG C 227 *********************** 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 152 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 100 time to evaluate : 1.842 Fit side-chains REVERT: F 118 THR cc_start: 0.8634 (p) cc_final: 0.8425 (m) outliers start: 52 outliers final: 39 residues processed: 132 average time/residue: 0.1975 time to fit residues: 44.9034 Evaluate side-chains 131 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 101 ILE 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 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 101 ILE 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 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 101 ILE 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 101 ILE 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 168 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15304 Z= 0.133 Angle : 0.429 6.284 20720 Z= 0.228 Chirality : 0.036 0.120 2340 Planarity : 0.002 0.018 2604 Dihedral : 4.515 55.323 2098 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.39 % Allowed : 8.91 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.20), residues: 1880 helix: 2.16 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.38 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 369 HIS 0.003 0.001 HIS D 108 PHE 0.020 0.001 PHE H 93 TYR 0.013 0.001 TYR C 534 ARG 0.002 0.000 ARG F 107 *********************** 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 136 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 1.773 Fit side-chains REVERT: F 118 THR cc_start: 0.8603 (p) cc_final: 0.8401 (m) outliers start: 36 outliers final: 24 residues processed: 120 average time/residue: 0.2014 time to fit residues: 41.1535 Evaluate side-chains 116 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 92 VAL Chi-restraints excluded: chain B residue 102 SER 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1506 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= 0.290 Angle : 0.502 6.896 20720 Z= 0.266 Chirality : 0.038 0.124 2340 Planarity : 0.003 0.018 2604 Dihedral : 4.479 56.445 2095 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.46 % Allowed : 8.78 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 1880 helix: 2.06 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.67 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 369 HIS 0.003 0.001 HIS G 230 PHE 0.010 0.001 PHE B 90 TYR 0.018 0.002 TYR C 534 ARG 0.002 0.000 ARG F 75 *********************** 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 148 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 96 time to evaluate : 1.930 Fit side-chains REVERT: F 118 THR cc_start: 0.8667 (p) cc_final: 0.8464 (m) outliers start: 52 outliers final: 40 residues processed: 124 average time/residue: 0.2069 time to fit residues: 43.9776 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 : 1.733 ------------------------------------------------------------------------------- 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 101 ILE 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 101 ILE 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 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 101 ILE 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 101 ILE Chi-restraints excluded: chain D residue 102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1485 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: