Starting phenix.real_space_refine on Sat Mar 16 12:46:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/03_2024/8asi_15616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/03_2024/8asi_15616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/03_2024/8asi_15616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/03_2024/8asi_15616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/03_2024/8asi_15616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/03_2024/8asi_15616_updated.pdb" } resolution = 2.9 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= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 12 5.49 5 S 74 5.16 5 C 9715 2.51 5 N 2338 2.21 5 O 2571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14720 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1342 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain: "B" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3477 Classifications: {'peptide': 433} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 404} Chain: "C" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1944 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 233} Chain: "D" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 222 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1357 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "F" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3471 Classifications: {'peptide': 432} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 403} Chain: "G" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1944 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 233} Chain: "H" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 203 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'FES': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "B" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 269 Unusual residues: {'HEM': 2, 'PEE': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'FES': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "F" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 280 Unusual residues: {'HEM': 2, 'PEE': 4, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 913 SG CYS A 129 34.336 79.448 51.034 1.00 77.73 S ATOM 1053 SG CYS A 149 37.178 80.949 52.834 1.00 72.20 S ATOM 7913 SG CYS E 129 71.785 34.949 77.937 1.00 98.47 S ATOM 8053 SG CYS E 149 69.114 33.393 76.251 1.00 97.18 S Time building chain proxies: 8.66, per 1000 atoms: 0.59 Number of scatterers: 14720 At special positions: 0 Unit cell: (120.695, 114.836, 117.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 74 16.00 P 12 15.00 O 2571 8.00 N 2338 7.00 C 9715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 151 " distance=2.02 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 151 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.89 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE2 FES A 201 " - pdb=" ND1 HIS A 152 " pdb="FE2 FES A 201 " - pdb=" ND1 HIS A 131 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 149 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 129 " pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" ND1 HIS E 152 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 149 " pdb="FE2 FES E 201 " - pdb=" ND1 HIS E 131 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 129 " Number of angles added : 6 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3254 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 11 sheets defined 51.8% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 removed outlier: 3.764A pdb=" N PHE A 14 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 19 " --> pdb=" O TYR A 16 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 25 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 27 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 29 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP A 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Proline residue: A 33 - end of helix removed outlier: 4.616A pdb=" N GLN A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 48 removed outlier: 3.731A pdb=" N ALA A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 removed outlier: 7.090A pdb=" N GLY A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'B' and resid 14 through 20 Processing helix chain 'B' and resid 25 through 33 Processing helix chain 'B' and resid 43 through 67 removed outlier: 3.914A pdb=" N TRP B 47 " --> pdb=" O MET B 44 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY B 48 " --> pdb=" O TRP B 45 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 55 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 58 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 60 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 61 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 63 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 90 through 118 removed outlier: 3.876A pdb=" N SER B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 149 Processing helix chain 'B' and resid 153 through 168 removed outlier: 4.112A pdb=" N PHE B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 188 through 217 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 244 through 269 removed outlier: 6.774A pdb=" N ILE B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 296 through 307 Proline residue: B 300 - end of helix Processing helix chain 'B' and resid 313 through 321 Processing helix chain 'B' and resid 328 through 349 removed outlier: 3.931A pdb=" N ILE B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 363 through 382 removed outlier: 3.851A pdb=" N ALA B 382 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 405 removed outlier: 3.714A pdb=" N PHE B 404 " --> pdb=" O TRP B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 4.072A pdb=" N ALA B 413 " --> pdb=" O PRO B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 431 Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 82 through 91 removed outlier: 3.917A pdb=" N GLN C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 149 through 157 Processing helix chain 'C' and resid 226 through 241 Processing helix chain 'C' and resid 245 through 277 removed outlier: 3.611A pdb=" N GLY C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 104 removed outlier: 4.069A pdb=" N LEU D 85 " --> pdb=" O ARG D 82 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY D 86 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 89 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 93 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 94 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 97 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 98 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE D 102 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 38 removed outlier: 3.572A pdb=" N ALA E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Proline residue: E 33 - end of helix removed outlier: 4.912A pdb=" N MET E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 79 through 87 Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'F' and resid 14 through 20 Processing helix chain 'F' and resid 25 through 34 Processing helix chain 'F' and resid 43 through 67 removed outlier: 3.947A pdb=" N TRP F 47 " --> pdb=" O MET F 44 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY F 48 " --> pdb=" O TRP F 45 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR F 61 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 66 " --> pdb=" O ILE F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 90 through 118 removed outlier: 3.944A pdb=" N SER F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 148 Processing helix chain 'F' and resid 153 through 168 removed outlier: 4.003A pdb=" N PHE F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY F 167 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.700A pdb=" N LEU F 181 " --> pdb=" O THR F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 219 Proline residue: F 202 - end of helix Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.580A pdb=" N LYS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 269 removed outlier: 6.766A pdb=" N ILE F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 280 Processing helix chain 'F' and resid 296 through 307 Proline residue: F 300 - end of helix Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 328 through 349 removed outlier: 4.333A pdb=" N ILE F 340 " --> pdb=" O MET F 336 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Proline residue: F 347 - end of helix Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 363 through 382 removed outlier: 3.783A pdb=" N ALA F 382 " --> pdb=" O THR F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 405 removed outlier: 3.734A pdb=" N PHE F 404 " --> pdb=" O TRP F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 414 removed outlier: 3.582A pdb=" N GLY F 412 " --> pdb=" O LEU F 408 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA F 413 " --> pdb=" O PRO F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 431 Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 58 through 60 No H-bonds generated for 'chain 'G' and resid 58 through 60' Processing helix chain 'G' and resid 69 through 73 Processing helix chain 'G' and resid 82 through 91 removed outlier: 3.726A pdb=" N GLN G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 149 through 157 Processing helix chain 'G' and resid 226 through 241 Processing helix chain 'G' and resid 245 through 277 removed outlier: 3.918A pdb=" N GLY G 276 " --> pdb=" O ARG G 272 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 104 removed outlier: 4.111A pdb=" N PHE H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.647A pdb=" N ILE A 74 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 removed outlier: 3.536A pdb=" N GLY A 187 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 54 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLN A 185 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLN A 185 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N PHE A 178 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= D, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= E, first strand: chain 'C' and resid 177 through 179 Processing sheet with id= F, first strand: chain 'E' and resid 50 through 53 Processing sheet with id= G, first strand: chain 'E' and resid 62 through 67 Processing sheet with id= H, first strand: chain 'E' and resid 145 through 149 removed outlier: 6.601A pdb=" N TYR E 156 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE E 148 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N SER E 154 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 36 through 38 Processing sheet with id= J, first strand: chain 'G' and resid 93 through 96 removed outlier: 3.749A pdb=" N GLU G 101 " --> pdb=" O ASP G 96 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 177 through 179 634 hydrogen bonds defined for protein. 1611 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: 4.28 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.39: 6181 1.39 - 1.59: 8841 1.59 - 1.80: 87 1.80 - 2.00: 60 2.00 - 2.20: 31 Bond restraints: 15200 Sorted by residual: bond pdb=" C18 PEE B 507 " pdb=" C19 PEE B 507 " ideal model delta sigma weight residual 1.523 1.318 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C38 PEE E 202 " pdb=" C39 PEE E 202 " ideal model delta sigma weight residual 1.523 1.335 0.188 2.00e-02 2.50e+03 8.88e+01 bond pdb=" C38 PEE F 507 " pdb=" C39 PEE F 507 " ideal model delta sigma weight residual 1.523 1.336 0.187 2.00e-02 2.50e+03 8.76e+01 bond pdb=" C38 PEE A 203 " pdb=" C39 PEE A 203 " ideal model delta sigma weight residual 1.523 1.339 0.184 2.00e-02 2.50e+03 8.50e+01 bond pdb=" C38 PEE B 507 " pdb=" C39 PEE B 507 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.40e+01 ... (remaining 15195 not shown) Histogram of bond angle deviations from ideal: 73.92 - 94.95: 30 94.95 - 115.99: 9753 115.99 - 137.03: 10938 137.03 - 158.07: 0 158.07 - 179.11: 13 Bond angle restraints: 20734 Sorted by residual: angle pdb=" C17 PEE B 507 " pdb=" C18 PEE B 507 " pdb=" C19 PEE B 507 " ideal model delta sigma weight residual 113.68 158.50 -44.82 3.00e+00 1.11e-01 2.23e+02 angle pdb=" C25 PEE A 203 " pdb=" C26 PEE A 203 " pdb=" C27 PEE A 203 " ideal model delta sigma weight residual 112.90 136.75 -23.85 3.00e+00 1.11e-01 6.32e+01 angle pdb=" C38 PEE F 507 " pdb=" C39 PEE F 507 " pdb=" C40 PEE F 507 " ideal model delta sigma weight residual 112.47 90.37 22.10 3.00e+00 1.11e-01 5.43e+01 angle pdb=" CG MET C 207 " pdb=" SD MET C 207 " pdb=" CE MET C 207 " ideal model delta sigma weight residual 100.90 86.04 14.86 2.20e+00 2.07e-01 4.56e+01 angle pdb=" C38 PEE B 503 " pdb=" C39 PEE B 503 " pdb=" C40 PEE B 503 " ideal model delta sigma weight residual 112.47 92.48 19.99 3.00e+00 1.11e-01 4.44e+01 ... (remaining 20729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 8403 34.61 - 69.22: 204 69.22 - 103.82: 59 103.82 - 138.43: 30 138.43 - 173.04: 14 Dihedral angle restraints: 8710 sinusoidal: 3605 harmonic: 5105 Sorted by residual: dihedral pdb=" C6 U10 F 503 " pdb=" C7 U10 F 503 " pdb=" C8 U10 F 503 " pdb=" C9 U10 F 503 " ideal model delta sinusoidal sigma weight residual 101.51 -103.09 -155.39 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" C2B HEC G 301 " pdb=" C3B HEC G 301 " pdb=" CAB HEC G 301 " pdb=" CBB HEC G 301 " ideal model delta sinusoidal sigma weight residual 240.00 174.57 65.43 2 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" C3M U10 F 503 " pdb=" C3 U10 F 503 " pdb=" O3 U10 F 503 " pdb=" C4 U10 F 503 " ideal model delta sinusoidal sigma weight residual 244.38 122.40 121.98 1 2.00e+01 2.50e-03 3.67e+01 ... (remaining 8707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1780 0.070 - 0.139: 327 0.139 - 0.209: 34 0.209 - 0.278: 4 0.278 - 0.348: 2 Chirality restraints: 2147 Sorted by residual: chirality pdb=" C2 PEE B 503 " pdb=" C1 PEE B 503 " pdb=" C3 PEE B 503 " pdb=" O2 PEE B 503 " both_signs ideal model delta sigma weight residual False -2.33 -1.98 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL B 108 " pdb=" CA VAL B 108 " pdb=" CG1 VAL B 108 " pdb=" CG2 VAL B 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2144 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 301 " 0.044 2.00e-02 2.50e+03 9.83e-02 2.17e+02 pdb=" C2C HEC C 301 " -0.267 2.00e-02 2.50e+03 pdb=" C3C HEC C 301 " 0.068 2.00e-02 2.50e+03 pdb=" C4C HEC C 301 " 0.014 2.00e-02 2.50e+03 pdb=" CAC HEC C 301 " 0.035 2.00e-02 2.50e+03 pdb=" CHC HEC C 301 " 0.037 2.00e-02 2.50e+03 pdb=" CHD HEC C 301 " -0.012 2.00e-02 2.50e+03 pdb=" CMC HEC C 301 " 0.077 2.00e-02 2.50e+03 pdb=" NC HEC C 301 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC G 301 " 0.023 2.00e-02 2.50e+03 6.68e-02 1.00e+02 pdb=" C2C HEC G 301 " -0.183 2.00e-02 2.50e+03 pdb=" C3C HEC G 301 " 0.035 2.00e-02 2.50e+03 pdb=" C4C HEC G 301 " 0.008 2.00e-02 2.50e+03 pdb=" CAC HEC G 301 " 0.030 2.00e-02 2.50e+03 pdb=" CHC HEC G 301 " 0.030 2.00e-02 2.50e+03 pdb=" CHD HEC G 301 " -0.006 2.00e-02 2.50e+03 pdb=" CMC HEC G 301 " 0.053 2.00e-02 2.50e+03 pdb=" NC HEC G 301 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 21 " 0.035 2.00e-02 2.50e+03 6.96e-02 4.84e+01 pdb=" C GLY A 21 " -0.120 2.00e-02 2.50e+03 pdb=" O GLY A 21 " 0.044 2.00e-02 2.50e+03 pdb=" N ALA A 22 " 0.041 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 29 2.52 - 3.12: 11395 3.12 - 3.71: 23816 3.71 - 4.31: 34601 4.31 - 4.90: 55917 Nonbonded interactions: 125758 Sorted by model distance: nonbonded pdb=" NE2 HIS G 62 " pdb="FE HEC G 301 " model vdw 1.929 3.080 nonbonded pdb=" NE2 HIS B 198 " pdb="FE HEM B 502 " model vdw 2.007 3.080 nonbonded pdb=" NE2 HIS C 62 " pdb="FE HEC C 301 " model vdw 2.022 3.080 nonbonded pdb=" NE2 HIS F 198 " pdb="FE HEM F 502 " model vdw 2.026 3.080 nonbonded pdb=" NE2 HIS F 111 " pdb="FE HEM F 501 " model vdw 2.156 3.080 ... (remaining 125753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 187 or resid 201 through 202)) selection = (chain 'E' and (resid 9 through 187 or resid 201 or (resid 202 and (name N or na \ me C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name C17 or name C18 or name C2 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )))) } ncs_group { reference = (chain 'B' and (resid 1 through 432 or resid 501 through 502 or resid 504 or (re \ sid 505 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C4 or name C5 or name O \ 1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name \ O5 or name P )) or resid 506 or (resid 507 and (name N or name C1 or name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name \ C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C \ 43 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )))) selection = (chain 'F' and (resid 1 through 432 or resid 501 through 502 or resid 504 or (re \ sid 505 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C4 or name C5 or name O \ 1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name \ O5 or name P )) or (resid 506 and (name N or name C1 or name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1P or name \ O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name \ P )) or resid 507)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 79 through 105) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.390 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 43.720 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.120 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 : 0.009 0.205 15200 Z= 0.564 Angle : 1.273 44.822 20734 Z= 0.581 Chirality : 0.054 0.348 2147 Planarity : 0.010 0.098 2582 Dihedral : 20.468 173.040 5450 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 1773 helix: -0.46 (0.15), residues: 912 sheet: -1.38 (0.60), residues: 62 loop : -0.39 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 348 HIS 0.012 0.002 HIS B 291 PHE 0.099 0.003 PHE D 88 TYR 0.035 0.005 TYR F 280 ARG 0.021 0.004 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.440 Fit side-chains REVERT: A 38 MET cc_start: 0.9055 (mtp) cc_final: 0.8736 (mtp) REVERT: A 63 LEU cc_start: 0.7711 (mt) cc_final: 0.7334 (tp) REVERT: B 6 HIS cc_start: 0.7923 (p-80) cc_final: 0.7555 (p-80) REVERT: B 92 MET cc_start: 0.7963 (mmt) cc_final: 0.7684 (tpt) REVERT: B 133 MET cc_start: 0.8676 (mmm) cc_final: 0.8314 (mmm) REVERT: B 154 MET cc_start: 0.8722 (mmm) cc_final: 0.8513 (mmt) REVERT: B 239 LYS cc_start: 0.7953 (mttt) cc_final: 0.7676 (mtpt) REVERT: B 292 ILE cc_start: 0.8496 (mm) cc_final: 0.8292 (mm) REVERT: B 393 SER cc_start: 0.8531 (t) cc_final: 0.8024 (p) REVERT: B 416 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7907 (mmtp) REVERT: C 52 GLN cc_start: 0.7976 (tt0) cc_final: 0.7390 (tt0) REVERT: C 56 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7457 (mp0) REVERT: C 101 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7203 (mt-10) REVERT: C 180 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7859 (ttp-110) REVERT: C 189 ASP cc_start: 0.6504 (p0) cc_final: 0.5971 (t0) REVERT: C 212 MET cc_start: 0.6956 (ttp) cc_final: 0.6619 (ttt) REVERT: C 214 ASP cc_start: 0.7295 (m-30) cc_final: 0.6744 (t0) REVERT: F 34 MET cc_start: 0.8800 (mmm) cc_final: 0.8452 (mmt) REVERT: F 92 MET cc_start: 0.7809 (tpt) cc_final: 0.7567 (tpt) REVERT: F 137 LEU cc_start: 0.7860 (mt) cc_final: 0.7465 (mt) REVERT: F 239 LYS cc_start: 0.8042 (mttt) cc_final: 0.7681 (mtmt) REVERT: F 313 TRP cc_start: 0.5592 (m-90) cc_final: 0.4408 (m-10) REVERT: F 394 LEU cc_start: 0.8446 (tp) cc_final: 0.8242 (tt) REVERT: F 428 PHE cc_start: 0.8466 (t80) cc_final: 0.8199 (t80) REVERT: G 136 MET cc_start: 0.6413 (tpp) cc_final: 0.6117 (tpt) outliers start: 0 outliers final: 1 residues processed: 283 average time/residue: 1.0926 time to fit residues: 343.3420 Evaluate side-chains 211 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 70 optimal weight: 0.0010 chunk 137 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 217 HIS B 276 HIS C 145 ASN C 183 GLN E 185 GLN F 319 ASN F 383 GLN F 431 HIS G 84 GLN G 118 ASN G 179 ASN G 183 GLN G 222 HIS G 227 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15200 Z= 0.190 Angle : 0.690 17.095 20734 Z= 0.312 Chirality : 0.044 0.224 2147 Planarity : 0.005 0.045 2582 Dihedral : 22.681 179.265 2395 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.53 % Allowed : 8.44 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1773 helix: 0.92 (0.17), residues: 918 sheet: -1.84 (0.53), residues: 72 loop : 0.22 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 147 HIS 0.007 0.001 HIS B 291 PHE 0.028 0.002 PHE D 88 TYR 0.015 0.001 TYR F 399 ARG 0.003 0.000 ARG G 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 232 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8995 (mtp) cc_final: 0.8510 (mtp) REVERT: A 63 LEU cc_start: 0.7649 (mt) cc_final: 0.7221 (tp) REVERT: A 180 ASP cc_start: 0.5477 (OUTLIER) cc_final: 0.4890 (p0) REVERT: B 1 MET cc_start: 0.2280 (OUTLIER) cc_final: 0.1629 (ttp) REVERT: B 6 HIS cc_start: 0.8007 (p-80) cc_final: 0.7743 (p-80) REVERT: B 92 MET cc_start: 0.8019 (mmt) cc_final: 0.7784 (tpt) REVERT: B 133 MET cc_start: 0.8552 (mmm) cc_final: 0.8292 (mmm) REVERT: B 239 LYS cc_start: 0.7844 (mttt) cc_final: 0.7557 (mtpt) REVERT: B 343 MET cc_start: 0.8374 (ttp) cc_final: 0.8155 (ttp) REVERT: B 416 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7865 (mmtp) REVERT: C 52 GLN cc_start: 0.8002 (tt0) cc_final: 0.7765 (tt0) REVERT: C 74 GLU cc_start: 0.7381 (tt0) cc_final: 0.6480 (mm-30) REVERT: C 180 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.7714 (ttp-110) REVERT: C 189 ASP cc_start: 0.6449 (p0) cc_final: 0.5786 (t0) REVERT: C 214 ASP cc_start: 0.7370 (m-30) cc_final: 0.7138 (m-30) REVERT: F 34 MET cc_start: 0.8801 (mmm) cc_final: 0.8544 (mmm) REVERT: F 137 LEU cc_start: 0.7855 (mt) cc_final: 0.7431 (mt) REVERT: F 187 ASP cc_start: 0.7548 (t0) cc_final: 0.6527 (p0) REVERT: F 239 LYS cc_start: 0.8051 (mttt) cc_final: 0.7565 (mttm) REVERT: F 252 ASP cc_start: 0.7667 (m-30) cc_final: 0.7450 (m-30) REVERT: F 313 TRP cc_start: 0.5691 (m-90) cc_final: 0.4461 (m-10) REVERT: G 136 MET cc_start: 0.6467 (tpp) cc_final: 0.6238 (tpt) REVERT: G 179 ASN cc_start: 0.8759 (t0) cc_final: 0.8454 (t0) outliers start: 22 outliers final: 8 residues processed: 240 average time/residue: 1.0775 time to fit residues: 288.4085 Evaluate side-chains 214 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 212 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.0020 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 0.0060 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 157 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.6808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN C 142 GLN C 183 GLN F 316 GLN F 383 GLN G 84 GLN G 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15200 Z= 0.174 Angle : 0.637 16.470 20734 Z= 0.279 Chirality : 0.043 0.212 2147 Planarity : 0.005 0.047 2582 Dihedral : 21.382 175.020 2395 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.09 % Allowed : 9.34 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1773 helix: 1.02 (0.17), residues: 928 sheet: -1.61 (0.58), residues: 72 loop : 0.35 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 147 HIS 0.007 0.001 HIS B 111 PHE 0.018 0.002 PHE B 216 TYR 0.014 0.001 TYR F 399 ARG 0.003 0.000 ARG G 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8927 (mtp) cc_final: 0.8384 (mtp) REVERT: B 1 MET cc_start: 0.2092 (OUTLIER) cc_final: 0.1656 (ttp) REVERT: B 6 HIS cc_start: 0.7902 (p-80) cc_final: 0.7695 (p-80) REVERT: B 20 HIS cc_start: 0.8759 (t-90) cc_final: 0.8477 (t70) REVERT: B 92 MET cc_start: 0.8075 (mmt) cc_final: 0.7754 (tpt) REVERT: B 239 LYS cc_start: 0.7926 (mttt) cc_final: 0.7599 (mtpt) REVERT: B 260 LEU cc_start: 0.7357 (mt) cc_final: 0.6960 (mp) REVERT: B 395 ILE cc_start: 0.8113 (mt) cc_final: 0.7913 (mt) REVERT: B 416 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7791 (mmtp) REVERT: C 52 GLN cc_start: 0.7982 (tt0) cc_final: 0.7772 (tt0) REVERT: C 74 GLU cc_start: 0.7445 (tt0) cc_final: 0.6610 (mm-30) REVERT: C 180 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7766 (ttp-110) REVERT: C 189 ASP cc_start: 0.6253 (p0) cc_final: 0.5846 (t0) REVERT: C 207 MET cc_start: 0.8330 (ttm) cc_final: 0.7881 (ttm) REVERT: C 214 ASP cc_start: 0.7345 (m-30) cc_final: 0.7109 (m-30) REVERT: E 111 ASP cc_start: 0.5739 (OUTLIER) cc_final: 0.5213 (t0) REVERT: F 137 LEU cc_start: 0.7902 (mt) cc_final: 0.7460 (mt) REVERT: F 187 ASP cc_start: 0.7603 (t0) cc_final: 0.6281 (p0) REVERT: F 239 LYS cc_start: 0.8008 (mttt) cc_final: 0.7628 (mttm) REVERT: F 252 ASP cc_start: 0.7588 (m-30) cc_final: 0.7354 (m-30) REVERT: F 313 TRP cc_start: 0.5711 (m-90) cc_final: 0.4463 (m-10) REVERT: G 74 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7581 (mt-10) REVERT: G 136 MET cc_start: 0.6468 (tpp) cc_final: 0.6070 (tpt) REVERT: G 232 ASP cc_start: 0.8401 (m-30) cc_final: 0.7992 (m-30) REVERT: G 271 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8263 (ttmm) outliers start: 30 outliers final: 10 residues processed: 235 average time/residue: 1.0715 time to fit residues: 281.6211 Evaluate side-chains 219 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 212 MET Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 0.0970 chunk 83 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 383 GLN C 183 GLN F 383 GLN G 84 GLN G 118 ASN G 179 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15200 Z= 0.160 Angle : 0.602 14.853 20734 Z= 0.262 Chirality : 0.042 0.204 2147 Planarity : 0.005 0.046 2582 Dihedral : 20.083 167.362 2395 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.44 % Allowed : 9.48 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1773 helix: 1.03 (0.17), residues: 941 sheet: -1.50 (0.55), residues: 77 loop : 0.39 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 147 HIS 0.006 0.001 HIS B 111 PHE 0.016 0.001 PHE B 105 TYR 0.013 0.001 TYR F 399 ARG 0.005 0.000 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 1.577 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8916 (mtp) cc_final: 0.8381 (mtp) REVERT: B 1 MET cc_start: 0.2096 (OUTLIER) cc_final: 0.1671 (ttp) REVERT: B 20 HIS cc_start: 0.8748 (t-90) cc_final: 0.8472 (t70) REVERT: B 92 MET cc_start: 0.8037 (mmt) cc_final: 0.7761 (tpt) REVERT: B 180 LEU cc_start: 0.8645 (tp) cc_final: 0.8285 (tp) REVERT: B 239 LYS cc_start: 0.7947 (mttt) cc_final: 0.7645 (mtpt) REVERT: B 260 LEU cc_start: 0.7351 (mt) cc_final: 0.6975 (mp) REVERT: B 276 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.7252 (m-70) REVERT: B 317 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6685 (mt) REVERT: B 343 MET cc_start: 0.8466 (ttp) cc_final: 0.8260 (ttp) REVERT: B 395 ILE cc_start: 0.8125 (mt) cc_final: 0.7921 (mt) REVERT: B 416 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7855 (mmtp) REVERT: B 431 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6878 (m-70) REVERT: C 74 GLU cc_start: 0.7319 (tt0) cc_final: 0.6618 (mm-30) REVERT: C 180 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7543 (ttp-110) REVERT: C 189 ASP cc_start: 0.6740 (p0) cc_final: 0.6061 (t0) REVERT: C 207 MET cc_start: 0.8443 (ttm) cc_final: 0.8043 (ttm) REVERT: C 214 ASP cc_start: 0.7334 (m-30) cc_final: 0.7098 (m-30) REVERT: F 17 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7920 (mtpp) REVERT: F 137 LEU cc_start: 0.7928 (mt) cc_final: 0.7469 (mt) REVERT: F 187 ASP cc_start: 0.7520 (t0) cc_final: 0.6199 (p0) REVERT: F 239 LYS cc_start: 0.7976 (mttt) cc_final: 0.7633 (mttm) REVERT: F 313 TRP cc_start: 0.5493 (m-90) cc_final: 0.4331 (m-10) REVERT: G 64 MET cc_start: 0.8903 (mtp) cc_final: 0.8698 (mtm) REVERT: G 74 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7411 (mt-10) REVERT: G 136 MET cc_start: 0.6449 (tpp) cc_final: 0.6040 (tpt) REVERT: G 271 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8253 (ttmm) outliers start: 35 outliers final: 13 residues processed: 239 average time/residue: 1.0111 time to fit residues: 271.1389 Evaluate side-chains 219 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 0.0670 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 151 optimal weight: 0.0030 chunk 42 optimal weight: 1.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN C 183 GLN F 316 GLN F 383 GLN G 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15200 Z= 0.149 Angle : 0.584 14.298 20734 Z= 0.253 Chirality : 0.041 0.196 2147 Planarity : 0.004 0.044 2582 Dihedral : 19.394 166.788 2393 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.88 % Allowed : 11.02 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1773 helix: 1.11 (0.17), residues: 936 sheet: -1.53 (0.56), residues: 77 loop : 0.42 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 122 HIS 0.005 0.001 HIS B 111 PHE 0.015 0.001 PHE B 216 TYR 0.012 0.001 TYR F 399 ARG 0.006 0.000 ARG G 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8902 (mtp) cc_final: 0.8377 (mtp) REVERT: A 47 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7874 (mm) REVERT: A 70 LYS cc_start: 0.8339 (mttp) cc_final: 0.8050 (mtmp) REVERT: A 122 TRP cc_start: 0.7088 (m100) cc_final: 0.5686 (m100) REVERT: A 137 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7745 (mm) REVERT: B 1 MET cc_start: 0.2122 (OUTLIER) cc_final: 0.1664 (ttp) REVERT: B 20 HIS cc_start: 0.8747 (t-90) cc_final: 0.8490 (t70) REVERT: B 92 MET cc_start: 0.8025 (mmt) cc_final: 0.7729 (tpt) REVERT: B 180 LEU cc_start: 0.8769 (tp) cc_final: 0.8333 (tp) REVERT: B 239 LYS cc_start: 0.7950 (mttt) cc_final: 0.7665 (mtpt) REVERT: B 260 LEU cc_start: 0.7414 (mt) cc_final: 0.7049 (mp) REVERT: B 317 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6675 (mt) REVERT: B 416 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7907 (mmtp) REVERT: C 29 GLU cc_start: 0.7490 (tt0) cc_final: 0.7278 (mm-30) REVERT: C 74 GLU cc_start: 0.7219 (tt0) cc_final: 0.6514 (mm-30) REVERT: C 180 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7501 (ttp-110) REVERT: C 189 ASP cc_start: 0.6760 (p0) cc_final: 0.6068 (t0) REVERT: C 207 MET cc_start: 0.8491 (ttm) cc_final: 0.8149 (ttm) REVERT: C 214 ASP cc_start: 0.7263 (m-30) cc_final: 0.7019 (m-30) REVERT: D 85 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.6925 (mt) REVERT: F 1 MET cc_start: 0.3126 (ppp) cc_final: 0.2883 (pp-130) REVERT: F 137 LEU cc_start: 0.7954 (mt) cc_final: 0.7464 (mt) REVERT: F 239 LYS cc_start: 0.7928 (mttt) cc_final: 0.7590 (mttm) REVERT: F 313 TRP cc_start: 0.5548 (m-90) cc_final: 0.4357 (m-10) REVERT: G 74 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7336 (mt-10) REVERT: G 136 MET cc_start: 0.6452 (tpp) cc_final: 0.6171 (tpt) REVERT: G 253 PHE cc_start: 0.8000 (m-80) cc_final: 0.6719 (t80) REVERT: G 271 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8256 (ttmm) outliers start: 27 outliers final: 9 residues processed: 226 average time/residue: 1.0558 time to fit residues: 266.5692 Evaluate side-chains 224 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.7980 chunk 152 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN E 155 HIS F 316 GLN F 383 GLN G 84 GLN G 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15200 Z= 0.167 Angle : 0.601 15.351 20734 Z= 0.258 Chirality : 0.042 0.199 2147 Planarity : 0.004 0.045 2582 Dihedral : 18.961 167.561 2393 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.16 % Allowed : 11.58 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1773 helix: 1.11 (0.17), residues: 931 sheet: -1.34 (0.57), residues: 77 loop : 0.40 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 147 HIS 0.006 0.001 HIS F 212 PHE 0.018 0.001 PHE B 216 TYR 0.013 0.001 TYR F 399 ARG 0.006 0.000 ARG G 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 219 time to evaluate : 1.627 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8854 (mtp) cc_final: 0.8327 (mtp) REVERT: A 47 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7888 (mm) REVERT: A 122 TRP cc_start: 0.7103 (m100) cc_final: 0.5771 (m100) REVERT: B 10 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6627 (mt-10) REVERT: B 20 HIS cc_start: 0.8749 (t-90) cc_final: 0.8492 (t70) REVERT: B 92 MET cc_start: 0.8018 (mmt) cc_final: 0.7746 (tpt) REVERT: B 180 LEU cc_start: 0.8691 (tp) cc_final: 0.8257 (tp) REVERT: B 239 LYS cc_start: 0.7974 (mttt) cc_final: 0.7697 (mtpt) REVERT: B 260 LEU cc_start: 0.7396 (mt) cc_final: 0.7106 (mp) REVERT: B 317 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6690 (mt) REVERT: B 416 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7813 (mmtp) REVERT: C 29 GLU cc_start: 0.7470 (tt0) cc_final: 0.7212 (mm-30) REVERT: C 74 GLU cc_start: 0.7247 (tt0) cc_final: 0.6531 (mm-30) REVERT: C 83 ASP cc_start: 0.7689 (p0) cc_final: 0.7379 (p0) REVERT: C 180 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7503 (ttp-110) REVERT: C 189 ASP cc_start: 0.6867 (p0) cc_final: 0.6129 (t0) REVERT: C 214 ASP cc_start: 0.7261 (m-30) cc_final: 0.7016 (m-30) REVERT: D 85 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.6873 (mt) REVERT: F 6 HIS cc_start: 0.8377 (p-80) cc_final: 0.8036 (p90) REVERT: F 137 LEU cc_start: 0.7936 (mt) cc_final: 0.7449 (mt) REVERT: F 239 LYS cc_start: 0.7930 (mttt) cc_final: 0.7452 (mttm) REVERT: F 313 TRP cc_start: 0.5477 (m-90) cc_final: 0.4287 (m-10) REVERT: F 416 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7532 (mmpt) REVERT: G 74 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7286 (mt-10) REVERT: G 136 MET cc_start: 0.6475 (tpp) cc_final: 0.6027 (tpt) REVERT: G 253 PHE cc_start: 0.8024 (m-80) cc_final: 0.6726 (t80) REVERT: G 271 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8256 (ttmm) outliers start: 31 outliers final: 11 residues processed: 233 average time/residue: 1.0662 time to fit residues: 277.7500 Evaluate side-chains 231 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 212 MET Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 104 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN F 383 GLN G 84 GLN G 222 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15200 Z= 0.257 Angle : 0.662 17.917 20734 Z= 0.285 Chirality : 0.044 0.238 2147 Planarity : 0.005 0.046 2582 Dihedral : 19.146 173.473 2393 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.30 % Allowed : 11.65 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1773 helix: 0.89 (0.17), residues: 937 sheet: -1.23 (0.57), residues: 77 loop : 0.29 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 147 HIS 0.011 0.001 HIS B 212 PHE 0.021 0.002 PHE B 216 TYR 0.017 0.002 TYR F 399 ARG 0.006 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8874 (mtp) cc_final: 0.8508 (mtp) REVERT: A 47 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7868 (mm) REVERT: A 122 TRP cc_start: 0.7099 (m100) cc_final: 0.5758 (m100) REVERT: A 170 ASN cc_start: 0.8170 (m-40) cc_final: 0.7807 (m-40) REVERT: B 10 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6555 (mt-10) REVERT: B 20 HIS cc_start: 0.8768 (t-90) cc_final: 0.8492 (t70) REVERT: B 92 MET cc_start: 0.7946 (mmt) cc_final: 0.7731 (tpt) REVERT: B 180 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8403 (tp) REVERT: B 239 LYS cc_start: 0.7986 (mttt) cc_final: 0.7670 (mtpt) REVERT: B 260 LEU cc_start: 0.7447 (mt) cc_final: 0.7194 (mp) REVERT: B 317 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6573 (mt) REVERT: B 416 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7813 (mmtm) REVERT: C 83 ASP cc_start: 0.7678 (p0) cc_final: 0.7446 (OUTLIER) REVERT: C 180 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7582 (ttm-80) REVERT: C 189 ASP cc_start: 0.6858 (p0) cc_final: 0.6128 (t0) REVERT: C 214 ASP cc_start: 0.7294 (m-30) cc_final: 0.7039 (m-30) REVERT: D 85 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6643 (mt) REVERT: F 6 HIS cc_start: 0.8322 (p-80) cc_final: 0.8066 (p90) REVERT: F 17 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7919 (mtpp) REVERT: F 137 LEU cc_start: 0.7980 (mt) cc_final: 0.7486 (mt) REVERT: F 239 LYS cc_start: 0.7983 (mttt) cc_final: 0.7540 (mttm) REVERT: F 245 TRP cc_start: 0.8474 (t-100) cc_final: 0.8214 (t-100) REVERT: F 313 TRP cc_start: 0.5589 (m-90) cc_final: 0.4400 (m-10) REVERT: F 416 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7623 (mmpt) REVERT: G 74 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7789 (mt-10) REVERT: G 136 MET cc_start: 0.6639 (tpp) cc_final: 0.6279 (tpt) REVERT: G 253 PHE cc_start: 0.8091 (m-80) cc_final: 0.6798 (t80) REVERT: G 271 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7720 (ttpp) outliers start: 33 outliers final: 19 residues processed: 236 average time/residue: 1.0041 time to fit residues: 265.4796 Evaluate side-chains 239 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 216 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 212 MET Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 132 optimal weight: 0.0040 chunk 153 optimal weight: 4.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 GLN C 183 GLN C 227 HIS F 316 GLN F 383 GLN G 84 GLN G 118 ASN G 222 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15200 Z= 0.206 Angle : 0.625 17.201 20734 Z= 0.270 Chirality : 0.043 0.228 2147 Planarity : 0.004 0.046 2582 Dihedral : 18.878 178.518 2393 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.16 % Allowed : 12.06 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1773 helix: 0.87 (0.17), residues: 940 sheet: -1.26 (0.56), residues: 79 loop : 0.21 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 147 HIS 0.008 0.001 HIS B 212 PHE 0.021 0.002 PHE B 216 TYR 0.015 0.001 TYR F 399 ARG 0.005 0.000 ARG G 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8866 (mtp) cc_final: 0.8498 (mtp) REVERT: A 47 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7872 (mm) REVERT: A 122 TRP cc_start: 0.7131 (m100) cc_final: 0.5822 (m100) REVERT: B 20 HIS cc_start: 0.8756 (t-90) cc_final: 0.8482 (t70) REVERT: B 239 LYS cc_start: 0.8037 (mttt) cc_final: 0.7721 (mtpt) REVERT: B 260 LEU cc_start: 0.7391 (mt) cc_final: 0.7166 (mp) REVERT: B 317 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6674 (mt) REVERT: B 416 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7700 (mmtp) REVERT: C 74 GLU cc_start: 0.7291 (tt0) cc_final: 0.6573 (mm-30) REVERT: C 180 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7557 (ttm-80) REVERT: C 189 ASP cc_start: 0.6860 (p0) cc_final: 0.6115 (t0) REVERT: C 214 ASP cc_start: 0.7308 (m-30) cc_final: 0.7050 (m-30) REVERT: D 85 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6545 (mt) REVERT: F 6 HIS cc_start: 0.8296 (p-80) cc_final: 0.8065 (p90) REVERT: F 17 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7923 (mtpp) REVERT: F 137 LEU cc_start: 0.7968 (mt) cc_final: 0.7521 (mt) REVERT: F 239 LYS cc_start: 0.7965 (mttt) cc_final: 0.7585 (mttm) REVERT: F 313 TRP cc_start: 0.5614 (m-90) cc_final: 0.4380 (m-10) REVERT: F 416 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7547 (mmpt) REVERT: G 74 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7452 (mt-10) REVERT: G 136 MET cc_start: 0.6729 (tpp) cc_final: 0.6420 (tpt) REVERT: G 253 PHE cc_start: 0.8060 (m-80) cc_final: 0.6786 (t80) REVERT: G 271 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7685 (ttpp) outliers start: 31 outliers final: 20 residues processed: 227 average time/residue: 1.0272 time to fit residues: 261.5069 Evaluate side-chains 230 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 206 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 148 optimal weight: 0.0370 chunk 156 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 GLN F 383 GLN G 222 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15200 Z= 0.174 Angle : 0.609 16.405 20734 Z= 0.262 Chirality : 0.042 0.206 2147 Planarity : 0.004 0.045 2582 Dihedral : 18.592 167.455 2393 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.09 % Allowed : 12.48 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1773 helix: 0.97 (0.17), residues: 935 sheet: -1.20 (0.57), residues: 79 loop : 0.24 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 147 HIS 0.006 0.001 HIS F 212 PHE 0.018 0.001 PHE B 216 TYR 0.014 0.001 TYR F 399 ARG 0.004 0.000 ARG G 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8854 (mtp) cc_final: 0.8436 (mtp) REVERT: A 122 TRP cc_start: 0.7168 (m100) cc_final: 0.5884 (m100) REVERT: B 1 MET cc_start: 0.2717 (OUTLIER) cc_final: 0.2043 (ttp) REVERT: B 20 HIS cc_start: 0.8754 (t-90) cc_final: 0.8480 (t70) REVERT: B 239 LYS cc_start: 0.8024 (mttt) cc_final: 0.7671 (mtpt) REVERT: B 317 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6560 (mt) REVERT: B 416 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7667 (mmtp) REVERT: C 74 GLU cc_start: 0.7303 (tt0) cc_final: 0.6568 (mm-30) REVERT: C 83 ASP cc_start: 0.7794 (p0) cc_final: 0.7572 (p0) REVERT: C 180 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7547 (ttm-80) REVERT: C 189 ASP cc_start: 0.6900 (p0) cc_final: 0.6134 (t0) REVERT: C 214 ASP cc_start: 0.7291 (m-30) cc_final: 0.7029 (m-30) REVERT: D 85 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6505 (mt) REVERT: F 6 HIS cc_start: 0.8316 (p-80) cc_final: 0.8052 (p90) REVERT: F 17 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7925 (mtpp) REVERT: F 137 LEU cc_start: 0.7982 (mt) cc_final: 0.7582 (mt) REVERT: F 239 LYS cc_start: 0.7939 (mttt) cc_final: 0.7576 (mttm) REVERT: F 313 TRP cc_start: 0.5541 (m-90) cc_final: 0.4382 (m-10) REVERT: F 416 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7605 (mmpt) REVERT: G 74 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7456 (mt-10) REVERT: G 136 MET cc_start: 0.6746 (tpp) cc_final: 0.6451 (tpt) REVERT: G 253 PHE cc_start: 0.8048 (m-80) cc_final: 0.6804 (t80) REVERT: G 271 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7673 (ttpp) outliers start: 30 outliers final: 17 residues processed: 225 average time/residue: 1.0402 time to fit residues: 262.1367 Evaluate side-chains 229 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.0670 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 GLN F 383 GLN G 118 ASN G 222 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15200 Z= 0.171 Angle : 0.606 15.831 20734 Z= 0.259 Chirality : 0.042 0.203 2147 Planarity : 0.004 0.045 2582 Dihedral : 18.165 167.375 2393 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.88 % Allowed : 12.76 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1773 helix: 1.07 (0.17), residues: 932 sheet: -1.18 (0.57), residues: 79 loop : 0.27 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 147 HIS 0.006 0.001 HIS F 212 PHE 0.018 0.001 PHE B 216 TYR 0.014 0.001 TYR F 399 ARG 0.003 0.000 ARG G 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8846 (mtp) cc_final: 0.8400 (mtp) REVERT: A 122 TRP cc_start: 0.7014 (m100) cc_final: 0.5774 (m100) REVERT: B 1 MET cc_start: 0.3155 (OUTLIER) cc_final: 0.2204 (ttp) REVERT: B 20 HIS cc_start: 0.8756 (t-90) cc_final: 0.8474 (t70) REVERT: B 239 LYS cc_start: 0.7932 (mttt) cc_final: 0.7581 (mtpt) REVERT: B 317 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6543 (mt) REVERT: B 416 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7647 (mmtp) REVERT: C 74 GLU cc_start: 0.7290 (tt0) cc_final: 0.6563 (mm-30) REVERT: C 180 ARG cc_start: 0.7855 (ttp-110) cc_final: 0.7493 (ttm-80) REVERT: C 189 ASP cc_start: 0.6899 (p0) cc_final: 0.6145 (t0) REVERT: D 85 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6458 (mt) REVERT: F 6 HIS cc_start: 0.8302 (p-80) cc_final: 0.8052 (p90) REVERT: F 17 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7935 (mtpp) REVERT: F 137 LEU cc_start: 0.8000 (mt) cc_final: 0.7640 (mt) REVERT: F 239 LYS cc_start: 0.7958 (mttt) cc_final: 0.7573 (mttm) REVERT: F 313 TRP cc_start: 0.5497 (m-90) cc_final: 0.4290 (m-10) REVERT: F 383 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: F 416 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7556 (mmpt) REVERT: G 74 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7352 (mt-10) REVERT: G 118 ASN cc_start: 0.7168 (t0) cc_final: 0.6960 (t0) REVERT: G 136 MET cc_start: 0.6762 (tpp) cc_final: 0.6456 (tpt) REVERT: G 253 PHE cc_start: 0.8077 (m-80) cc_final: 0.6806 (t80) REVERT: G 271 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7685 (ttpp) outliers start: 27 outliers final: 16 residues processed: 225 average time/residue: 1.0514 time to fit residues: 265.1871 Evaluate side-chains 229 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN F 316 GLN G 84 GLN G 222 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.151349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.103323 restraints weight = 15969.815| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.68 r_work: 0.2773 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 15200 Z= 0.204 Angle : 0.816 59.187 20734 Z= 0.422 Chirality : 0.042 0.201 2147 Planarity : 0.004 0.045 2582 Dihedral : 18.163 167.375 2393 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.74 % Allowed : 13.25 % Favored : 85.01 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1773 helix: 1.07 (0.17), residues: 932 sheet: -1.18 (0.57), residues: 79 loop : 0.27 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 147 HIS 0.006 0.001 HIS F 212 PHE 0.018 0.001 PHE B 216 TYR 0.014 0.001 TYR F 399 ARG 0.004 0.000 ARG G 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5223.12 seconds wall clock time: 93 minutes 0.08 seconds (5580.08 seconds total)