Starting phenix.real_space_refine on Fri Sep 27 09:05:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/09_2024/8asi_15616.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/09_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_15616/09_2024/8asi_15616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/09_2024/8asi_15616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/09_2024/8asi_15616.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asi_15616/09_2024/8asi_15616.cif" } 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. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.93, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.43 Conformation dependent library (CDL) restraints added in 1.9 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... Secondary structure from input PDB file: 76 helices and 13 sheets defined 57.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 37 Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.857A pdb=" N LEU A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 66 removed outlier: 3.750A pdb=" N VAL B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.707A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 119 removed outlier: 3.876A pdb=" N SER B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 149 Processing helix chain 'B' and resid 152 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 172 through 182 Processing helix chain 'B' and resid 187 through 218 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 244 through 270 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 276 through 281 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 298 through 308 removed outlier: 4.123A pdb=" N PHE B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 Processing helix chain 'B' and resid 327 through 345 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) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 362 through 381 removed outlier: 3.577A pdb=" N TYR B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.714A pdb=" N PHE B 404 " --> pdb=" O TRP B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 415 removed outlier: 4.072A pdb=" N ALA B 413 " --> pdb=" O PRO B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 432 Processing helix chain 'C' and resid 43 through 57 Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 139 through 146 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 225 through 242 Processing helix chain 'C' and resid 244 through 276 removed outlier: 3.611A pdb=" N GLY C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 278 No H-bonds generated for 'chain 'C' and resid 277 through 278' Processing helix chain 'D' and resid 79 through 79 No H-bonds generated for 'chain 'D' and resid 79 through 79' Processing helix chain 'D' and resid 80 through 103 removed outlier: 3.739A pdb=" N ARG D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 37 removed outlier: 3.572A pdb=" N ALA E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 78 through 88 removed outlier: 3.814A pdb=" N VAL E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 24 through 35 Processing helix chain 'F' and resid 42 through 45 Processing helix chain 'F' and resid 46 through 66 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 89 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 125 through 149 removed outlier: 3.571A pdb=" N LEU F 149 " --> pdb=" O MET F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 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 182 Processing helix chain 'F' and resid 187 through 220 Proline residue: F 202 - end of helix Processing helix chain 'F' and resid 233 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 270 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 276 through 281 Processing helix chain 'F' and resid 295 through 297 No H-bonds generated for 'chain 'F' and resid 295 through 297' Processing helix chain 'F' and resid 298 through 308 removed outlier: 4.092A pdb=" N PHE F 308 " --> pdb=" O ILE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 322 Processing helix chain 'F' and resid 327 through 345 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) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 356 through 360 Processing helix chain 'F' and resid 362 through 382 removed outlier: 3.636A pdb=" N TYR F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA F 382 " --> pdb=" O THR F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 406 removed outlier: 3.734A pdb=" N PHE F 404 " --> pdb=" O TRP F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 415 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 423 through 432 Processing helix chain 'G' and resid 43 through 57 Processing helix chain 'G' and resid 58 through 61 Processing helix chain 'G' and resid 68 through 74 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 148 through 158 Processing helix chain 'G' and resid 225 through 242 Processing helix chain 'G' and resid 244 through 278 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 83 through 105 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=AA1, first strand: chain 'A' and resid 52 through 54 removed outlier: 5.915A pdb=" N VAL A 52 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing sheet with id=AA2, 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=AA3, first strand: chain 'A' and resid 147 through 148 removed outlier: 6.595A pdb=" N HIS A 155 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA5, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AA6, first strand: chain 'C' and resid 177 through 179 Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 193 Processing sheet with id=AA8, first strand: chain 'E' and resid 50 through 53 Processing sheet with id=AA9, first strand: chain 'E' and resid 62 through 67 Processing sheet with id=AB1, first strand: chain 'E' and resid 145 through 149 removed outlier: 3.687A pdb=" N SER E 154 " --> pdb=" O CYS E 149 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS E 155 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 36 through 38 Processing sheet with id=AB3, first strand: chain 'G' and resid 93 through 95 Processing sheet with id=AB4, first strand: chain 'G' and resid 177 through 179 751 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 4.80 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: 0.00 - 8.96: 20677 8.96 - 17.93: 52 17.93 - 26.89: 4 26.89 - 35.86: 0 35.86 - 44.82: 1 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: 11251 3.12 - 3.71: 23788 3.71 - 4.31: 34332 4.31 - 4.90: 55890 Nonbonded interactions: 125290 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 125285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.580 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.910 ------------------------------------------------------------------------------- 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= 0.602 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 : 1.538 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: 1.0617 time to fit residues: 335.6250 Evaluate side-chains 211 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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: 3.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 0.0570 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 F 319 ASN F 383 GLN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1833 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= 0.200 Angle : 0.704 16.899 20734 Z= 0.323 Chirality : 0.045 0.223 2147 Planarity : 0.005 0.047 2582 Dihedral : 22.504 178.279 2395 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.60 % Allowed : 8.37 % 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: 0.84 (0.20), residues: 1773 helix: 1.15 (0.17), residues: 923 sheet: -1.88 (0.52), residues: 72 loop : 0.24 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 147 HIS 0.006 0.001 HIS B 291 PHE 0.040 0.002 PHE D 88 TYR 0.015 0.001 TYR F 399 ARG 0.004 0.001 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 261 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 238 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9045 (mtp) cc_final: 0.8640 (mtp) REVERT: A 70 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8016 (mtmp) REVERT: A 77 ARG cc_start: 0.6596 (mtm180) cc_final: 0.5993 (mtp180) REVERT: A 180 ASP cc_start: 0.5872 (OUTLIER) cc_final: 0.5634 (p0) REVERT: B 1 MET cc_start: 0.2353 (OUTLIER) cc_final: 0.1676 (ttp) REVERT: B 6 HIS cc_start: 0.7996 (p-80) cc_final: 0.7700 (p-80) REVERT: B 92 MET cc_start: 0.8022 (mmt) cc_final: 0.7773 (tpt) REVERT: B 133 MET cc_start: 0.8568 (mmm) cc_final: 0.8306 (mmm) REVERT: B 239 LYS cc_start: 0.7870 (mttt) cc_final: 0.7586 (mtpt) REVERT: B 343 MET cc_start: 0.8371 (ttp) cc_final: 0.8145 (ttp) REVERT: B 416 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7826 (mmtp) REVERT: C 74 GLU cc_start: 0.7341 (tt0) cc_final: 0.6454 (mm-30) REVERT: C 140 ILE cc_start: 0.6996 (pt) cc_final: 0.6786 (pp) REVERT: C 180 ARG cc_start: 0.8075 (ttp-110) cc_final: 0.7708 (ttp-110) REVERT: C 189 ASP cc_start: 0.6461 (p0) cc_final: 0.5764 (t0) REVERT: C 214 ASP cc_start: 0.7354 (m-30) cc_final: 0.7094 (m-30) REVERT: F 137 LEU cc_start: 0.7864 (mt) cc_final: 0.7438 (mt) REVERT: F 239 LYS cc_start: 0.8062 (mttt) cc_final: 0.7586 (mttm) REVERT: F 313 TRP cc_start: 0.5705 (m-90) cc_final: 0.4449 (m-10) REVERT: F 414 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7749 (mp) REVERT: G 136 MET cc_start: 0.6481 (tpp) cc_final: 0.6263 (tpt) REVERT: G 179 ASN cc_start: 0.8773 (t0) cc_final: 0.8457 (t0) outliers start: 23 outliers final: 8 residues processed: 249 average time/residue: 1.0319 time to fit residues: 288.8586 Evaluate side-chains 224 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL 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 431 HIS 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 F residue 414 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: 0.9990 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 383 GLN G 84 GLN G 118 ASN G 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15200 Z= 0.216 Angle : 0.669 16.361 20734 Z= 0.300 Chirality : 0.045 0.186 2147 Planarity : 0.005 0.049 2582 Dihedral : 21.344 173.000 2395 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.86 % Allowed : 9.27 % Favored : 87.87 % 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: 1.02 (0.20), residues: 1773 helix: 1.27 (0.17), residues: 941 sheet: -1.59 (0.56), residues: 72 loop : 0.33 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 147 HIS 0.018 0.001 HIS B 431 PHE 0.026 0.002 PHE D 88 TYR 0.015 0.001 TYR F 399 ARG 0.004 0.000 ARG F 12 *********************** 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 274 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 233 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9057 (mtp) cc_final: 0.8622 (mtp) REVERT: A 180 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5626 (p0) REVERT: B 6 HIS cc_start: 0.7789 (p-80) cc_final: 0.7564 (p-80) REVERT: B 20 HIS cc_start: 0.8754 (t-90) cc_final: 0.8429 (t70) REVERT: B 92 MET cc_start: 0.7994 (mmt) cc_final: 0.7706 (tpt) REVERT: B 133 MET cc_start: 0.8582 (mmm) cc_final: 0.8311 (mmm) REVERT: B 239 LYS cc_start: 0.7896 (mttt) cc_final: 0.7561 (mtpt) REVERT: B 260 LEU cc_start: 0.7473 (mt) cc_final: 0.7139 (mp) REVERT: B 317 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6629 (mt) REVERT: B 416 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7846 (mmtp) REVERT: B 423 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7777 (p) REVERT: B 426 GLU cc_start: 0.7506 (tt0) cc_final: 0.7256 (tt0) REVERT: B 431 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.6723 (m170) REVERT: C 74 GLU cc_start: 0.7446 (tt0) cc_final: 0.6503 (mm-30) REVERT: C 99 THR cc_start: 0.6482 (OUTLIER) cc_final: 0.6212 (p) REVERT: C 140 ILE cc_start: 0.7047 (pt) cc_final: 0.6778 (pp) REVERT: C 180 ARG cc_start: 0.8050 (ttp-110) cc_final: 0.7680 (ttp-110) REVERT: C 189 ASP cc_start: 0.6370 (p0) cc_final: 0.5979 (t0) REVERT: C 207 MET cc_start: 0.8182 (ttm) cc_final: 0.7703 (ttm) REVERT: C 214 ASP cc_start: 0.7378 (m-30) cc_final: 0.7100 (m-30) REVERT: E 90 LEU cc_start: 0.5259 (tm) cc_final: 0.4944 (tt) REVERT: F 137 LEU cc_start: 0.7926 (mt) cc_final: 0.7464 (mt) REVERT: F 239 LYS cc_start: 0.8038 (mttt) cc_final: 0.7578 (mttm) REVERT: F 270 MET cc_start: 0.8836 (ptp) cc_final: 0.8586 (ptp) REVERT: F 313 TRP cc_start: 0.5694 (m-90) cc_final: 0.4437 (m-10) REVERT: F 432 TYR cc_start: 0.5386 (m-80) cc_final: 0.4734 (m-80) REVERT: G 136 MET cc_start: 0.6518 (tpp) cc_final: 0.6267 (tpt) REVERT: G 232 ASP cc_start: 0.8425 (m-30) cc_final: 0.7938 (m-30) REVERT: G 246 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7291 (mpp) REVERT: G 271 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7730 (ttpp) outliers start: 41 outliers final: 12 residues processed: 252 average time/residue: 0.9699 time to fit residues: 275.0549 Evaluate side-chains 227 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 208 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 212 MET Chi-restraints excluded: chain G residue 246 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: 0.7980 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN C 171 HIS C 183 GLN F 383 GLN G 84 GLN G 118 ASN G 142 GLN G 179 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2573 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= 0.182 Angle : 0.634 16.399 20734 Z= 0.281 Chirality : 0.043 0.183 2147 Planarity : 0.005 0.048 2582 Dihedral : 20.281 169.566 2393 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.37 % Allowed : 10.32 % Favored : 87.31 % 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: 1.12 (0.20), residues: 1773 helix: 1.37 (0.17), residues: 949 sheet: -1.41 (0.54), residues: 77 loop : 0.33 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 147 HIS 0.007 0.001 HIS B 431 PHE 0.024 0.001 PHE D 88 TYR 0.014 0.001 TYR F 399 ARG 0.002 0.000 ARG G 49 *********************** 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 259 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9028 (mtp) cc_final: 0.8595 (mtp) REVERT: B 1 MET cc_start: 0.2640 (OUTLIER) cc_final: 0.1962 (ttp) REVERT: B 20 HIS cc_start: 0.8777 (t-90) cc_final: 0.8471 (t70) REVERT: B 92 MET cc_start: 0.7984 (mmt) cc_final: 0.7672 (tpt) REVERT: B 180 LEU cc_start: 0.8674 (tp) cc_final: 0.8297 (tp) REVERT: B 239 LYS cc_start: 0.7914 (mttt) cc_final: 0.7585 (mtpt) REVERT: B 317 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6664 (mt) REVERT: B 416 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7856 (mmtp) REVERT: B 423 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7656 (p) REVERT: C 52 GLN cc_start: 0.8020 (tt0) cc_final: 0.7498 (tt0) REVERT: C 70 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.6527 (ptt-90) REVERT: C 74 GLU cc_start: 0.7292 (tt0) cc_final: 0.6480 (mm-30) REVERT: C 180 ARG cc_start: 0.8003 (ttp-110) cc_final: 0.7544 (ttp-110) REVERT: C 189 ASP cc_start: 0.6498 (p0) cc_final: 0.5941 (t0) REVERT: C 207 MET cc_start: 0.8280 (ttm) cc_final: 0.7855 (ttm) REVERT: C 214 ASP cc_start: 0.7309 (m-30) cc_final: 0.7051 (m-30) REVERT: F 137 LEU cc_start: 0.7965 (mt) cc_final: 0.7483 (mt) REVERT: F 239 LYS cc_start: 0.7976 (mttt) cc_final: 0.7556 (mttm) REVERT: F 252 ASP cc_start: 0.7644 (m-30) cc_final: 0.7436 (m-30) REVERT: F 270 MET cc_start: 0.8865 (ptp) cc_final: 0.8596 (ptp) REVERT: F 313 TRP cc_start: 0.5608 (m-90) cc_final: 0.4438 (m-10) REVERT: F 350 ASP cc_start: 0.8344 (t0) cc_final: 0.8049 (t70) REVERT: F 432 TYR cc_start: 0.5463 (m-80) cc_final: 0.4971 (m-80) REVERT: G 136 MET cc_start: 0.6474 (tpp) cc_final: 0.6187 (tpt) REVERT: G 271 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7721 (ttpp) outliers start: 34 outliers final: 12 residues processed: 246 average time/residue: 1.0856 time to fit residues: 298.9437 Evaluate side-chains 222 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL 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 108 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain E residue 125 MET 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: 3.9990 chunk 96 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 151 optimal weight: 0.0170 chunk 42 optimal weight: 0.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2744 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= 0.259 Angle : 0.680 17.853 20734 Z= 0.301 Chirality : 0.045 0.192 2147 Planarity : 0.005 0.049 2582 Dihedral : 19.870 173.816 2393 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.65 % Allowed : 11.16 % Favored : 86.19 % 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: 0.97 (0.20), residues: 1773 helix: 1.29 (0.17), residues: 945 sheet: -1.19 (0.61), residues: 62 loop : 0.12 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 147 HIS 0.011 0.001 HIS B 212 PHE 0.025 0.002 PHE D 88 TYR 0.018 0.002 TYR F 399 ARG 0.004 0.000 ARG F 114 *********************** 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 257 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 219 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9067 (mtp) cc_final: 0.8729 (mtp) REVERT: A 70 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7989 (mtmp) REVERT: B 1 MET cc_start: 0.2367 (OUTLIER) cc_final: 0.1711 (ttp) REVERT: B 20 HIS cc_start: 0.8787 (t-90) cc_final: 0.8461 (t70) REVERT: B 92 MET cc_start: 0.7950 (mmt) cc_final: 0.7732 (tpt) REVERT: B 180 LEU cc_start: 0.8719 (tp) cc_final: 0.8343 (tp) REVERT: B 239 LYS cc_start: 0.7932 (mttt) cc_final: 0.7570 (mtpt) REVERT: B 317 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6600 (mt) REVERT: B 416 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7850 (mmtp) REVERT: B 432 TYR cc_start: 0.6973 (m-80) cc_final: 0.6150 (m-80) REVERT: C 70 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.6508 (ptt-90) REVERT: C 180 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7509 (ttp-110) REVERT: C 189 ASP cc_start: 0.6465 (p0) cc_final: 0.5889 (t0) REVERT: C 207 MET cc_start: 0.8382 (ttm) cc_final: 0.7957 (ttm) REVERT: C 214 ASP cc_start: 0.7310 (m-30) cc_final: 0.7054 (m-30) REVERT: E 90 LEU cc_start: 0.5119 (tm) cc_final: 0.4788 (tt) REVERT: F 137 LEU cc_start: 0.7981 (mt) cc_final: 0.7495 (mt) REVERT: F 238 GLN cc_start: 0.7702 (mt0) cc_final: 0.7445 (mt0) REVERT: F 239 LYS cc_start: 0.7998 (mttt) cc_final: 0.7595 (mttm) REVERT: F 270 MET cc_start: 0.8922 (ptp) cc_final: 0.8573 (ptp) REVERT: F 272 ASN cc_start: 0.8624 (m-40) cc_final: 0.8406 (m-40) REVERT: F 313 TRP cc_start: 0.5602 (m-90) cc_final: 0.4429 (m-10) REVERT: F 394 LEU cc_start: 0.8534 (tt) cc_final: 0.8186 (tm) REVERT: G 136 MET cc_start: 0.6613 (tpp) cc_final: 0.6261 (tpt) REVERT: G 253 PHE cc_start: 0.8122 (m-80) cc_final: 0.6786 (t80) REVERT: G 271 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7718 (ttpp) outliers start: 38 outliers final: 20 residues processed: 235 average time/residue: 1.0471 time to fit residues: 274.6852 Evaluate side-chains 235 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 70 ARG 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 116 LEU Chi-restraints excluded: chain E residue 125 MET 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 261 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 212 MET 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: 0.7980 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 169 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 276 HIS C 46 GLN C 183 GLN F 383 GLN G 118 ASN G 222 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15200 Z= 0.179 Angle : 0.622 16.826 20734 Z= 0.272 Chirality : 0.042 0.175 2147 Planarity : 0.005 0.047 2582 Dihedral : 19.377 179.086 2393 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.16 % Allowed : 11.72 % Favored : 86.12 % 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: 1.19 (0.20), residues: 1773 helix: 1.49 (0.17), residues: 941 sheet: -1.00 (0.59), residues: 67 loop : 0.20 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 147 HIS 0.006 0.001 HIS G 227 PHE 0.025 0.001 PHE D 88 TYR 0.013 0.001 TYR F 399 ARG 0.002 0.000 ARG C 86 *********************** 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 252 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 221 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8978 (mtp) cc_final: 0.8599 (mtp) REVERT: A 47 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7793 (mm) REVERT: A 70 LYS cc_start: 0.8335 (mtmt) cc_final: 0.8076 (mtmp) REVERT: B 10 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6649 (mt-10) REVERT: B 20 HIS cc_start: 0.8782 (t-90) cc_final: 0.8457 (t70) REVERT: B 180 LEU cc_start: 0.8816 (tp) cc_final: 0.8469 (tp) REVERT: B 239 LYS cc_start: 0.7932 (mttt) cc_final: 0.7658 (mtpt) REVERT: B 317 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6573 (mt) REVERT: B 343 MET cc_start: 0.8530 (ttp) cc_final: 0.8309 (ttp) REVERT: B 416 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7857 (mmtp) REVERT: B 432 TYR cc_start: 0.6915 (m-80) cc_final: 0.6106 (m-80) REVERT: C 70 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.6531 (ptt-90) REVERT: C 180 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.7456 (ttp-110) REVERT: C 189 ASP cc_start: 0.6433 (p0) cc_final: 0.5892 (t0) REVERT: C 207 MET cc_start: 0.8311 (ttp) cc_final: 0.7894 (ttm) REVERT: C 214 ASP cc_start: 0.7283 (m-30) cc_final: 0.7021 (m-30) REVERT: E 90 LEU cc_start: 0.5068 (tm) cc_final: 0.4754 (tt) REVERT: F 137 LEU cc_start: 0.7988 (mt) cc_final: 0.7506 (mt) REVERT: F 239 LYS cc_start: 0.7957 (mttt) cc_final: 0.7584 (mttm) REVERT: F 245 TRP cc_start: 0.8425 (t-100) cc_final: 0.8107 (t-100) REVERT: F 270 MET cc_start: 0.8900 (ptp) cc_final: 0.8592 (ptp) REVERT: F 313 TRP cc_start: 0.5542 (m-90) cc_final: 0.4387 (m-10) REVERT: F 394 LEU cc_start: 0.8545 (tt) cc_final: 0.8191 (tm) REVERT: G 136 MET cc_start: 0.6610 (tpp) cc_final: 0.6366 (tpt) REVERT: G 246 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7318 (mpp) REVERT: G 253 PHE cc_start: 0.8025 (m-80) cc_final: 0.6791 (t80) REVERT: G 271 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7688 (ttpp) outliers start: 31 outliers final: 14 residues processed: 236 average time/residue: 1.0378 time to fit residues: 274.0302 Evaluate side-chains 231 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 212 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 108 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain E residue 125 MET 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 G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 246 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: 0.7980 chunk 96 optimal weight: 7.9990 chunk 123 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN C 46 GLN C 183 GLN F 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 15200 Z= 0.331 Angle : 0.707 18.640 20734 Z= 0.311 Chirality : 0.047 0.179 2147 Planarity : 0.005 0.049 2582 Dihedral : 19.712 178.565 2393 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.72 % Allowed : 11.58 % Favored : 85.70 % 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: 0.85 (0.20), residues: 1773 helix: 1.23 (0.17), residues: 942 sheet: -0.97 (0.60), residues: 70 loop : -0.00 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 147 HIS 0.009 0.001 HIS B 212 PHE 0.024 0.002 PHE D 88 TYR 0.019 0.002 TYR F 399 ARG 0.007 0.001 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 242 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9064 (mtp) cc_final: 0.8763 (mtp) REVERT: A 47 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7773 (mm) REVERT: B 20 HIS cc_start: 0.8793 (t-90) cc_final: 0.8441 (t70) REVERT: B 180 LEU cc_start: 0.8824 (tp) cc_final: 0.8523 (tp) REVERT: B 238 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: B 239 LYS cc_start: 0.7978 (mttt) cc_final: 0.7592 (mtpt) REVERT: B 317 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6535 (mt) REVERT: B 416 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7824 (mmtp) REVERT: B 432 TYR cc_start: 0.6981 (m-80) cc_final: 0.5995 (m-80) REVERT: C 70 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6477 (ptt-90) REVERT: C 180 ARG cc_start: 0.7988 (ttp-110) cc_final: 0.7524 (ttp-110) REVERT: C 189 ASP cc_start: 0.6471 (p0) cc_final: 0.5899 (t0) REVERT: C 214 ASP cc_start: 0.7361 (m-30) cc_final: 0.7084 (m-30) REVERT: F 137 LEU cc_start: 0.7987 (mt) cc_final: 0.7508 (mt) REVERT: F 238 GLN cc_start: 0.7695 (mt0) cc_final: 0.7447 (mt0) REVERT: F 239 LYS cc_start: 0.8008 (mttt) cc_final: 0.7629 (mttm) REVERT: F 270 MET cc_start: 0.8926 (ptp) cc_final: 0.8604 (ptp) REVERT: F 313 TRP cc_start: 0.5625 (m-90) cc_final: 0.4441 (m-10) REVERT: G 271 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7696 (ttpp) outliers start: 39 outliers final: 20 residues processed: 226 average time/residue: 1.0512 time to fit residues: 265.6963 Evaluate side-chains 224 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain C residue 70 ARG 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 116 LEU Chi-restraints excluded: chain E residue 125 MET 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 F residue 278 ASP Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain G residue 199 THR 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: 3.9990 chunk 100 optimal weight: 0.0030 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 153 optimal weight: 0.1980 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 227 HIS F 221 ASN F 383 GLN G 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15200 Z= 0.157 Angle : 0.599 15.227 20734 Z= 0.265 Chirality : 0.042 0.167 2147 Planarity : 0.004 0.047 2582 Dihedral : 19.003 175.154 2393 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.74 % Allowed : 12.62 % Favored : 85.63 % 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: 1.18 (0.20), residues: 1773 helix: 1.53 (0.17), residues: 942 sheet: -0.92 (0.60), residues: 70 loop : 0.11 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 147 HIS 0.006 0.001 HIS G 227 PHE 0.021 0.001 PHE D 88 TYR 0.011 0.001 TYR B 359 ARG 0.002 0.000 ARG A 77 *********************** 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 243 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8993 (mtp) cc_final: 0.8618 (mtp) REVERT: A 47 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7824 (mm) REVERT: A 70 LYS cc_start: 0.8257 (mttp) cc_final: 0.8027 (mtmp) REVERT: B 10 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6710 (mt-10) REVERT: B 20 HIS cc_start: 0.8792 (t-90) cc_final: 0.8504 (t70) REVERT: B 154 MET cc_start: 0.8992 (mmt) cc_final: 0.8702 (mmp) REVERT: B 180 LEU cc_start: 0.8827 (tp) cc_final: 0.8479 (tp) REVERT: B 238 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: B 239 LYS cc_start: 0.7942 (mttt) cc_final: 0.7563 (mtpt) REVERT: B 317 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6559 (mt) REVERT: B 416 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7674 (mmtp) REVERT: B 432 TYR cc_start: 0.7074 (m-80) cc_final: 0.6085 (m-80) REVERT: C 56 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: C 70 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.6523 (ptt-90) REVERT: C 74 GLU cc_start: 0.7213 (tt0) cc_final: 0.6381 (mm-30) REVERT: C 180 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7430 (ttp-110) REVERT: C 189 ASP cc_start: 0.6479 (p0) cc_final: 0.5946 (t0) REVERT: F 137 LEU cc_start: 0.8001 (mt) cc_final: 0.7531 (mt) REVERT: F 239 LYS cc_start: 0.7958 (mttt) cc_final: 0.7635 (mttm) REVERT: F 270 MET cc_start: 0.8858 (ptp) cc_final: 0.8488 (ptp) REVERT: F 313 TRP cc_start: 0.5479 (m-90) cc_final: 0.4347 (m-10) REVERT: F 350 ASP cc_start: 0.8391 (t0) cc_final: 0.8122 (t70) REVERT: F 394 LEU cc_start: 0.8484 (tt) cc_final: 0.8152 (tm) REVERT: G 48 GLN cc_start: 0.7298 (mt0) cc_final: 0.7071 (mt0) REVERT: G 253 PHE cc_start: 0.8007 (m-80) cc_final: 0.6722 (t80) REVERT: G 271 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7667 (ttpp) outliers start: 25 outliers final: 11 residues processed: 233 average time/residue: 1.0789 time to fit residues: 280.4744 Evaluate side-chains 215 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 261 LEU 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: 0.8980 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 0.0870 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 142 optimal weight: 0.5980 chunk 148 optimal weight: 0.0770 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 276 HIS C 46 GLN F 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15200 Z= 0.158 Angle : 0.606 14.637 20734 Z= 0.264 Chirality : 0.042 0.167 2147 Planarity : 0.004 0.044 2582 Dihedral : 18.725 173.617 2393 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.74 % Allowed : 12.90 % 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: 1.30 (0.20), residues: 1773 helix: 1.63 (0.17), residues: 942 sheet: -1.09 (0.57), residues: 80 loop : 0.21 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 147 HIS 0.005 0.001 HIS G 227 PHE 0.020 0.001 PHE D 88 TYR 0.013 0.001 TYR B 359 ARG 0.003 0.000 ARG C 103 *********************** 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 229 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8990 (mtp) cc_final: 0.8556 (mtp) REVERT: A 47 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7851 (mm) REVERT: B 1 MET cc_start: 0.2750 (OUTLIER) cc_final: 0.1871 (ttp) REVERT: B 20 HIS cc_start: 0.8783 (t-90) cc_final: 0.8471 (t70) REVERT: B 154 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8723 (mmp) REVERT: B 180 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8457 (tp) REVERT: B 238 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: B 239 LYS cc_start: 0.7904 (mttt) cc_final: 0.7548 (mtpt) REVERT: B 317 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6560 (mt) REVERT: B 416 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7624 (mmtp) REVERT: C 56 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: C 70 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.6501 (ptt-90) REVERT: C 74 GLU cc_start: 0.7186 (tt0) cc_final: 0.6330 (mm-30) REVERT: C 189 ASP cc_start: 0.6479 (p0) cc_final: 0.5940 (t0) REVERT: F 137 LEU cc_start: 0.7973 (mt) cc_final: 0.7489 (mt) REVERT: F 239 LYS cc_start: 0.7944 (mttt) cc_final: 0.7624 (mttm) REVERT: F 270 MET cc_start: 0.8873 (ptp) cc_final: 0.8493 (ptp) REVERT: F 313 TRP cc_start: 0.5380 (m-90) cc_final: 0.4322 (m-10) REVERT: F 394 LEU cc_start: 0.8501 (tt) cc_final: 0.8158 (tm) REVERT: G 74 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7161 (mm-30) REVERT: G 253 PHE cc_start: 0.7984 (m-80) cc_final: 0.6739 (t80) REVERT: G 271 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7679 (ttpp) outliers start: 25 outliers final: 11 residues processed: 218 average time/residue: 1.0720 time to fit residues: 261.8936 Evaluate side-chains 215 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 212 MET 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: 3.9990 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 0.0050 chunk 115 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN F 383 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15200 Z= 0.221 Angle : 0.649 16.874 20734 Z= 0.282 Chirality : 0.044 0.173 2147 Planarity : 0.005 0.046 2582 Dihedral : 18.769 178.266 2393 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.60 % Allowed : 13.53 % Favored : 84.87 % 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: 1.20 (0.20), residues: 1773 helix: 1.56 (0.17), residues: 940 sheet: -1.01 (0.58), residues: 80 loop : 0.14 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 147 HIS 0.008 0.001 HIS B 212 PHE 0.027 0.002 PHE G 258 TYR 0.016 0.001 TYR F 399 ARG 0.005 0.000 ARG G 103 ********************** 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 224 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9026 (mtp) cc_final: 0.8668 (mtp) REVERT: A 47 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7832 (mm) REVERT: B 1 MET cc_start: 0.2711 (OUTLIER) cc_final: 0.1857 (ttp) REVERT: B 10 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6752 (mt-10) REVERT: B 20 HIS cc_start: 0.8787 (t-90) cc_final: 0.8455 (t70) REVERT: B 180 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8483 (tp) REVERT: B 236 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 238 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7302 (mt0) REVERT: B 239 LYS cc_start: 0.7924 (mttt) cc_final: 0.7554 (mtpt) REVERT: B 317 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6575 (mt) REVERT: B 416 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7635 (mmtp) REVERT: C 56 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: C 70 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6548 (ptt-90) REVERT: C 189 ASP cc_start: 0.6486 (p0) cc_final: 0.5914 (t0) REVERT: C 214 ASP cc_start: 0.7525 (m-30) cc_final: 0.7126 (m-30) REVERT: F 137 LEU cc_start: 0.7988 (mt) cc_final: 0.7533 (mt) REVERT: F 238 GLN cc_start: 0.7631 (mt0) cc_final: 0.7377 (mt0) REVERT: F 239 LYS cc_start: 0.7973 (mttt) cc_final: 0.7639 (mttm) REVERT: F 270 MET cc_start: 0.8929 (ptp) cc_final: 0.8609 (ptp) REVERT: F 313 TRP cc_start: 0.5406 (m-90) cc_final: 0.4316 (m-10) REVERT: F 394 LEU cc_start: 0.8529 (tt) cc_final: 0.8189 (tm) REVERT: G 253 PHE cc_start: 0.8055 (m-80) cc_final: 0.6828 (t80) REVERT: G 271 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7676 (ttpp) outliers start: 23 outliers final: 10 residues processed: 213 average time/residue: 1.1260 time to fit residues: 269.5257 Evaluate side-chains 216 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 261 LEU 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: 1.9990 chunk 42 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 chunk 142 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN C 46 GLN F 383 GLN G 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.150547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.102942 restraints weight = 15940.569| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.70 r_work: 0.2765 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3282 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= 0.177 Angle : 0.627 16.096 20734 Z= 0.271 Chirality : 0.042 0.173 2147 Planarity : 0.005 0.045 2582 Dihedral : 18.610 179.166 2393 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.53 % Allowed : 13.53 % Favored : 84.94 % 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: 1.26 (0.20), residues: 1773 helix: 1.61 (0.17), residues: 940 sheet: -1.00 (0.58), residues: 80 loop : 0.16 (0.23), residues: 753 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 0.028 0.001 PHE G 258 TYR 0.014 0.001 TYR B 359 ARG 0.009 0.000 ARG C 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5203.79 seconds wall clock time: 91 minutes 52.83 seconds (5512.83 seconds total)