Starting phenix.real_space_refine on Tue Dec 31 11:17:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8asj_15617/12_2024/8asj_15617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asj_15617/12_2024/8asj_15617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8asj_15617/12_2024/8asj_15617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asj_15617/12_2024/8asj_15617.map" model { file = "/net/cci-nas-00/data/ceres_data/8asj_15617/12_2024/8asj_15617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asj_15617/12_2024/8asj_15617.cif" } resolution = 3.75 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 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'FES': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 316 Unusual residues: {'HEM': 2, 'PEE': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 76 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: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 265 Unusual residues: {'HEM': 2, 'PEE': 4, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 84 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 34.288 79.492 51.048 1.00 88.05 S ATOM 1053 SG CYS A 149 37.103 81.000 52.863 1.00 83.58 S ATOM 7913 SG CYS E 129 63.956 35.852 87.115 1.00178.24 S ATOM 8053 SG CYS E 149 59.607 34.141 86.774 1.00191.63 S Time building chain proxies: 8.99, per 1000 atoms: 0.61 Number of scatterers: 14720 At special positions: 0 Unit cell: (119.524, 114.836, 119.524, 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=2.03 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.66 Conformation dependent library (CDL) restraints added in 2.0 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=" NE2 HIS E 131 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 149 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 129 " pdb="FE2 FES E 201 " - pdb=" ND1 HIS E 152 " 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: 77 helices and 12 sheets defined 57.9% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 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: 3.747A 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 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 89 through 119 removed outlier: 3.693A 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 167 removed outlier: 4.139A pdb=" N PHE B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 182 removed outlier: 4.520A pdb=" N SER B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 220 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: 6.675A pdb=" N ILE B 249 " --> pdb=" O TRP B 245 " (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: 3.895A 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: 4.015A pdb=" N ILE B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 3.588A 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: 3.532A pdb=" N TYR B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.686A pdb=" N PHE B 404 " --> pdb=" O TRP B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 415 removed outlier: 3.556A pdb=" N GLY B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 413 " --> pdb=" O PRO B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 432 removed outlier: 3.554A pdb=" N HIS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) 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 168 through 172 removed outlier: 4.307A pdb=" N GLU C 172 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 242 Processing helix chain 'C' and resid 244 through 276 removed outlier: 3.705A 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 78 through 78 No H-bonds generated for 'chain 'D' and resid 78 through 78' Processing helix chain 'D' and resid 79 through 102 removed outlier: 3.635A pdb=" N ARG D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 37 removed outlier: 3.539A pdb=" N LEU E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.772A 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 42 through 47 removed outlier: 3.687A pdb=" N GLN E 45 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU E 47 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.514A pdb=" N VAL E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 86 Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 24 through 34 Processing helix chain 'F' and resid 42 through 45 Processing helix chain 'F' and resid 46 through 67 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 89 through 118 removed outlier: 3.732A pdb=" N SER F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 149 Processing helix chain 'F' and resid 152 through 168 removed outlier: 3.777A pdb=" N PHE F 166 " --> pdb=" O ILE F 162 " (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: 3.505A pdb=" N LYS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 270 removed outlier: 6.741A pdb=" N ILE F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) removed outlier: 3.753A 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: 3.952A 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: 4.350A pdb=" N ILE F 340 " --> pdb=" O MET F 336 " (cutoff:3.500A) removed outlier: 3.800A 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: 3.571A pdb=" N TYR F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA F 382 " --> pdb=" O THR F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 406 removed outlier: 3.777A pdb=" N PHE F 404 " --> pdb=" O TRP F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 415 removed outlier: 3.704A 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 91 removed outlier: 3.738A pdb=" N GLN G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) 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: 4.142A pdb=" N GLY G 276 " --> pdb=" O ARG G 272 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 105 removed outlier: 3.572A pdb=" N LEU H 85 " --> pdb=" O TYR H 81 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY H 86 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 3.921A 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: 6.063A 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: 3.678A pdb=" N VAL A 61 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.661A 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: 6.553A 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 66 through 67 Processing sheet with id=AA9, first strand: chain 'E' and resid 145 through 148 removed outlier: 3.598A pdb=" N TRP E 147 " --> pdb=" O TYR E 156 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS E 164 " --> pdb=" O HIS E 155 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP E 157 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE E 162 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 36 through 38 Processing sheet with id=AB2, first strand: chain 'G' and resid 93 through 95 Processing sheet with id=AB3, first strand: chain 'G' and resid 177 through 179 739 hydrogen bonds defined for protein. 2109 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: 4.45 Time building geometry restraints manager: 5.16 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: 6218 1.39 - 1.60: 8804 1.60 - 1.80: 112 1.80 - 2.01: 34 2.01 - 2.21: 32 Bond restraints: 15200 Sorted by residual: bond pdb=" C18 PEE B 508 " pdb=" C19 PEE B 508 " ideal model delta sigma weight residual 1.523 1.328 0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" C38 PEE B 503 " pdb=" C39 PEE B 503 " ideal model delta sigma weight residual 1.523 1.334 0.189 2.00e-02 2.50e+03 8.88e+01 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 8.82e+01 bond pdb=" C38 PEE B 507 " pdb=" C39 PEE B 507 " ideal model delta sigma weight residual 1.523 1.335 0.188 2.00e-02 2.50e+03 8.82e+01 bond pdb=" C38 PEE B 508 " pdb=" C39 PEE B 508 " ideal model delta sigma weight residual 1.523 1.338 0.185 2.00e-02 2.50e+03 8.52e+01 ... (remaining 15195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.11: 20630 6.11 - 12.22: 84 12.22 - 18.33: 16 18.33 - 24.44: 1 24.44 - 30.54: 3 Bond angle restraints: 20734 Sorted by residual: angle pdb=" C17 PEE B 508 " pdb=" C18 PEE B 508 " pdb=" C19 PEE B 508 " ideal model delta sigma weight residual 113.68 144.22 -30.54 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C38 PEE B 503 " pdb=" C39 PEE B 503 " pdb=" C40 PEE B 503 " ideal model delta sigma weight residual 112.47 85.91 26.56 3.00e+00 1.11e-01 7.84e+01 angle pdb=" C38 PEE B 507 " pdb=" C39 PEE B 507 " pdb=" C40 PEE B 507 " ideal model delta sigma weight residual 112.47 86.07 26.40 3.00e+00 1.11e-01 7.74e+01 angle pdb=" C38 PEE B 508 " pdb=" C39 PEE B 508 " pdb=" C40 PEE B 508 " ideal model delta sigma weight residual 112.47 91.41 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" O3P PEE F 503 " pdb=" P PEE F 503 " pdb=" O4P PEE F 503 " ideal model delta sigma weight residual 92.91 110.59 -17.68 3.00e+00 1.11e-01 3.47e+01 ... (remaining 20729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 8381 33.84 - 67.68: 215 67.68 - 101.52: 67 101.52 - 135.35: 28 135.35 - 169.19: 19 Dihedral angle restraints: 8710 sinusoidal: 3605 harmonic: 5105 Sorted by residual: dihedral pdb=" C6 U10 F 507 " pdb=" C7 U10 F 507 " pdb=" C8 U10 F 507 " pdb=" C9 U10 F 507 " ideal model delta sinusoidal sigma weight residual 101.51 -104.74 -153.75 1 2.00e+01 2.50e-03 4.55e+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 240.00 172.21 67.79 2 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" C2C HEC G 301 " pdb=" C3C HEC G 301 " pdb=" CAC HEC G 301 " pdb=" CBC HEC G 301 " ideal model delta sinusoidal sigma weight residual 240.00 179.16 60.84 2 1.00e+01 1.00e-02 3.66e+01 ... (remaining 8707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1542 0.043 - 0.087: 456 0.087 - 0.130: 127 0.130 - 0.173: 15 0.173 - 0.217: 7 Chirality restraints: 2147 Sorted by residual: chirality pdb=" C2 PEE A 202 " pdb=" C1 PEE A 202 " pdb=" C3 PEE A 202 " pdb=" O2 PEE A 202 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL F 242 " pdb=" CA VAL F 242 " pdb=" CG1 VAL F 242 " pdb=" CG2 VAL F 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2 PEE F 504 " pdb=" C1 PEE F 504 " pdb=" C3 PEE F 504 " pdb=" O2 PEE F 504 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2144 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 301 " 0.024 2.00e-02 2.50e+03 8.25e-02 1.53e+02 pdb=" C2C HEC C 301 " -0.225 2.00e-02 2.50e+03 pdb=" C3C HEC C 301 " 0.052 2.00e-02 2.50e+03 pdb=" C4C HEC C 301 " 0.012 2.00e-02 2.50e+03 pdb=" CAC HEC C 301 " 0.032 2.00e-02 2.50e+03 pdb=" CHC HEC C 301 " 0.037 2.00e-02 2.50e+03 pdb=" CHD HEC C 301 " -0.008 2.00e-02 2.50e+03 pdb=" CMC HEC C 301 " 0.069 2.00e-02 2.50e+03 pdb=" NC HEC C 301 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC G 301 " 0.025 2.00e-02 2.50e+03 8.20e-02 1.51e+02 pdb=" C2C HEC G 301 " -0.225 2.00e-02 2.50e+03 pdb=" C3C HEC G 301 " 0.044 2.00e-02 2.50e+03 pdb=" C4C HEC G 301 " 0.012 2.00e-02 2.50e+03 pdb=" CAC HEC G 301 " 0.038 2.00e-02 2.50e+03 pdb=" CHC HEC G 301 " 0.040 2.00e-02 2.50e+03 pdb=" CHD HEC G 301 " -0.008 2.00e-02 2.50e+03 pdb=" CMC HEC G 301 " 0.064 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=" CD ARG B 230 " -0.203 9.50e-02 1.11e+02 9.16e-02 6.68e+00 pdb=" NE ARG B 230 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 230 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 230 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 230 " -0.000 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 393 2.71 - 3.26: 15409 3.26 - 3.81: 25093 3.81 - 4.35: 31843 4.35 - 4.90: 52010 Nonbonded interactions: 124748 Sorted by model distance: nonbonded pdb=" NE2 HIS F 97 " pdb="FE HEM F 502 " model vdw 2.165 3.080 nonbonded pdb=" CE MET C 207 " pdb="FE HEC C 301 " model vdw 2.200 3.420 nonbonded pdb=" SD MET G 207 " pdb="FE HEC G 301 " model vdw 2.210 3.360 nonbonded pdb=" NE2 HIS B 97 " pdb="FE HEM B 502 " model vdw 2.217 3.080 nonbonded pdb=" OD1 ASN B 272 " pdb=" OH TYR B 280 " model vdw 2.247 3.040 ... (remaining 124743 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 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 \ C38 or name C39 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 )))) selection = (chain 'E' and (resid 9 through 187 or resid 201 through 202)) } ncs_group { reference = (chain 'B' and (resid 1 through 432 or resid 502 or resid 504 or (resid 505 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r 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 O1P or name O \ 2 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 C17 or name C1 \ 8 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 name C31 or n \ ame 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 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 or resid 503 or (resid 504 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r 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 O1P or name O \ 2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P \ )) or resid 505 through 506)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 78 through 104) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.030 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 : 0.008 0.195 15200 Z= 0.539 Angle : 1.092 30.544 20734 Z= 0.464 Chirality : 0.045 0.217 2147 Planarity : 0.009 0.092 2582 Dihedral : 20.537 169.193 5450 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 0.21 % Allowed : 3.63 % Favored : 96.16 % 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: -0.91 (0.18), residues: 1773 helix: -0.36 (0.15), residues: 933 sheet: -1.68 (0.58), residues: 61 loop : -0.64 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 147 HIS 0.007 0.001 HIS B 291 PHE 0.042 0.002 PHE D 87 TYR 0.019 0.004 TYR E 156 ARG 0.022 0.004 ARG B 230 *********************** 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 330 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 327 time to evaluate : 1.575 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.6307 (tp) cc_final: 0.5986 (tt) REVERT: A 76 ARG cc_start: 0.6714 (ttt180) cc_final: 0.6386 (mtp85) REVERT: A 89 GLN cc_start: 0.7314 (mt0) cc_final: 0.7075 (tp40) REVERT: A 113 ASN cc_start: 0.7524 (m-40) cc_final: 0.7261 (m-40) REVERT: A 184 ILE cc_start: 0.6547 (mt) cc_final: 0.6302 (mt) REVERT: B 34 MET cc_start: 0.8460 (mmm) cc_final: 0.8236 (mmt) REVERT: B 84 MET cc_start: 0.8076 (mmm) cc_final: 0.7647 (mmt) REVERT: B 133 MET cc_start: 0.7778 (mmm) cc_final: 0.7341 (mmm) REVERT: B 137 LEU cc_start: 0.7340 (mt) cc_final: 0.7057 (mt) REVERT: B 180 LEU cc_start: 0.7848 (mt) cc_final: 0.7586 (tp) REVERT: B 306 ARG cc_start: 0.6934 (mtm180) cc_final: 0.6719 (mmt180) REVERT: B 317 ILE cc_start: 0.6793 (mp) cc_final: 0.6348 (mt) REVERT: B 342 VAL cc_start: 0.8098 (p) cc_final: 0.7794 (m) REVERT: B 393 SER cc_start: 0.8428 (t) cc_final: 0.8010 (p) REVERT: B 431 HIS cc_start: 0.6475 (m-70) cc_final: 0.6151 (m170) REVERT: C 64 MET cc_start: 0.7671 (mtt) cc_final: 0.7460 (mtm) REVERT: C 70 ARG cc_start: 0.7513 (ptt90) cc_final: 0.7180 (ptt90) REVERT: C 79 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7443 (mt-10) REVERT: C 86 ARG cc_start: 0.6599 (ttm110) cc_final: 0.6259 (mtm-85) REVERT: C 141 SER cc_start: 0.8327 (t) cc_final: 0.8101 (t) REVERT: F 137 LEU cc_start: 0.7106 (mt) cc_final: 0.6530 (mt) REVERT: F 270 MET cc_start: 0.8622 (ptm) cc_final: 0.8289 (ptp) REVERT: F 282 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7393 (mt-10) REVERT: F 325 ILE cc_start: 0.8047 (mm) cc_final: 0.7820 (tt) REVERT: F 352 SER cc_start: 0.7327 (t) cc_final: 0.7039 (m) REVERT: F 426 GLU cc_start: 0.7482 (tt0) cc_final: 0.6491 (tp30) REVERT: F 431 HIS cc_start: 0.6176 (m-70) cc_final: 0.5720 (m-70) REVERT: G 136 MET cc_start: 0.6402 (tpp) cc_final: 0.5616 (mtm) REVERT: G 164 PRO cc_start: 0.6686 (Cg_exo) cc_final: 0.6364 (Cg_endo) REVERT: G 223 ASP cc_start: 0.7174 (t0) cc_final: 0.6893 (t70) REVERT: G 257 MET cc_start: 0.6781 (mmp) cc_final: 0.6570 (mmt) REVERT: G 267 TYR cc_start: 0.8117 (t80) cc_final: 0.7883 (t80) outliers start: 3 outliers final: 1 residues processed: 330 average time/residue: 0.2747 time to fit residues: 134.5478 Evaluate side-chains 228 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR 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: 0.9980 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 158 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 217 HIS C 113 HIS C 171 HIS F 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1714 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= 0.206 Angle : 0.658 14.367 20734 Z= 0.313 Chirality : 0.045 0.209 2147 Planarity : 0.005 0.046 2582 Dihedral : 22.410 177.411 2394 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.14 % Favored : 97.74 % Rotamer: Outliers : 1.39 % Allowed : 8.72 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.75 (0.20), residues: 1773 helix: 1.21 (0.17), residues: 946 sheet: -2.06 (0.51), residues: 72 loop : -0.03 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 157 HIS 0.005 0.001 HIS B 111 PHE 0.030 0.002 PHE D 87 TYR 0.016 0.001 TYR B 359 ARG 0.014 0.001 ARG A 77 *********************** 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 259 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 1.614 Fit side-chains REVERT: A 63 LEU cc_start: 0.7557 (mt) cc_final: 0.7156 (mm) REVERT: A 68 LEU cc_start: 0.6540 (tp) cc_final: 0.6128 (tt) REVERT: A 113 ASN cc_start: 0.7476 (m-40) cc_final: 0.7208 (m-40) REVERT: A 140 VAL cc_start: 0.7528 (t) cc_final: 0.7313 (t) REVERT: B 34 MET cc_start: 0.8466 (mmm) cc_final: 0.8204 (mmm) REVERT: B 137 LEU cc_start: 0.7333 (mt) cc_final: 0.7045 (mt) REVERT: B 154 MET cc_start: 0.8478 (mmm) cc_final: 0.8217 (mmm) REVERT: B 180 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7695 (tp) REVERT: B 227 VAL cc_start: 0.7391 (t) cc_final: 0.7154 (m) REVERT: B 317 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6309 (mt) REVERT: B 342 VAL cc_start: 0.8124 (p) cc_final: 0.7863 (m) REVERT: C 70 ARG cc_start: 0.7561 (ptt90) cc_final: 0.7328 (ptt90) REVERT: C 74 GLU cc_start: 0.7178 (tt0) cc_final: 0.6435 (mm-30) REVERT: C 86 ARG cc_start: 0.6602 (ttm110) cc_final: 0.6320 (mtm-85) REVERT: C 207 MET cc_start: 0.8480 (ttt) cc_final: 0.8272 (ttp) REVERT: C 212 MET cc_start: 0.6864 (mmt) cc_final: 0.6573 (mtm) REVERT: F 325 ILE cc_start: 0.8055 (mm) cc_final: 0.7716 (tt) REVERT: F 352 SER cc_start: 0.7442 (t) cc_final: 0.7010 (m) REVERT: G 64 MET cc_start: 0.7655 (mtt) cc_final: 0.7405 (mtm) REVERT: G 74 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6228 (mt-10) REVERT: G 94 VAL cc_start: 0.7746 (m) cc_final: 0.7543 (p) REVERT: G 136 MET cc_start: 0.5740 (tpp) cc_final: 0.5087 (mtm) REVERT: G 223 ASP cc_start: 0.7165 (t0) cc_final: 0.6949 (t70) REVERT: G 246 MET cc_start: 0.8027 (mmt) cc_final: 0.7464 (mmt) REVERT: G 257 MET cc_start: 0.7113 (mmp) cc_final: 0.6848 (mmt) REVERT: G 258 PHE cc_start: 0.7691 (m-10) cc_final: 0.7463 (m-10) outliers start: 20 outliers final: 12 residues processed: 250 average time/residue: 0.2605 time to fit residues: 98.1611 Evaluate side-chains 226 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 83 ASP 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: 9.9990 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2271 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= 0.195 Angle : 0.608 12.423 20734 Z= 0.287 Chirality : 0.043 0.212 2147 Planarity : 0.005 0.046 2582 Dihedral : 20.766 174.313 2394 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.29 % Rotamer: Outliers : 2.16 % Allowed : 8.93 % Favored : 88.91 % 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: 0.96 (0.20), residues: 1773 helix: 1.44 (0.17), residues: 944 sheet: -1.94 (0.50), residues: 77 loop : -0.01 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 147 HIS 0.005 0.001 HIS F 212 PHE 0.022 0.002 PHE D 87 TYR 0.016 0.001 TYR B 359 ARG 0.004 0.000 ARG A 86 *********************** 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 254 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 1.659 Fit side-chains REVERT: A 68 LEU cc_start: 0.6451 (tp) cc_final: 0.6073 (tt) REVERT: A 89 GLN cc_start: 0.6764 (pt0) cc_final: 0.6287 (tp40) REVERT: A 113 ASN cc_start: 0.7570 (m-40) cc_final: 0.7359 (m-40) REVERT: A 140 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7237 (t) REVERT: A 170 ASN cc_start: 0.7573 (m-40) cc_final: 0.7301 (m-40) REVERT: B 12 ARG cc_start: 0.6707 (mmp-170) cc_final: 0.5956 (mtm110) REVERT: B 306 ARG cc_start: 0.6853 (mtm180) cc_final: 0.6644 (mmt180) REVERT: B 317 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6346 (mp) REVERT: B 342 VAL cc_start: 0.8351 (p) cc_final: 0.8061 (m) REVERT: B 362 MET cc_start: 0.7627 (mtp) cc_final: 0.7058 (ttm) REVERT: C 27 HIS cc_start: 0.5183 (m-70) cc_final: 0.4801 (p90) REVERT: C 74 GLU cc_start: 0.7154 (tt0) cc_final: 0.6414 (mm-30) REVERT: C 99 THR cc_start: 0.6419 (OUTLIER) cc_final: 0.6192 (p) REVERT: C 246 MET cc_start: 0.7285 (mmm) cc_final: 0.6549 (mmm) REVERT: E 52 VAL cc_start: 0.2493 (OUTLIER) cc_final: 0.2259 (t) REVERT: F 325 ILE cc_start: 0.7991 (mm) cc_final: 0.7678 (tt) REVERT: F 352 SER cc_start: 0.7550 (t) cc_final: 0.7074 (m) REVERT: F 431 HIS cc_start: 0.5818 (m-70) cc_final: 0.5264 (m-70) REVERT: G 125 MET cc_start: 0.8369 (tpp) cc_final: 0.7956 (tpp) REVERT: G 136 MET cc_start: 0.6039 (tpp) cc_final: 0.5165 (mtm) REVERT: G 163 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7474 (mm-30) REVERT: G 223 ASP cc_start: 0.7295 (t0) cc_final: 0.7063 (t70) REVERT: G 246 MET cc_start: 0.7991 (mmt) cc_final: 0.7431 (mmt) REVERT: G 257 MET cc_start: 0.7103 (mmp) cc_final: 0.6856 (mmt) outliers start: 31 outliers final: 18 residues processed: 242 average time/residue: 0.2598 time to fit residues: 94.8926 Evaluate side-chains 235 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 45 optimal weight: 0.0570 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2623 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= 0.186 Angle : 0.579 10.828 20734 Z= 0.272 Chirality : 0.042 0.199 2147 Planarity : 0.004 0.040 2582 Dihedral : 19.618 174.424 2394 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 2.30 % Allowed : 8.86 % Favored : 88.84 % 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: 1.08 (0.20), residues: 1773 helix: 1.50 (0.17), residues: 945 sheet: -1.98 (0.50), residues: 77 loop : 0.13 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 157 HIS 0.005 0.001 HIS F 212 PHE 0.026 0.001 PHE D 87 TYR 0.014 0.001 TYR G 267 ARG 0.004 0.000 ARG C 70 *********************** 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 269 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 1.594 Fit side-chains REVERT: A 47 LEU cc_start: 0.5224 (OUTLIER) cc_final: 0.4995 (mm) REVERT: A 68 LEU cc_start: 0.6463 (tp) cc_final: 0.6221 (tt) REVERT: A 108 GLU cc_start: 0.5193 (mp0) cc_final: 0.4990 (mp0) REVERT: A 113 ASN cc_start: 0.7589 (m-40) cc_final: 0.7388 (m-40) REVERT: A 140 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7144 (t) REVERT: A 170 ASN cc_start: 0.7567 (m-40) cc_final: 0.7230 (m-40) REVERT: B 317 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6214 (mt) REVERT: B 342 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8124 (m) REVERT: B 362 MET cc_start: 0.7585 (mtp) cc_final: 0.7170 (ttm) REVERT: C 27 HIS cc_start: 0.5062 (m-70) cc_final: 0.4658 (p90) REVERT: C 74 GLU cc_start: 0.7137 (tt0) cc_final: 0.6373 (mm-30) REVERT: C 246 MET cc_start: 0.7365 (mmm) cc_final: 0.6585 (mmm) REVERT: E 52 VAL cc_start: 0.2524 (OUTLIER) cc_final: 0.2290 (t) REVERT: F 249 ILE cc_start: 0.7221 (mt) cc_final: 0.6979 (tp) REVERT: F 325 ILE cc_start: 0.7914 (mm) cc_final: 0.7672 (tt) REVERT: F 352 SER cc_start: 0.7540 (t) cc_final: 0.7028 (m) REVERT: F 431 HIS cc_start: 0.5815 (m-70) cc_final: 0.5217 (m-70) REVERT: G 136 MET cc_start: 0.6026 (tpp) cc_final: 0.5201 (mtm) REVERT: G 163 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7377 (mm-30) REVERT: G 223 ASP cc_start: 0.7297 (t0) cc_final: 0.7057 (t70) REVERT: G 246 MET cc_start: 0.7954 (mmt) cc_final: 0.7418 (mmt) REVERT: G 262 LEU cc_start: 0.7152 (tp) cc_final: 0.6933 (tp) outliers start: 33 outliers final: 19 residues processed: 260 average time/residue: 0.2831 time to fit residues: 112.2947 Evaluate side-chains 245 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 0.0050 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN F 272 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15200 Z= 0.224 Angle : 0.603 11.801 20734 Z= 0.281 Chirality : 0.043 0.194 2147 Planarity : 0.004 0.039 2582 Dihedral : 19.248 173.458 2393 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.46 % Rotamer: Outliers : 2.09 % Allowed : 9.62 % Favored : 88.28 % 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: 1.03 (0.20), residues: 1773 helix: 1.43 (0.17), residues: 945 sheet: -1.72 (0.52), residues: 78 loop : 0.11 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 147 HIS 0.007 0.001 HIS F 212 PHE 0.025 0.002 PHE D 87 TYR 0.016 0.001 TYR F 399 ARG 0.003 0.000 ARG C 248 *********************** 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 253 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 1.594 Fit side-chains REVERT: A 70 LYS cc_start: 0.7204 (mttm) cc_final: 0.6847 (mttp) REVERT: A 113 ASN cc_start: 0.7616 (m-40) cc_final: 0.7415 (m-40) REVERT: A 140 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6966 (t) REVERT: A 170 ASN cc_start: 0.7579 (m-40) cc_final: 0.7278 (m-40) REVERT: B 317 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6272 (mt) REVERT: B 342 VAL cc_start: 0.8461 (p) cc_final: 0.8137 (m) REVERT: B 362 MET cc_start: 0.7692 (mtp) cc_final: 0.7112 (ttm) REVERT: C 74 GLU cc_start: 0.7034 (tt0) cc_final: 0.6255 (mm-30) REVERT: C 246 MET cc_start: 0.7352 (mmm) cc_final: 0.6529 (mmm) REVERT: F 325 ILE cc_start: 0.7939 (mm) cc_final: 0.7690 (tt) REVERT: F 352 SER cc_start: 0.7609 (t) cc_final: 0.7076 (m) REVERT: F 431 HIS cc_start: 0.5861 (m-70) cc_final: 0.5223 (m-70) REVERT: G 96 ASP cc_start: 0.5932 (t70) cc_final: 0.5699 (p0) REVERT: G 125 MET cc_start: 0.8304 (tpp) cc_final: 0.7700 (tpp) REVERT: G 136 MET cc_start: 0.6249 (tpp) cc_final: 0.5332 (mtm) REVERT: G 163 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7390 (mm-30) REVERT: G 223 ASP cc_start: 0.7308 (t0) cc_final: 0.7067 (t70) outliers start: 30 outliers final: 23 residues processed: 246 average time/residue: 0.2553 time to fit residues: 94.6919 Evaluate side-chains 244 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 0.0050 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS B 279 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15200 Z= 0.306 Angle : 0.664 14.731 20734 Z= 0.309 Chirality : 0.046 0.186 2147 Planarity : 0.005 0.039 2582 Dihedral : 19.241 162.603 2393 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 2.58 % Allowed : 9.27 % Favored : 88.15 % 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: 0.73 (0.20), residues: 1773 helix: 1.20 (0.17), residues: 946 sheet: -1.66 (0.52), residues: 78 loop : -0.08 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 157 HIS 0.008 0.001 HIS B 111 PHE 0.029 0.002 PHE D 87 TYR 0.020 0.002 TYR F 399 ARG 0.005 0.001 ARG C 248 *********************** 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 262 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.4916 (OUTLIER) cc_final: 0.4521 (mm) REVERT: A 70 LYS cc_start: 0.7418 (mttm) cc_final: 0.6769 (mtmm) REVERT: A 140 VAL cc_start: 0.7107 (OUTLIER) cc_final: 0.6774 (t) REVERT: A 170 ASN cc_start: 0.7688 (m-40) cc_final: 0.7382 (m-40) REVERT: B 274 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8102 (mm) REVERT: B 317 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6322 (mt) REVERT: B 362 MET cc_start: 0.7817 (mtp) cc_final: 0.7287 (ttm) REVERT: C 74 GLU cc_start: 0.7001 (tt0) cc_final: 0.6288 (mm-30) REVERT: C 84 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: C 246 MET cc_start: 0.7380 (mmm) cc_final: 0.6520 (mmm) REVERT: E 125 MET cc_start: 0.5681 (OUTLIER) cc_final: 0.4697 (ttm) REVERT: E 149 CYS cc_start: 0.1688 (OUTLIER) cc_final: 0.0847 (t) REVERT: F 352 SER cc_start: 0.7696 (t) cc_final: 0.7185 (m) REVERT: F 362 MET cc_start: 0.6773 (ttm) cc_final: 0.6564 (ttm) REVERT: F 425 GLU cc_start: 0.7632 (tt0) cc_final: 0.7206 (tt0) REVERT: F 431 HIS cc_start: 0.5716 (m-70) cc_final: 0.5047 (m-70) REVERT: G 125 MET cc_start: 0.8326 (tpp) cc_final: 0.7739 (tpp) REVERT: G 136 MET cc_start: 0.6383 (tpp) cc_final: 0.5417 (mtm) REVERT: G 207 MET cc_start: 0.7611 (ttp) cc_final: 0.7350 (tpp) REVERT: G 223 ASP cc_start: 0.7318 (t0) cc_final: 0.7109 (t70) outliers start: 37 outliers final: 26 residues processed: 253 average time/residue: 0.2616 time to fit residues: 99.5703 Evaluate side-chains 252 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 149 CYS Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 123 optimal weight: 0.4980 chunk 95 optimal weight: 0.0870 chunk 142 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 105 optimal weight: 0.0170 chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 0.0170 chunk 104 optimal weight: 6.9990 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 HIS F 272 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15200 Z= 0.160 Angle : 0.565 11.900 20734 Z= 0.265 Chirality : 0.041 0.180 2147 Planarity : 0.004 0.041 2582 Dihedral : 18.406 163.202 2393 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 2.02 % Allowed : 10.88 % 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: 1.09 (0.20), residues: 1773 helix: 1.56 (0.17), residues: 943 sheet: -1.80 (0.54), residues: 80 loop : 0.04 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 157 HIS 0.004 0.001 HIS E 131 PHE 0.028 0.001 PHE D 87 TYR 0.016 0.001 TYR B 359 ARG 0.002 0.000 ARG F 94 *********************** 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 257 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.4637 (mm) REVERT: A 70 LYS cc_start: 0.7301 (mttm) cc_final: 0.6664 (mtmm) REVERT: A 140 VAL cc_start: 0.7301 (OUTLIER) cc_final: 0.6977 (t) REVERT: A 170 ASN cc_start: 0.7540 (m-40) cc_final: 0.7160 (m-40) REVERT: A 186 LEU cc_start: 0.6091 (mt) cc_final: 0.5478 (tp) REVERT: B 12 ARG cc_start: 0.7068 (mmp-170) cc_final: 0.6622 (mmp-170) REVERT: B 317 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6409 (mp) REVERT: B 342 VAL cc_start: 0.8440 (p) cc_final: 0.8132 (m) REVERT: B 362 MET cc_start: 0.7709 (mtp) cc_final: 0.7138 (ttm) REVERT: C 74 GLU cc_start: 0.6972 (tt0) cc_final: 0.6221 (mm-30) REVERT: C 84 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7366 (mt0) REVERT: C 246 MET cc_start: 0.7390 (mmm) cc_final: 0.6611 (mmm) REVERT: E 125 MET cc_start: 0.5306 (OUTLIER) cc_final: 0.4378 (ttm) REVERT: F 352 SER cc_start: 0.7636 (t) cc_final: 0.7085 (m) REVERT: F 362 MET cc_start: 0.6578 (ttm) cc_final: 0.6375 (ttm) REVERT: F 431 HIS cc_start: 0.5634 (m-70) cc_final: 0.4859 (m-70) REVERT: G 125 MET cc_start: 0.8461 (tpp) cc_final: 0.7924 (tpp) REVERT: G 136 MET cc_start: 0.6453 (tpp) cc_final: 0.5595 (mtm) REVERT: G 223 ASP cc_start: 0.7334 (t0) cc_final: 0.7098 (t70) REVERT: G 246 MET cc_start: 0.7844 (mmm) cc_final: 0.7354 (mmp) outliers start: 29 outliers final: 15 residues processed: 250 average time/residue: 0.2577 time to fit residues: 96.9171 Evaluate side-chains 241 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 83 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.0570 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 153 optimal weight: 0.4980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15200 Z= 0.169 Angle : 0.570 12.559 20734 Z= 0.264 Chirality : 0.041 0.165 2147 Planarity : 0.004 0.041 2582 Dihedral : 18.087 162.802 2393 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.88 % Allowed : 11.23 % Favored : 86.89 % 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: 1.62 (0.17), residues: 943 sheet: -1.75 (0.54), residues: 80 loop : 0.11 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 157 HIS 0.005 0.001 HIS F 212 PHE 0.029 0.001 PHE A 67 TYR 0.015 0.001 TYR B 359 ARG 0.003 0.000 ARG F 94 *********************** 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 254 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 1.721 Fit side-chains REVERT: A 47 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.4627 (mm) REVERT: A 70 LYS cc_start: 0.7306 (mttm) cc_final: 0.6613 (mtmm) REVERT: A 140 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.6954 (t) REVERT: A 170 ASN cc_start: 0.7455 (m-40) cc_final: 0.7128 (m-40) REVERT: A 186 LEU cc_start: 0.6067 (mt) cc_final: 0.5392 (tp) REVERT: B 12 ARG cc_start: 0.6982 (mmp-170) cc_final: 0.6496 (mmp-170) REVERT: B 295 GLU cc_start: 0.7376 (pm20) cc_final: 0.7080 (mm-30) REVERT: B 317 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6384 (mp) REVERT: B 342 VAL cc_start: 0.8444 (p) cc_final: 0.8112 (m) REVERT: B 362 MET cc_start: 0.7765 (mtp) cc_final: 0.7198 (ttm) REVERT: C 74 GLU cc_start: 0.6991 (tt0) cc_final: 0.6229 (mm-30) REVERT: C 84 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: C 246 MET cc_start: 0.7359 (mmm) cc_final: 0.6586 (mmm) REVERT: E 125 MET cc_start: 0.5087 (mtm) cc_final: 0.3998 (ttm) REVERT: F 352 SER cc_start: 0.7637 (t) cc_final: 0.7098 (m) REVERT: F 362 MET cc_start: 0.6582 (ttm) cc_final: 0.6373 (ttm) REVERT: F 431 HIS cc_start: 0.5784 (m-70) cc_final: 0.4931 (m-70) REVERT: G 96 ASP cc_start: 0.5812 (t70) cc_final: 0.5610 (t0) REVERT: G 125 MET cc_start: 0.8368 (tpp) cc_final: 0.7742 (tpp) REVERT: G 136 MET cc_start: 0.6478 (tpp) cc_final: 0.5587 (mtm) REVERT: G 223 ASP cc_start: 0.7351 (t0) cc_final: 0.7105 (t70) outliers start: 27 outliers final: 20 residues processed: 247 average time/residue: 0.2613 time to fit residues: 96.7705 Evaluate side-chains 248 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 253 PHE 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: 0.9980 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 148 optimal weight: 0.0010 chunk 156 optimal weight: 0.0050 chunk 103 optimal weight: 6.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15200 Z= 0.155 Angle : 0.553 13.878 20734 Z= 0.257 Chirality : 0.041 0.159 2147 Planarity : 0.004 0.041 2582 Dihedral : 17.827 162.370 2393 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 1.74 % Allowed : 11.58 % Favored : 86.68 % 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: 1.31 (0.20), residues: 1773 helix: 1.73 (0.17), residues: 938 sheet: -1.69 (0.56), residues: 80 loop : 0.18 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 157 HIS 0.004 0.001 HIS E 131 PHE 0.025 0.001 PHE A 67 TYR 0.017 0.001 TYR G 267 ARG 0.003 0.000 ARG C 129 *********************** 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 247 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 1.652 Fit side-chains REVERT: A 47 LEU cc_start: 0.4861 (OUTLIER) cc_final: 0.4544 (mm) REVERT: A 70 LYS cc_start: 0.7319 (mttm) cc_final: 0.6571 (mtmm) REVERT: A 140 VAL cc_start: 0.7234 (OUTLIER) cc_final: 0.6941 (t) REVERT: A 170 ASN cc_start: 0.7416 (m-40) cc_final: 0.7098 (m-40) REVERT: A 186 LEU cc_start: 0.6173 (mt) cc_final: 0.5511 (tp) REVERT: B 12 ARG cc_start: 0.7151 (mmp-170) cc_final: 0.6659 (mmp-170) REVERT: B 166 PHE cc_start: 0.8216 (m-80) cc_final: 0.7976 (m-80) REVERT: B 295 GLU cc_start: 0.7432 (pm20) cc_final: 0.7136 (mm-30) REVERT: B 317 ILE cc_start: 0.6642 (OUTLIER) cc_final: 0.6334 (mp) REVERT: B 342 VAL cc_start: 0.8418 (p) cc_final: 0.8098 (m) REVERT: B 362 MET cc_start: 0.7750 (mtp) cc_final: 0.7190 (ttm) REVERT: C 74 GLU cc_start: 0.6972 (tt0) cc_final: 0.6228 (mm-30) REVERT: C 84 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: E 125 MET cc_start: 0.5325 (OUTLIER) cc_final: 0.4037 (ttm) REVERT: F 352 SER cc_start: 0.7643 (t) cc_final: 0.7117 (m) REVERT: F 362 MET cc_start: 0.6559 (ttm) cc_final: 0.6349 (ttm) REVERT: G 96 ASP cc_start: 0.5900 (t70) cc_final: 0.5680 (t0) REVERT: G 104 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6156 (tt0) REVERT: G 125 MET cc_start: 0.8379 (tpp) cc_final: 0.7768 (tpp) REVERT: G 136 MET cc_start: 0.6490 (tpp) cc_final: 0.5625 (mtm) REVERT: G 246 MET cc_start: 0.7897 (mmm) cc_final: 0.7460 (mmp) outliers start: 25 outliers final: 15 residues processed: 239 average time/residue: 0.2694 time to fit residues: 96.1522 Evaluate side-chains 240 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 253 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.3980 chunk 101 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3448 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= 0.194 Angle : 0.592 13.983 20734 Z= 0.270 Chirality : 0.042 0.162 2147 Planarity : 0.004 0.041 2582 Dihedral : 17.778 161.114 2393 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 1.67 % Allowed : 11.85 % Favored : 86.47 % 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: 1.21 (0.20), residues: 1773 helix: 1.61 (0.17), residues: 943 sheet: -1.49 (0.61), residues: 70 loop : 0.11 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 157 HIS 0.006 0.001 HIS F 212 PHE 0.023 0.001 PHE D 87 TYR 0.016 0.001 TYR B 359 ARG 0.005 0.000 ARG C 129 ********************** 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 247 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 1.680 Fit side-chains REVERT: A 140 VAL cc_start: 0.7271 (OUTLIER) cc_final: 0.6971 (t) REVERT: A 170 ASN cc_start: 0.7524 (m-40) cc_final: 0.7180 (m-40) REVERT: A 186 LEU cc_start: 0.6254 (mt) cc_final: 0.5507 (tp) REVERT: B 12 ARG cc_start: 0.7099 (mmp-170) cc_final: 0.6573 (mmp-170) REVERT: B 295 GLU cc_start: 0.7495 (pm20) cc_final: 0.7130 (mm-30) REVERT: B 317 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6391 (mp) REVERT: B 342 VAL cc_start: 0.8455 (p) cc_final: 0.8082 (m) REVERT: B 362 MET cc_start: 0.7757 (mtp) cc_final: 0.7183 (ttm) REVERT: B 429 ASN cc_start: 0.7030 (m-40) cc_final: 0.6727 (m-40) REVERT: C 56 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7011 (mt-10) REVERT: C 74 GLU cc_start: 0.6981 (tt0) cc_final: 0.6234 (mm-30) REVERT: C 84 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7311 (mt0) REVERT: C 246 MET cc_start: 0.7417 (mmm) cc_final: 0.6653 (mmm) REVERT: E 47 LEU cc_start: 0.4538 (mm) cc_final: 0.4199 (mm) REVERT: E 125 MET cc_start: 0.5286 (OUTLIER) cc_final: 0.3944 (ttm) REVERT: F 352 SER cc_start: 0.7664 (t) cc_final: 0.7143 (m) REVERT: F 362 MET cc_start: 0.6656 (ttm) cc_final: 0.6456 (ttm) REVERT: F 431 HIS cc_start: 0.5840 (m-70) cc_final: 0.5006 (m-70) REVERT: G 104 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6162 (tt0) REVERT: G 125 MET cc_start: 0.8330 (tpp) cc_final: 0.7665 (tpp) REVERT: G 136 MET cc_start: 0.6495 (tpp) cc_final: 0.5642 (mtm) outliers start: 24 outliers final: 17 residues processed: 240 average time/residue: 0.2561 time to fit residues: 93.5121 Evaluate side-chains 242 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 253 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.141512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.129248 restraints weight = 15994.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.102078 restraints weight = 43677.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.101652 restraints weight = 35924.208| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15200 Z= 0.205 Angle : 0.805 59.198 20734 Z= 0.433 Chirality : 0.042 0.261 2147 Planarity : 0.004 0.041 2582 Dihedral : 17.779 161.105 2393 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.53 % Allowed : 11.99 % Favored : 86.47 % 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: 1.20 (0.20), residues: 1773 helix: 1.60 (0.17), residues: 943 sheet: -1.48 (0.61), residues: 70 loop : 0.10 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 157 HIS 0.006 0.001 HIS F 212 PHE 0.023 0.001 PHE D 87 TYR 0.024 0.001 TYR B 280 ARG 0.005 0.000 ARG C 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2953.11 seconds wall clock time: 55 minutes 0.68 seconds (3300.68 seconds total)