Starting phenix.real_space_refine on Sat Aug 23 23:53:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8asj_15617/08_2025/8asj_15617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asj_15617/08_2025/8asj_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_15617/08_2025/8asj_15617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asj_15617/08_2025/8asj_15617.map" model { file = "/net/cci-nas-00/data/ceres_data/8asj_15617/08_2025/8asj_15617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asj_15617/08_2025/8asj_15617.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.44, per 1000 atoms: 0.30 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: 1.51 Conformation dependent library (CDL) restraints added in 709.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.48 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: 3.747A 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: 2.58 Time building geometry restraints manager: 1.91 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 201 or (resid 202 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 C2 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O \ 3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'E' and resid 9 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 501 or resid 503 or (resid 504 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 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 O2 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: 1.030 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.940 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- 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 : 0.011 0.526 15218 Z= 0.621 Angle : 1.215 53.710 20744 Z= 0.468 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 : 3.80 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.022 0.004 ARG B 230 TYR 0.019 0.004 TYR E 156 PHE 0.042 0.002 PHE D 87 TRP 0.029 0.002 TRP E 147 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd covalent geometry : bond 0.00840 (15200) covalent geometry : angle 1.09206 (20734) SS BOND : bond 0.00314 ( 2) SS BOND : angle 1.38754 ( 4) hydrogen bonds : bond 0.13448 ( 739) hydrogen bonds : angle 6.03654 ( 2109) metal coordination : bond 0.18856 ( 8) metal coordination : angle 31.33780 ( 6) Misc. bond : bond 0.21226 ( 8) *********************** 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 : 0.559 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: 0.5615 (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: 0.1204 time to fit residues: 59.5206 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 : 0.513 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.140188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.128038 restraints weight = 15859.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.102443 restraints weight = 43603.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.100188 restraints weight = 57060.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.099862 restraints weight = 40517.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.100584 restraints weight = 29513.378| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.311 15218 Z= 0.187 Angle : 0.791 30.140 20744 Z= 0.343 Chirality : 0.047 0.240 2147 Planarity : 0.005 0.050 2582 Dihedral : 22.412 178.351 2394 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.26 % Favored : 97.63 % Rotamer: Outliers : 1.88 % Allowed : 8.16 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.20), residues: 1773 helix: 1.00 (0.17), residues: 942 sheet: -1.96 (0.49), residues: 77 loop : -0.18 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 230 TYR 0.020 0.002 TYR F 302 PHE 0.036 0.002 PHE D 87 TRP 0.018 0.002 TRP F 157 HIS 0.009 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00447 (15200) covalent geometry : angle 0.72891 (20734) SS BOND : bond 0.00326 ( 2) SS BOND : angle 0.40892 ( 4) hydrogen bonds : bond 0.05523 ( 739) hydrogen bonds : angle 4.53851 ( 2109) metal coordination : bond 0.02964 ( 8) metal coordination : angle 18.15420 ( 6) Misc. bond : bond 0.20515 ( 8) *********************** 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 266 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.514 Fit side-chains REVERT: A 63 LEU cc_start: 0.7603 (mt) cc_final: 0.7301 (mm) REVERT: A 92 GLN cc_start: 0.6672 (pt0) cc_final: 0.6357 (pt0) REVERT: A 113 ASN cc_start: 0.7113 (m-40) cc_final: 0.6874 (m-40) REVERT: B 133 MET cc_start: 0.8327 (mmm) cc_final: 0.7606 (mmm) REVERT: B 137 LEU cc_start: 0.8104 (mt) cc_final: 0.7841 (mt) REVERT: B 180 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8204 (tp) REVERT: B 260 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7280 (mt) REVERT: B 317 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6676 (mt) REVERT: B 342 VAL cc_start: 0.8916 (p) cc_final: 0.8624 (m) REVERT: B 362 MET cc_start: 0.7520 (mtp) cc_final: 0.7223 (ttm) REVERT: B 378 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8472 (m) REVERT: C 86 ARG cc_start: 0.7120 (ttm110) cc_final: 0.6895 (mtm-85) REVERT: C 158 THR cc_start: 0.8563 (m) cc_final: 0.8361 (m) REVERT: E 45 GLN cc_start: 0.6495 (mp10) cc_final: 0.6036 (mp10) REVERT: F 325 ILE cc_start: 0.8044 (mm) cc_final: 0.7781 (tt) REVERT: F 352 SER cc_start: 0.7870 (t) cc_final: 0.7387 (m) REVERT: G 74 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6697 (mt-10) REVERT: G 125 MET cc_start: 0.8743 (tpp) cc_final: 0.8381 (tpp) REVERT: G 136 MET cc_start: 0.6107 (tpp) cc_final: 0.5681 (mtm) REVERT: G 222 HIS cc_start: 0.7003 (m90) cc_final: 0.6802 (m90) REVERT: G 246 MET cc_start: 0.8129 (mmt) cc_final: 0.7642 (mmt) REVERT: G 257 MET cc_start: 0.7732 (mmp) cc_final: 0.7458 (mmt) outliers start: 27 outliers final: 16 residues processed: 255 average time/residue: 0.1168 time to fit residues: 45.0693 Evaluate side-chains 233 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 187 VAL 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 Chi-restraints excluded: chain G residue 261 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 0.0060 chunk 91 optimal weight: 0.0060 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.0020 chunk 143 optimal weight: 0.0070 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 121 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.0238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 HIS B 384 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.146833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.134979 restraints weight = 15890.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.106681 restraints weight = 39879.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.106592 restraints weight = 36261.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.106422 restraints weight = 32279.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.106662 restraints weight = 27952.096| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.266 15218 Z= 0.113 Angle : 0.626 26.106 20744 Z= 0.276 Chirality : 0.042 0.212 2147 Planarity : 0.005 0.039 2582 Dihedral : 20.604 171.202 2394 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.26 % Favored : 97.63 % Rotamer: Outliers : 1.74 % Allowed : 9.14 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.20), residues: 1773 helix: 1.55 (0.17), residues: 946 sheet: -1.88 (0.50), residues: 77 loop : 0.09 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 86 TYR 0.012 0.001 TYR B 297 PHE 0.022 0.001 PHE D 87 TRP 0.013 0.001 TRP F 157 HIS 0.004 0.001 HIS B 291 Details of bonding type rmsd covalent geometry : bond 0.00242 (15200) covalent geometry : angle 0.57721 (20734) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.35476 ( 4) hydrogen bonds : bond 0.04105 ( 739) hydrogen bonds : angle 4.05329 ( 2109) metal coordination : bond 0.01299 ( 8) metal coordination : angle 14.26932 ( 6) Misc. bond : bond 0.15272 ( 8) *********************** 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 261 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.530 Fit side-chains REVERT: A 70 LYS cc_start: 0.7658 (mttt) cc_final: 0.7286 (mtmm) REVERT: A 92 GLN cc_start: 0.6834 (pt0) cc_final: 0.6589 (pt0) REVERT: A 170 ASN cc_start: 0.7977 (m-40) cc_final: 0.7699 (m-40) REVERT: B 1 MET cc_start: 0.2238 (ptt) cc_final: 0.1943 (ptm) REVERT: B 12 ARG cc_start: 0.6772 (mmp-170) cc_final: 0.6226 (mtm110) REVERT: B 84 MET cc_start: 0.8644 (mmm) cc_final: 0.8296 (mmt) REVERT: B 180 LEU cc_start: 0.8314 (mt) cc_final: 0.8114 (tp) REVERT: B 233 SER cc_start: 0.8345 (p) cc_final: 0.8067 (m) REVERT: B 260 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7324 (mt) REVERT: B 279 ASN cc_start: 0.8597 (t0) cc_final: 0.8268 (t0) REVERT: B 317 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6545 (mp) REVERT: B 342 VAL cc_start: 0.8865 (p) cc_final: 0.8660 (m) REVERT: B 362 MET cc_start: 0.7566 (mtp) cc_final: 0.7247 (ttm) REVERT: C 82 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6967 (mm-30) REVERT: C 86 ARG cc_start: 0.7088 (ttm110) cc_final: 0.6819 (mtm-85) REVERT: C 246 MET cc_start: 0.7625 (mmm) cc_final: 0.7119 (mmm) REVERT: E 52 VAL cc_start: 0.2484 (OUTLIER) cc_final: 0.2215 (t) REVERT: F 140 MET cc_start: 0.6526 (mtp) cc_final: 0.6215 (mtm) REVERT: F 325 ILE cc_start: 0.8023 (mm) cc_final: 0.7746 (tt) REVERT: F 352 SER cc_start: 0.7885 (t) cc_final: 0.7403 (m) REVERT: F 431 HIS cc_start: 0.5779 (m-70) cc_final: 0.5369 (m-70) REVERT: G 125 MET cc_start: 0.8816 (tpp) cc_final: 0.8556 (tpp) REVERT: G 136 MET cc_start: 0.6120 (tpp) cc_final: 0.5517 (mtm) REVERT: G 246 MET cc_start: 0.8280 (mmt) cc_final: 0.8034 (mmt) REVERT: G 257 MET cc_start: 0.7707 (mmp) cc_final: 0.7489 (mmt) REVERT: G 258 PHE cc_start: 0.8343 (m-10) cc_final: 0.8132 (m-10) outliers start: 25 outliers final: 12 residues processed: 250 average time/residue: 0.1108 time to fit residues: 42.5102 Evaluate side-chains 241 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 260 LEU 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 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 F residue 287 SER 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 40 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.139660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.128035 restraints weight = 16046.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.099850 restraints weight = 38757.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.099248 restraints weight = 37117.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.098599 restraints weight = 32692.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.098518 restraints weight = 28813.859| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.297 15218 Z= 0.167 Angle : 0.685 23.955 20744 Z= 0.303 Chirality : 0.045 0.197 2147 Planarity : 0.005 0.039 2582 Dihedral : 20.083 178.233 2394 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.71 % Favored : 97.18 % Rotamer: Outliers : 2.37 % Allowed : 8.51 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.20), residues: 1773 helix: 1.31 (0.17), residues: 950 sheet: -1.86 (0.49), residues: 78 loop : 0.06 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 114 TYR 0.019 0.002 TYR F 399 PHE 0.025 0.002 PHE D 87 TRP 0.018 0.001 TRP A 147 HIS 0.011 0.001 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00409 (15200) covalent geometry : angle 0.64787 (20734) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.33585 ( 4) hydrogen bonds : bond 0.05102 ( 739) hydrogen bonds : angle 4.17821 ( 2109) metal coordination : bond 0.01396 ( 8) metal coordination : angle 13.11532 ( 6) Misc. bond : bond 0.17431 ( 8) *********************** 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 to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.596 Fit side-chains REVERT: A 47 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5336 (mm) REVERT: A 68 LEU cc_start: 0.6404 (mt) cc_final: 0.5912 (tt) REVERT: B 10 GLU cc_start: 0.5557 (pt0) cc_final: 0.5260 (pt0) REVERT: B 180 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8320 (tp) REVERT: B 260 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7294 (mt) REVERT: B 279 ASN cc_start: 0.8555 (t0) cc_final: 0.8221 (t0) REVERT: B 317 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6526 (mt) REVERT: B 342 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8590 (m) REVERT: B 362 MET cc_start: 0.7606 (mtp) cc_final: 0.7330 (ttm) REVERT: C 246 MET cc_start: 0.7727 (mmm) cc_final: 0.7185 (mmm) REVERT: E 45 GLN cc_start: 0.6551 (mp10) cc_final: 0.6337 (mp10) REVERT: F 325 ILE cc_start: 0.7982 (mm) cc_final: 0.7753 (tt) REVERT: F 352 SER cc_start: 0.7914 (t) cc_final: 0.7411 (m) REVERT: F 431 HIS cc_start: 0.5874 (m-70) cc_final: 0.5539 (m-70) REVERT: G 83 ASP cc_start: 0.6626 (OUTLIER) cc_final: 0.6356 (t0) REVERT: G 125 MET cc_start: 0.8809 (tpp) cc_final: 0.8511 (tpp) REVERT: G 136 MET cc_start: 0.6104 (tpp) cc_final: 0.5607 (mtm) outliers start: 34 outliers final: 22 residues processed: 247 average time/residue: 0.1163 time to fit residues: 43.9079 Evaluate side-chains 241 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 260 LEU 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 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 261 VAL 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 77 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.141550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.129753 restraints weight = 15891.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.102198 restraints weight = 39163.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.102335 restraints weight = 34633.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.101003 restraints weight = 29583.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.101249 restraints weight = 25948.454| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.310 15218 Z= 0.125 Angle : 0.621 23.002 20744 Z= 0.276 Chirality : 0.043 0.196 2147 Planarity : 0.004 0.038 2582 Dihedral : 19.342 173.976 2393 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.65 % Favored : 97.24 % Rotamer: Outliers : 2.09 % Allowed : 9.48 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.20), residues: 1773 helix: 1.43 (0.17), residues: 947 sheet: -1.91 (0.49), residues: 78 loop : 0.11 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.015 0.001 TYR B 359 PHE 0.026 0.001 PHE D 87 TRP 0.013 0.001 TRP F 157 HIS 0.006 0.001 HIS B 291 Details of bonding type rmsd covalent geometry : bond 0.00293 (15200) covalent geometry : angle 0.58357 (20734) SS BOND : bond 0.00178 ( 2) SS BOND : angle 0.27917 ( 4) hydrogen bonds : bond 0.04538 ( 739) hydrogen bonds : angle 4.03703 ( 2109) metal coordination : bond 0.01188 ( 8) metal coordination : angle 12.43191 ( 6) Misc. bond : bond 0.17136 ( 8) *********************** 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 252 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.539 Fit side-chains REVERT: A 68 LEU cc_start: 0.6312 (mt) cc_final: 0.5856 (tt) REVERT: A 186 LEU cc_start: 0.6027 (mt) cc_final: 0.5393 (tp) REVERT: B 180 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8244 (tp) REVERT: B 260 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7216 (mt) REVERT: B 279 ASN cc_start: 0.8528 (t0) cc_final: 0.8197 (t0) REVERT: B 317 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6417 (mt) REVERT: B 342 VAL cc_start: 0.8884 (p) cc_final: 0.8628 (m) REVERT: B 362 MET cc_start: 0.7634 (mtp) cc_final: 0.7270 (ttm) REVERT: C 246 MET cc_start: 0.7797 (mmm) cc_final: 0.7204 (mmm) REVERT: E 45 GLN cc_start: 0.6692 (mp10) cc_final: 0.6413 (mp10) REVERT: F 352 SER cc_start: 0.7983 (t) cc_final: 0.7509 (m) REVERT: F 431 HIS cc_start: 0.5865 (m-70) cc_final: 0.5456 (m-70) REVERT: G 125 MET cc_start: 0.8799 (tpp) cc_final: 0.8522 (tpp) REVERT: G 136 MET cc_start: 0.6366 (tpp) cc_final: 0.5727 (mtm) REVERT: G 262 LEU cc_start: 0.8019 (tp) cc_final: 0.7687 (tp) outliers start: 30 outliers final: 22 residues processed: 240 average time/residue: 0.1127 time to fit residues: 41.6231 Evaluate side-chains 243 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 180 LEU 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 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 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 G residue 83 ASP Chi-restraints excluded: chain G residue 253 PHE 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 144 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.137295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.125838 restraints weight = 16039.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.097536 restraints weight = 38606.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.096608 restraints weight = 37913.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.096375 restraints weight = 33683.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.096494 restraints weight = 30840.628| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.439 15218 Z= 0.200 Angle : 0.712 22.335 20744 Z= 0.316 Chirality : 0.046 0.190 2147 Planarity : 0.005 0.041 2582 Dihedral : 19.425 163.124 2393 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 2.51 % Allowed : 9.97 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.20), residues: 1773 helix: 1.15 (0.17), residues: 944 sheet: -1.66 (0.54), residues: 68 loop : -0.12 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 248 TYR 0.021 0.002 TYR F 399 PHE 0.029 0.002 PHE D 87 TRP 0.014 0.002 TRP F 157 HIS 0.009 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00491 (15200) covalent geometry : angle 0.68509 (20734) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.45789 ( 4) hydrogen bonds : bond 0.05554 ( 739) hydrogen bonds : angle 4.24551 ( 2109) metal coordination : bond 0.01431 ( 8) metal coordination : angle 11.46554 ( 6) Misc. bond : bond 0.21520 ( 8) *********************** 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 258 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.570 Fit side-chains REVERT: A 47 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4897 (mm) REVERT: A 68 LEU cc_start: 0.6245 (mt) cc_final: 0.5968 (tt) REVERT: A 186 LEU cc_start: 0.6159 (mt) cc_final: 0.5583 (tp) REVERT: B 180 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8167 (tp) REVERT: B 260 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7229 (mt) REVERT: B 279 ASN cc_start: 0.8501 (t0) cc_final: 0.8195 (t0) REVERT: B 317 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6478 (mt) REVERT: B 362 MET cc_start: 0.7824 (mtp) cc_final: 0.7508 (ttm) REVERT: C 246 MET cc_start: 0.7847 (mmm) cc_final: 0.7194 (mmm) REVERT: E 45 GLN cc_start: 0.6566 (mp10) cc_final: 0.6255 (mp10) REVERT: E 149 CYS cc_start: 0.0580 (OUTLIER) cc_final: -0.0131 (t) REVERT: F 352 SER cc_start: 0.7970 (t) cc_final: 0.7526 (m) REVERT: F 425 GLU cc_start: 0.7955 (tt0) cc_final: 0.7584 (tt0) REVERT: F 431 HIS cc_start: 0.5908 (m-70) cc_final: 0.5480 (m-70) REVERT: G 136 MET cc_start: 0.6479 (tpp) cc_final: 0.5752 (mtm) REVERT: G 177 TYR cc_start: 0.8352 (m-80) cc_final: 0.8021 (m-80) outliers start: 36 outliers final: 27 residues processed: 248 average time/residue: 0.1177 time to fit residues: 44.5324 Evaluate side-chains 246 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 33 ILE 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 249 ILE Chi-restraints excluded: chain B residue 260 LEU 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 C residue 277 VAL 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 65 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 F 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.140138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.127894 restraints weight = 15904.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.103383 restraints weight = 43041.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.100348 restraints weight = 49740.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.100035 restraints weight = 40120.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.100476 restraints weight = 28625.221| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.332 15218 Z= 0.128 Angle : 0.620 22.179 20744 Z= 0.278 Chirality : 0.042 0.179 2147 Planarity : 0.004 0.037 2582 Dihedral : 18.830 163.436 2393 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 2.51 % Allowed : 10.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.20), residues: 1773 helix: 1.39 (0.17), residues: 943 sheet: -1.65 (0.55), residues: 68 loop : -0.04 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.017 0.001 TYR B 359 PHE 0.029 0.001 PHE D 87 TRP 0.015 0.001 TRP F 157 HIS 0.006 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00302 (15200) covalent geometry : angle 0.59125 (20734) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.38474 ( 4) hydrogen bonds : bond 0.04673 ( 739) hydrogen bonds : angle 4.04125 ( 2109) metal coordination : bond 0.01118 ( 8) metal coordination : angle 11.04475 ( 6) Misc. bond : bond 0.17515 ( 8) *********************** 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 256 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.758 Fit side-chains REVERT: A 47 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.5027 (mm) REVERT: A 68 LEU cc_start: 0.6148 (mt) cc_final: 0.5902 (tt) REVERT: A 186 LEU cc_start: 0.5979 (mt) cc_final: 0.5543 (tp) REVERT: B 12 ARG cc_start: 0.6969 (mmp-170) cc_final: 0.6677 (mmp-170) REVERT: B 180 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8157 (tp) REVERT: B 279 ASN cc_start: 0.8494 (t0) cc_final: 0.8157 (t0) REVERT: B 317 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6795 (mp) REVERT: B 342 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8651 (m) REVERT: B 362 MET cc_start: 0.7685 (mtp) cc_final: 0.7310 (ttm) REVERT: C 246 MET cc_start: 0.7834 (mmm) cc_final: 0.7243 (mmm) REVERT: E 45 GLN cc_start: 0.6456 (mp10) cc_final: 0.6199 (mp10) REVERT: E 125 MET cc_start: 0.4875 (pmm) cc_final: 0.4613 (ttm) REVERT: E 149 CYS cc_start: 0.0557 (OUTLIER) cc_final: -0.0133 (t) REVERT: F 140 MET cc_start: 0.6622 (mtp) cc_final: 0.6351 (mtm) REVERT: F 352 SER cc_start: 0.8005 (t) cc_final: 0.7529 (m) REVERT: F 431 HIS cc_start: 0.5891 (m-70) cc_final: 0.5441 (m-70) REVERT: G 125 MET cc_start: 0.8811 (tpp) cc_final: 0.8428 (tpp) REVERT: G 136 MET cc_start: 0.6384 (tpp) cc_final: 0.5942 (mtm) REVERT: G 177 TYR cc_start: 0.8248 (m-80) cc_final: 0.7910 (m-80) outliers start: 36 outliers final: 26 residues processed: 243 average time/residue: 0.1151 time to fit residues: 42.8871 Evaluate side-chains 248 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 28 LEU 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 249 ILE 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 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 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN F 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.140162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.128406 restraints weight = 15948.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.101251 restraints weight = 40826.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.100086 restraints weight = 35140.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.099158 restraints weight = 32532.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.099740 restraints weight = 26641.341| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.324 15218 Z= 0.129 Angle : 0.616 21.399 20744 Z= 0.276 Chirality : 0.042 0.170 2147 Planarity : 0.004 0.038 2582 Dihedral : 18.625 163.156 2393 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 2.51 % Allowed : 10.88 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.20), residues: 1773 helix: 1.41 (0.17), residues: 945 sheet: -1.75 (0.55), residues: 70 loop : -0.01 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.017 0.001 TYR B 359 PHE 0.027 0.001 PHE D 87 TRP 0.015 0.001 TRP F 157 HIS 0.006 0.001 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00304 (15200) covalent geometry : angle 0.58877 (20734) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.31588 ( 4) hydrogen bonds : bond 0.04642 ( 739) hydrogen bonds : angle 4.00165 ( 2109) metal coordination : bond 0.01048 ( 8) metal coordination : angle 10.60594 ( 6) Misc. bond : bond 0.17305 ( 8) *********************** 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 251 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.552 Fit side-chains REVERT: A 68 LEU cc_start: 0.6215 (mt) cc_final: 0.5958 (tt) REVERT: A 186 LEU cc_start: 0.6194 (mt) cc_final: 0.5591 (tp) REVERT: B 12 ARG cc_start: 0.6943 (mmp-170) cc_final: 0.6573 (mmp-170) REVERT: B 180 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8058 (tp) REVERT: B 279 ASN cc_start: 0.8499 (t0) cc_final: 0.8184 (t0) REVERT: B 317 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6566 (mp) REVERT: B 342 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8565 (m) REVERT: B 362 MET cc_start: 0.7772 (mtp) cc_final: 0.7397 (ttm) REVERT: C 246 MET cc_start: 0.7776 (mmm) cc_final: 0.7190 (mmm) REVERT: E 45 GLN cc_start: 0.6484 (mp10) cc_final: 0.6146 (mp10) REVERT: E 125 MET cc_start: 0.5171 (pmm) cc_final: 0.4549 (ttm) REVERT: F 140 MET cc_start: 0.6770 (mtp) cc_final: 0.6497 (mtm) REVERT: F 352 SER cc_start: 0.7958 (t) cc_final: 0.7471 (m) REVERT: F 431 HIS cc_start: 0.5890 (m-70) cc_final: 0.5332 (m-70) REVERT: G 125 MET cc_start: 0.8822 (tpp) cc_final: 0.8432 (tpp) REVERT: G 136 MET cc_start: 0.6433 (tpp) cc_final: 0.5783 (mtm) REVERT: G 177 TYR cc_start: 0.8299 (m-80) cc_final: 0.7942 (m-80) outliers start: 36 outliers final: 27 residues processed: 240 average time/residue: 0.1023 time to fit residues: 37.7214 Evaluate side-chains 245 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 33 ILE 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 249 ILE 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 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 217 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 148 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 0.0270 chunk 144 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 F 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.141573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.130124 restraints weight = 15952.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.104936 restraints weight = 37495.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.103250 restraints weight = 45954.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.103154 restraints weight = 37706.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.103878 restraints weight = 26920.070| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.278 15218 Z= 0.113 Angle : 0.608 28.062 20744 Z= 0.268 Chirality : 0.042 0.163 2147 Planarity : 0.004 0.038 2582 Dihedral : 18.331 162.811 2393 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.81 % Allowed : 11.65 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.20), residues: 1773 helix: 1.51 (0.17), residues: 945 sheet: -1.69 (0.57), residues: 70 loop : 0.03 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.016 0.001 TYR B 359 PHE 0.026 0.001 PHE D 87 TRP 0.016 0.001 TRP F 157 HIS 0.004 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00257 (15200) covalent geometry : angle 0.56703 (20734) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.27102 ( 4) hydrogen bonds : bond 0.04346 ( 739) hydrogen bonds : angle 3.91587 ( 2109) metal coordination : bond 0.01425 ( 8) metal coordination : angle 12.86052 ( 6) Misc. bond : bond 0.16002 ( 8) *********************** 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: 26 poor density : 221 time to evaluate : 0.326 Fit side-chains REVERT: A 68 LEU cc_start: 0.6114 (mt) cc_final: 0.5865 (tt) REVERT: A 186 LEU cc_start: 0.5886 (mt) cc_final: 0.5499 (tp) REVERT: B 12 ARG cc_start: 0.6967 (mmp-170) cc_final: 0.6651 (mmp-170) REVERT: B 180 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8061 (tp) REVERT: B 260 LEU cc_start: 0.8063 (mp) cc_final: 0.7604 (mt) REVERT: B 279 ASN cc_start: 0.8447 (t0) cc_final: 0.8147 (t0) REVERT: B 317 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6806 (mp) REVERT: B 342 VAL cc_start: 0.8862 (p) cc_final: 0.8607 (m) REVERT: B 362 MET cc_start: 0.7615 (mtp) cc_final: 0.7289 (ttm) REVERT: C 246 MET cc_start: 0.7730 (mmm) cc_final: 0.7199 (mmm) REVERT: E 45 GLN cc_start: 0.6447 (mp10) cc_final: 0.6178 (mp10) REVERT: E 125 MET cc_start: 0.4953 (pmm) cc_final: 0.4702 (ttm) REVERT: F 140 MET cc_start: 0.6683 (mtp) cc_final: 0.6396 (mtm) REVERT: F 352 SER cc_start: 0.7990 (t) cc_final: 0.7502 (m) REVERT: F 431 HIS cc_start: 0.5947 (m-70) cc_final: 0.5435 (m-70) REVERT: G 125 MET cc_start: 0.8785 (tpp) cc_final: 0.8399 (tpp) REVERT: G 136 MET cc_start: 0.6367 (tpp) cc_final: 0.6001 (mtm) outliers start: 26 outliers final: 23 residues processed: 240 average time/residue: 0.0996 time to fit residues: 36.6154 Evaluate side-chains 241 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU 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 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 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 217 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 101 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 87 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 148 optimal weight: 0.0570 chunk 174 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 117 optimal weight: 0.0060 chunk 79 optimal weight: 2.9990 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.143766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.132424 restraints weight = 15941.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.103962 restraints weight = 34406.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.103640 restraints weight = 33349.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.103570 restraints weight = 26885.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.103882 restraints weight = 22496.847| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.261 15218 Z= 0.108 Angle : 0.583 23.918 20744 Z= 0.259 Chirality : 0.041 0.160 2147 Planarity : 0.004 0.038 2582 Dihedral : 17.811 161.246 2393 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 1.39 % Allowed : 11.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.20), residues: 1773 helix: 1.67 (0.17), residues: 940 sheet: -1.67 (0.56), residues: 80 loop : 0.20 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 77 TYR 0.014 0.001 TYR B 359 PHE 0.024 0.001 PHE D 87 TRP 0.018 0.001 TRP F 157 HIS 0.008 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00247 (15200) covalent geometry : angle 0.55007 (20734) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.21651 ( 4) hydrogen bonds : bond 0.04088 ( 739) hydrogen bonds : angle 3.80817 ( 2109) metal coordination : bond 0.01147 ( 8) metal coordination : angle 11.35814 ( 6) Misc. bond : bond 0.14754 ( 8) ********************** 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 244 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.435 Fit side-chains REVERT: A 68 LEU cc_start: 0.6168 (mt) cc_final: 0.5951 (tt) REVERT: A 70 LYS cc_start: 0.7586 (mttt) cc_final: 0.7341 (mttp) REVERT: A 186 LEU cc_start: 0.6055 (mt) cc_final: 0.5571 (tp) REVERT: B 12 ARG cc_start: 0.6961 (mmp-170) cc_final: 0.6609 (mmp-170) REVERT: B 180 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8244 (tp) REVERT: B 260 LEU cc_start: 0.8034 (mp) cc_final: 0.7548 (mt) REVERT: B 279 ASN cc_start: 0.8425 (t0) cc_final: 0.8066 (t0) REVERT: B 317 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6625 (mp) REVERT: B 342 VAL cc_start: 0.8824 (p) cc_final: 0.8558 (m) REVERT: B 362 MET cc_start: 0.7634 (mtp) cc_final: 0.7311 (ttm) REVERT: C 144 PHE cc_start: 0.7559 (m-80) cc_final: 0.7313 (m-80) REVERT: E 125 MET cc_start: 0.5023 (pmm) cc_final: 0.4593 (ttm) REVERT: F 352 SER cc_start: 0.7944 (t) cc_final: 0.7466 (m) REVERT: G 125 MET cc_start: 0.8824 (tpp) cc_final: 0.8441 (tpp) REVERT: G 136 MET cc_start: 0.6459 (tpp) cc_final: 0.5907 (mtm) REVERT: G 246 MET cc_start: 0.8170 (mmm) cc_final: 0.7582 (mmp) outliers start: 20 outliers final: 18 residues processed: 238 average time/residue: 0.0899 time to fit residues: 33.2928 Evaluate side-chains 235 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 28 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN F 272 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.143987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.128466 restraints weight = 15606.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.107779 restraints weight = 39050.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.104345 restraints weight = 36951.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.103430 restraints weight = 34855.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.104056 restraints weight = 25444.689| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.247 15218 Z= 0.111 Angle : 0.593 24.163 20744 Z= 0.261 Chirality : 0.041 0.159 2147 Planarity : 0.004 0.039 2582 Dihedral : 17.659 160.686 2393 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 1.46 % Allowed : 11.58 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.20), residues: 1773 helix: 1.64 (0.17), residues: 945 sheet: -1.59 (0.63), residues: 65 loop : 0.14 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.017 0.001 TYR G 267 PHE 0.023 0.001 PHE D 87 TRP 0.015 0.001 TRP F 157 HIS 0.005 0.001 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00258 (15200) covalent geometry : angle 0.56036 (20734) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.27256 ( 4) hydrogen bonds : bond 0.04237 ( 739) hydrogen bonds : angle 3.82050 ( 2109) metal coordination : bond 0.01114 ( 8) metal coordination : angle 11.36754 ( 6) Misc. bond : bond 0.14449 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.38 seconds wall clock time: 37 minutes 59.59 seconds (2279.59 seconds total)