Starting phenix.real_space_refine on Fri Dec 27 13:26:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gt6_34245/12_2024/8gt6_34245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gt6_34245/12_2024/8gt6_34245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gt6_34245/12_2024/8gt6_34245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gt6_34245/12_2024/8gt6_34245.map" model { file = "/net/cci-nas-00/data/ceres_data/8gt6_34245/12_2024/8gt6_34245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gt6_34245/12_2024/8gt6_34245.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 140 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3160 2.51 5 N 859 2.21 5 O 877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4922 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2429 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain breaks: 5 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2429 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain breaks: 5 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'WJ6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.86, per 1000 atoms: 0.78 Number of scatterers: 4922 At special positions: 0 Unit cell: (65.331, 86.751, 102.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 877 8.00 N 859 7.00 C 3160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 624.7 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 60.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 16 through 36 removed outlier: 3.621A pdb=" N LEU A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 33 " --> pdb=" O CYS A 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 70 removed outlier: 4.142A pdb=" N TYR A 46 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.852A pdb=" N THR A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 108 removed outlier: 4.431A pdb=" N LEU A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 134 removed outlier: 4.114A pdb=" N LEU A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.606A pdb=" N CYS A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 167 through 186 Proline residue: A 173 - end of helix removed outlier: 4.224A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 3.573A pdb=" N GLN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 299 removed outlier: 3.646A pdb=" N GLN A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.968A pdb=" N GLU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 36 removed outlier: 3.621A pdb=" N LEU B 23 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 33 " --> pdb=" O CYS B 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 70 removed outlier: 4.142A pdb=" N TYR B 46 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 80 through 88 removed outlier: 3.852A pdb=" N THR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 108 removed outlier: 4.431A pdb=" N LEU B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 removed outlier: 4.114A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.606A pdb=" N CYS B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 167 through 186 Proline residue: B 173 - end of helix removed outlier: 4.224A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.573A pdb=" N GLN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 299 removed outlier: 3.646A pdb=" N GLN B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.968A pdb=" N GLU B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 249 removed outlier: 3.538A pdb=" N CYS A 257 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 255 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU A 249 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR A 314 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 202 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 249 removed outlier: 3.570A pdb=" N CYS B 257 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 255 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU B 249 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ARG B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 198 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE B 312 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE B 200 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR B 314 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 202 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 666 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: 1.16 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 778 1.30 - 1.43: 1362 1.43 - 1.56: 2859 1.56 - 1.68: 0 1.68 - 1.81: 32 Bond restraints: 5031 Sorted by residual: bond pdb=" C20 WJ6 A 401 " pdb=" C21 WJ6 A 401 " ideal model delta sigma weight residual 1.325 1.535 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C39 WJ6 A 401 " pdb=" N13 WJ6 A 401 " ideal model delta sigma weight residual 1.465 1.307 0.158 2.00e-02 2.50e+03 6.27e+01 bond pdb=" C41 WJ6 A 401 " pdb=" N13 WJ6 A 401 " ideal model delta sigma weight residual 1.468 1.314 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C27 WJ6 A 401 " pdb=" C28 WJ6 A 401 " ideal model delta sigma weight residual 1.410 1.259 0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C44 WJ6 A 401 " pdb=" N13 WJ6 A 401 " ideal model delta sigma weight residual 1.464 1.318 0.146 2.00e-02 2.50e+03 5.32e+01 ... (remaining 5026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 6686 3.31 - 6.62: 117 6.62 - 9.93: 21 9.93 - 13.25: 3 13.25 - 16.56: 4 Bond angle restraints: 6831 Sorted by residual: angle pdb=" C20 WJ6 A 401 " pdb=" C21 WJ6 A 401 " pdb=" C22 WJ6 A 401 " ideal model delta sigma weight residual 126.79 110.23 16.56 3.00e+00 1.11e-01 3.05e+01 angle pdb=" C4 WJ6 A 401 " pdb=" N1 WJ6 A 401 " pdb=" C9 WJ6 A 401 " ideal model delta sigma weight residual 106.05 119.41 -13.36 3.00e+00 1.11e-01 1.98e+01 angle pdb=" C3 WJ6 A 401 " pdb=" C8 WJ6 A 401 " pdb=" C7 WJ6 A 401 " ideal model delta sigma weight residual 106.52 119.75 -13.23 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C19 WJ6 A 401 " pdb=" C20 WJ6 A 401 " pdb=" C21 WJ6 A 401 " ideal model delta sigma weight residual 124.95 112.69 12.26 3.00e+00 1.11e-01 1.67e+01 angle pdb=" CA LEU B 89 " pdb=" CB LEU B 89 " pdb=" CG LEU B 89 " ideal model delta sigma weight residual 116.30 130.03 -13.73 3.50e+00 8.16e-02 1.54e+01 ... (remaining 6826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 2646 17.49 - 34.97: 280 34.97 - 52.46: 51 52.46 - 69.95: 22 69.95 - 87.44: 6 Dihedral angle restraints: 3005 sinusoidal: 1205 harmonic: 1800 Sorted by residual: dihedral pdb=" CA ASP B 205 " pdb=" C ASP B 205 " pdb=" N CYS B 206 " pdb=" CA CYS B 206 " ideal model delta harmonic sigma weight residual -180.00 -136.05 -43.95 0 5.00e+00 4.00e-02 7.73e+01 dihedral pdb=" CA ASP A 205 " pdb=" C ASP A 205 " pdb=" N CYS A 206 " pdb=" CA CYS A 206 " ideal model delta harmonic sigma weight residual -180.00 -136.05 -43.95 0 5.00e+00 4.00e-02 7.73e+01 dihedral pdb=" CA CYS A 206 " pdb=" C CYS A 206 " pdb=" N GLY A 207 " pdb=" CA GLY A 207 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 3002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 496 0.043 - 0.087: 188 0.087 - 0.130: 50 0.130 - 0.173: 19 0.173 - 0.216: 13 Chirality restraints: 766 Sorted by residual: chirality pdb=" CA ILE B 244 " pdb=" N ILE B 244 " pdb=" C ILE B 244 " pdb=" CB ILE B 244 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR B 256 " pdb=" CA THR B 256 " pdb=" OG1 THR B 256 " pdb=" CG2 THR B 256 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB THR A 256 " pdb=" CA THR A 256 " pdb=" OG1 THR A 256 " pdb=" CG2 THR A 256 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 763 not shown) Planarity restraints: 859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 WJ6 A 401 " 0.048 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" C20 WJ6 A 401 " -0.050 2.00e-02 2.50e+03 pdb=" C21 WJ6 A 401 " -0.045 2.00e-02 2.50e+03 pdb=" C22 WJ6 A 401 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 205 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ASP A 205 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP A 205 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS A 206 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 205 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ASP B 205 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP B 205 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS B 206 " 0.018 2.00e-02 2.50e+03 ... (remaining 856 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1630 2.84 - 3.35: 4628 3.35 - 3.87: 7795 3.87 - 4.38: 9040 4.38 - 4.90: 14963 Nonbonded interactions: 38056 Sorted by model distance: nonbonded pdb=" O PRO B 264 " pdb=" OG1 THR B 267 " model vdw 2.322 3.040 nonbonded pdb=" O PRO A 264 " pdb=" OG1 THR A 267 " model vdw 2.322 3.040 nonbonded pdb=" O PHE B 269 " pdb=" OG SER B 272 " model vdw 2.326 3.040 nonbonded pdb=" O PHE A 269 " pdb=" OG SER A 272 " model vdw 2.326 3.040 nonbonded pdb=" OE1 GLU A 246 " pdb=" CD ARG A 253 " model vdw 2.356 3.440 ... (remaining 38051 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 5 through 337) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.000 Extract box with map and model: 0.840 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 15.160 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 0.210 5031 Z= 0.679 Angle : 1.125 16.558 6831 Z= 0.535 Chirality : 0.056 0.216 766 Planarity : 0.007 0.061 859 Dihedral : 16.017 87.436 1845 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.77 % Allowed : 7.53 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.26), residues: 594 helix: -3.69 (0.15), residues: 306 sheet: -2.07 (0.54), residues: 74 loop : -1.98 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.004 0.001 HIS A 7 PHE 0.009 0.002 PHE A 291 TYR 0.018 0.002 TYR A 77 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.713 Fit side-chains REVERT: A 56 LEU cc_start: 0.9596 (mt) cc_final: 0.9380 (mt) REVERT: A 120 MET cc_start: 0.7522 (mpp) cc_final: 0.7286 (mpp) REVERT: A 174 GLU cc_start: 0.7738 (tp30) cc_final: 0.7512 (tp30) REVERT: A 223 ASP cc_start: 0.8192 (t0) cc_final: 0.7617 (t0) REVERT: A 238 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6302 (mmt-90) REVERT: B 56 LEU cc_start: 0.9596 (mt) cc_final: 0.9379 (mt) REVERT: B 120 MET cc_start: 0.7526 (mpp) cc_final: 0.7289 (mpp) REVERT: B 174 GLU cc_start: 0.7745 (tp30) cc_final: 0.7514 (tp30) REVERT: B 218 ASN cc_start: 0.7978 (t0) cc_final: 0.7665 (t0) REVERT: B 223 ASP cc_start: 0.8426 (t0) cc_final: 0.7851 (t0) REVERT: B 237 ASP cc_start: 0.6115 (m-30) cc_final: 0.5220 (p0) outliers start: 4 outliers final: 2 residues processed: 142 average time/residue: 0.1792 time to fit residues: 32.9149 Evaluate side-chains 128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 244 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 24 optimal weight: 0.0670 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 61 ASN A 266 GLN A 335 GLN B 7 HIS B 61 ASN B 266 GLN B 335 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5031 Z= 0.168 Angle : 0.708 11.961 6831 Z= 0.328 Chirality : 0.040 0.137 766 Planarity : 0.005 0.044 859 Dihedral : 7.136 62.694 729 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.54 % Allowed : 15.83 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.31), residues: 594 helix: -1.59 (0.23), residues: 350 sheet: -1.07 (0.80), residues: 46 loop : -1.70 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 119 HIS 0.001 0.000 HIS B 42 PHE 0.003 0.001 PHE B 269 TYR 0.009 0.001 TYR A 107 ARG 0.002 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.465 Fit side-chains REVERT: A 119 TRP cc_start: 0.7832 (t60) cc_final: 0.7538 (t60) REVERT: A 120 MET cc_start: 0.7770 (mpp) cc_final: 0.7388 (mpp) REVERT: A 224 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8887 (mmmt) REVERT: A 257 CYS cc_start: 0.7746 (p) cc_final: 0.7542 (p) REVERT: A 292 CYS cc_start: 0.8587 (m) cc_final: 0.8385 (m) REVERT: B 119 TRP cc_start: 0.7833 (t60) cc_final: 0.7541 (t60) REVERT: B 120 MET cc_start: 0.7766 (mpp) cc_final: 0.7385 (mpp) REVERT: B 224 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8783 (mmmt) REVERT: B 237 ASP cc_start: 0.6386 (m-30) cc_final: 0.5443 (p0) REVERT: B 257 CYS cc_start: 0.7799 (p) cc_final: 0.7582 (p) REVERT: B 292 CYS cc_start: 0.8597 (m) cc_final: 0.8390 (m) outliers start: 8 outliers final: 4 residues processed: 154 average time/residue: 0.1614 time to fit residues: 31.7376 Evaluate side-chains 136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.0270 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5031 Z= 0.154 Angle : 0.653 11.277 6831 Z= 0.299 Chirality : 0.040 0.160 766 Planarity : 0.004 0.037 859 Dihedral : 6.414 61.821 721 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.32 % Allowed : 17.37 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.33), residues: 594 helix: -0.61 (0.24), residues: 350 sheet: -1.79 (0.59), residues: 74 loop : -1.15 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 34 HIS 0.001 0.000 HIS B 157 PHE 0.003 0.001 PHE A 221 TYR 0.018 0.001 TYR A 104 ARG 0.005 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TRP cc_start: 0.7986 (t60) cc_final: 0.7424 (t60) REVERT: A 224 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8847 (mmmt) REVERT: A 246 GLU cc_start: 0.5320 (pp20) cc_final: 0.5063 (pp20) REVERT: A 292 CYS cc_start: 0.8542 (m) cc_final: 0.8330 (m) REVERT: B 119 TRP cc_start: 0.7987 (t60) cc_final: 0.7426 (t60) REVERT: B 224 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8758 (mmmt) REVERT: B 237 ASP cc_start: 0.6432 (m-30) cc_final: 0.5679 (p0) REVERT: B 292 CYS cc_start: 0.8546 (m) cc_final: 0.8341 (m) outliers start: 12 outliers final: 6 residues processed: 144 average time/residue: 0.1454 time to fit residues: 28.1728 Evaluate side-chains 134 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 74 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5031 Z= 0.151 Angle : 0.678 11.882 6831 Z= 0.298 Chirality : 0.041 0.169 766 Planarity : 0.004 0.034 859 Dihedral : 6.217 61.385 721 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.70 % Allowed : 20.66 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.34), residues: 594 helix: 0.07 (0.26), residues: 350 sheet: -1.91 (0.56), residues: 74 loop : -0.91 (0.54), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 161 HIS 0.002 0.001 HIS A 74 PHE 0.023 0.001 PHE A 117 TYR 0.009 0.001 TYR A 199 ARG 0.004 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.583 Fit side-chains REVERT: A 119 TRP cc_start: 0.7937 (t60) cc_final: 0.7446 (t60) REVERT: A 224 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8775 (mmmt) REVERT: A 292 CYS cc_start: 0.8473 (m) cc_final: 0.8262 (m) REVERT: B 119 TRP cc_start: 0.7938 (t60) cc_final: 0.7448 (t60) REVERT: B 224 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8771 (mmmt) REVERT: B 237 ASP cc_start: 0.6488 (m-30) cc_final: 0.5765 (p0) REVERT: B 246 GLU cc_start: 0.5520 (pp20) cc_final: 0.5214 (pp20) REVERT: B 292 CYS cc_start: 0.8479 (m) cc_final: 0.8262 (m) outliers start: 14 outliers final: 10 residues processed: 137 average time/residue: 0.1426 time to fit residues: 26.1149 Evaluate side-chains 131 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 132 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 0.0020 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.006 0.064 5031 Z= 0.374 Angle : 0.771 10.828 6831 Z= 0.350 Chirality : 0.045 0.172 766 Planarity : 0.004 0.037 859 Dihedral : 6.583 61.188 721 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.09 % Allowed : 20.08 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.34), residues: 594 helix: 0.17 (0.26), residues: 350 sheet: -1.84 (0.73), residues: 46 loop : -1.22 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 34 HIS 0.002 0.001 HIS A 72 PHE 0.008 0.002 PHE B 279 TYR 0.011 0.002 TYR B 77 ARG 0.003 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.645 Fit side-chains REVERT: A 119 TRP cc_start: 0.8052 (t60) cc_final: 0.7816 (t60) REVERT: A 150 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8264 (ttpp) REVERT: A 224 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8882 (mmmt) REVERT: A 292 CYS cc_start: 0.8563 (m) cc_final: 0.8313 (m) REVERT: B 119 TRP cc_start: 0.8053 (t60) cc_final: 0.7816 (t60) REVERT: B 150 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8265 (ttpp) REVERT: B 224 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8788 (mmmt) REVERT: B 237 ASP cc_start: 0.6604 (m-30) cc_final: 0.5876 (p0) REVERT: B 292 CYS cc_start: 0.8557 (m) cc_final: 0.8311 (m) outliers start: 16 outliers final: 10 residues processed: 122 average time/residue: 0.1485 time to fit residues: 23.9899 Evaluate side-chains 114 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5031 Z= 0.157 Angle : 0.684 11.221 6831 Z= 0.304 Chirality : 0.042 0.201 766 Planarity : 0.004 0.037 859 Dihedral : 6.316 61.834 721 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.12 % Allowed : 21.81 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 594 helix: 0.52 (0.27), residues: 350 sheet: -2.96 (0.78), residues: 32 loop : -1.14 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 119 HIS 0.002 0.000 HIS A 74 PHE 0.029 0.002 PHE A 117 TYR 0.008 0.001 TYR B 199 ARG 0.007 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.645 Fit side-chains REVERT: A 119 TRP cc_start: 0.8045 (t60) cc_final: 0.7458 (t60) REVERT: A 150 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8228 (ttpp) REVERT: A 224 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8820 (mmmt) REVERT: A 292 CYS cc_start: 0.8466 (m) cc_final: 0.8253 (m) REVERT: B 119 TRP cc_start: 0.8046 (t60) cc_final: 0.7458 (t60) REVERT: B 150 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8229 (ttpp) REVERT: B 224 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8819 (mmmt) REVERT: B 237 ASP cc_start: 0.6494 (m-30) cc_final: 0.6010 (p0) REVERT: B 292 CYS cc_start: 0.8475 (m) cc_final: 0.8259 (m) outliers start: 11 outliers final: 9 residues processed: 127 average time/residue: 0.1565 time to fit residues: 26.4176 Evaluate side-chains 127 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 261 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5031 Z= 0.200 Angle : 0.712 11.003 6831 Z= 0.313 Chirality : 0.043 0.178 766 Planarity : 0.004 0.038 859 Dihedral : 6.267 61.098 721 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.54 % Allowed : 23.36 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.35), residues: 594 helix: 0.60 (0.27), residues: 350 sheet: -3.04 (0.77), residues: 32 loop : -1.12 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 119 HIS 0.001 0.000 HIS A 42 PHE 0.004 0.001 PHE A 117 TYR 0.008 0.001 TYR A 199 ARG 0.005 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.666 Fit side-chains REVERT: A 119 TRP cc_start: 0.8056 (t60) cc_final: 0.7428 (t60) REVERT: A 150 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8219 (ttpp) REVERT: A 224 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8835 (mmmt) REVERT: A 292 CYS cc_start: 0.8483 (m) cc_final: 0.8244 (m) REVERT: B 119 TRP cc_start: 0.8055 (t60) cc_final: 0.7426 (t60) REVERT: B 150 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8228 (ttpp) REVERT: B 218 ASN cc_start: 0.7397 (t0) cc_final: 0.7063 (t0) REVERT: B 224 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8831 (mmmt) REVERT: B 237 ASP cc_start: 0.6464 (m-30) cc_final: 0.6028 (p0) REVERT: B 292 CYS cc_start: 0.8491 (m) cc_final: 0.8250 (m) outliers start: 8 outliers final: 8 residues processed: 122 average time/residue: 0.1987 time to fit residues: 33.3963 Evaluate side-chains 127 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5031 Z= 0.157 Angle : 0.703 11.961 6831 Z= 0.306 Chirality : 0.043 0.227 766 Planarity : 0.004 0.037 859 Dihedral : 6.181 61.404 721 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.32 % Allowed : 22.59 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.35), residues: 594 helix: 0.69 (0.27), residues: 350 sheet: -3.07 (0.77), residues: 32 loop : -1.05 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 119 HIS 0.001 0.000 HIS A 74 PHE 0.005 0.001 PHE B 105 TYR 0.008 0.001 TYR B 199 ARG 0.005 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.641 Fit side-chains REVERT: A 119 TRP cc_start: 0.8149 (t60) cc_final: 0.7434 (t60) REVERT: A 150 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8218 (ttpp) REVERT: A 224 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8808 (mmmt) REVERT: A 292 CYS cc_start: 0.8459 (m) cc_final: 0.8237 (m) REVERT: B 119 TRP cc_start: 0.8150 (t60) cc_final: 0.7434 (t60) REVERT: B 150 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8220 (ttpp) REVERT: B 214 MET cc_start: 0.7893 (ppp) cc_final: 0.7693 (ppp) REVERT: B 218 ASN cc_start: 0.7489 (t0) cc_final: 0.7176 (t0) REVERT: B 224 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8812 (mmmt) REVERT: B 237 ASP cc_start: 0.6341 (m-30) cc_final: 0.6084 (p0) REVERT: B 292 CYS cc_start: 0.8466 (m) cc_final: 0.8246 (m) outliers start: 12 outliers final: 10 residues processed: 129 average time/residue: 0.1427 time to fit residues: 24.8194 Evaluate side-chains 128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 47 optimal weight: 7.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5031 Z= 0.150 Angle : 0.772 12.020 6831 Z= 0.325 Chirality : 0.044 0.259 766 Planarity : 0.004 0.037 859 Dihedral : 6.067 60.520 721 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.32 % Allowed : 21.81 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.35), residues: 594 helix: 0.52 (0.26), residues: 354 sheet: -3.08 (0.77), residues: 32 loop : -0.96 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 161 HIS 0.002 0.000 HIS A 74 PHE 0.005 0.001 PHE B 105 TYR 0.009 0.001 TYR B 199 ARG 0.005 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.612 Fit side-chains REVERT: A 119 TRP cc_start: 0.8161 (t60) cc_final: 0.7502 (t60) REVERT: A 120 MET cc_start: 0.7275 (mpt) cc_final: 0.6956 (mpt) REVERT: A 224 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8779 (mmmt) REVERT: A 292 CYS cc_start: 0.8432 (m) cc_final: 0.8219 (m) REVERT: B 119 TRP cc_start: 0.8161 (t60) cc_final: 0.7503 (t60) REVERT: B 120 MET cc_start: 0.7275 (mpt) cc_final: 0.6954 (mpt) REVERT: B 218 ASN cc_start: 0.7597 (t0) cc_final: 0.7270 (t0) REVERT: B 224 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8770 (mmmt) REVERT: B 292 CYS cc_start: 0.8442 (m) cc_final: 0.8238 (m) outliers start: 12 outliers final: 10 residues processed: 133 average time/residue: 0.1404 time to fit residues: 25.1605 Evaluate side-chains 129 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 147 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5031 Z= 0.179 Angle : 0.781 11.816 6831 Z= 0.333 Chirality : 0.045 0.276 766 Planarity : 0.004 0.037 859 Dihedral : 6.093 60.300 721 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.93 % Allowed : 22.20 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.35), residues: 594 helix: 0.57 (0.26), residues: 350 sheet: -3.00 (0.77), residues: 32 loop : -0.88 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.002 0.000 HIS A 74 PHE 0.004 0.001 PHE A 105 TYR 0.008 0.001 TYR B 199 ARG 0.005 0.000 ARG B 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.530 Fit side-chains REVERT: A 119 TRP cc_start: 0.8149 (t60) cc_final: 0.7809 (t60) REVERT: A 120 MET cc_start: 0.7188 (mpt) cc_final: 0.6892 (mpt) REVERT: A 224 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8796 (mmmt) REVERT: A 292 CYS cc_start: 0.8455 (m) cc_final: 0.8232 (m) REVERT: B 119 TRP cc_start: 0.8149 (t60) cc_final: 0.7808 (t60) REVERT: B 120 MET cc_start: 0.7187 (mpt) cc_final: 0.6892 (mpt) REVERT: B 224 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8804 (mmmt) REVERT: B 271 MET cc_start: 0.7907 (mtp) cc_final: 0.7562 (mtp) REVERT: B 292 CYS cc_start: 0.8455 (m) cc_final: 0.8244 (m) outliers start: 10 outliers final: 10 residues processed: 124 average time/residue: 0.1535 time to fit residues: 25.2311 Evaluate side-chains 124 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 147 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.0870 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.125890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.095253 restraints weight = 11200.584| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.71 r_work: 0.3209 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5031 Z= 0.189 Angle : 0.760 11.741 6831 Z= 0.331 Chirality : 0.045 0.279 766 Planarity : 0.004 0.037 859 Dihedral : 6.171 61.260 721 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.93 % Allowed : 22.97 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.35), residues: 594 helix: 0.63 (0.26), residues: 354 sheet: -2.90 (0.78), residues: 32 loop : -0.86 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 161 HIS 0.002 0.000 HIS B 74 PHE 0.005 0.001 PHE B 105 TYR 0.008 0.001 TYR A 199 ARG 0.005 0.000 ARG B 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1574.59 seconds wall clock time: 29 minutes 52.48 seconds (1792.48 seconds total)