Starting phenix.real_space_refine on Thu Mar 6 05:34:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gt6_34245/03_2025/8gt6_34245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gt6_34245/03_2025/8gt6_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_34245/03_2025/8gt6_34245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gt6_34245/03_2025/8gt6_34245.map" model { file = "/net/cci-nas-00/data/ceres_data/8gt6_34245/03_2025/8gt6_34245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gt6_34245/03_2025/8gt6_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.76, per 1000 atoms: 1.37 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: 1.33 Conformation dependent library (CDL) restraints added in 702.9 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: 0.62 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: 1.35 Time building geometry restraints manager: 1.64 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:3.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- 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 : 0.669 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: 0.2029 time to fit residues: 37.1073 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 : 0.878 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 3.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.126203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094699 restraints weight = 10842.972| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.76 r_work: 0.3219 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 62.695 729 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 : 0.641 Fit side-chains REVERT: A 119 TRP cc_start: 0.7885 (t60) cc_final: 0.7579 (t60) REVERT: A 120 MET cc_start: 0.7894 (mpp) cc_final: 0.7494 (mpp) REVERT: A 218 ASN cc_start: 0.7736 (t0) cc_final: 0.7527 (t0) REVERT: A 224 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8894 (mmmt) REVERT: A 238 ARG cc_start: 0.7569 (mpp-170) cc_final: 0.7223 (mmt-90) REVERT: A 257 CYS cc_start: 0.8316 (p) cc_final: 0.8069 (p) REVERT: B 119 TRP cc_start: 0.7885 (t60) cc_final: 0.7581 (t60) REVERT: B 120 MET cc_start: 0.7870 (mpp) cc_final: 0.7479 (mpp) REVERT: B 218 ASN cc_start: 0.7765 (t0) cc_final: 0.7559 (t0) REVERT: B 224 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8824 (mmmt) REVERT: B 237 ASP cc_start: 0.6464 (m-30) cc_final: 0.5397 (p0) REVERT: B 238 ARG cc_start: 0.7519 (mpp-170) cc_final: 0.7127 (mtm-85) REVERT: B 257 CYS cc_start: 0.8307 (p) cc_final: 0.8054 (p) outliers start: 8 outliers final: 4 residues processed: 154 average time/residue: 0.2188 time to fit residues: 43.4433 Evaluate side-chains 138 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.0270 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.124259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092912 restraints weight = 10945.610| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.66 r_work: 0.3181 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5031 Z= 0.209 Angle : 0.678 11.161 6831 Z= 0.312 Chirality : 0.041 0.175 766 Planarity : 0.004 0.037 859 Dihedral : 6.524 61.240 721 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.93 % Allowed : 19.11 % Favored : 78.96 % 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: -1.51 (0.33), residues: 594 helix: -0.59 (0.24), residues: 350 sheet: -1.31 (0.80), residues: 46 loop : -1.41 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 34 HIS 0.001 0.000 HIS A 157 PHE 0.004 0.001 PHE B 279 TYR 0.017 0.001 TYR A 104 ARG 0.002 0.000 ARG A 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 133 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TRP cc_start: 0.8079 (t60) cc_final: 0.7504 (t60) REVERT: A 224 LYS cc_start: 0.9115 (mmtt) cc_final: 0.8894 (mmmt) REVERT: A 238 ARG cc_start: 0.7633 (mpp-170) cc_final: 0.7221 (mmt-90) REVERT: A 246 GLU cc_start: 0.5979 (pp20) cc_final: 0.5584 (pp20) REVERT: B 119 TRP cc_start: 0.8071 (t60) cc_final: 0.7491 (t60) REVERT: B 224 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8828 (mmmt) REVERT: B 237 ASP cc_start: 0.6604 (m-30) cc_final: 0.5663 (p0) REVERT: B 238 ARG cc_start: 0.7519 (mpp-170) cc_final: 0.7204 (mtm-85) REVERT: B 246 GLU cc_start: 0.6157 (pp20) cc_final: 0.5688 (pp20) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.1801 time to fit residues: 31.1540 Evaluate side-chains 126 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 38 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 1.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.123622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.091981 restraints weight = 11388.410| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.82 r_work: 0.3158 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5031 Z= 0.235 Angle : 0.706 11.432 6831 Z= 0.315 Chirality : 0.042 0.170 766 Planarity : 0.004 0.035 859 Dihedral : 6.483 61.640 721 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.32 % Allowed : 20.66 % Favored : 77.03 % 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: -0.89 (0.34), residues: 594 helix: 0.01 (0.26), residues: 350 sheet: -1.68 (0.76), residues: 46 loop : -1.19 (0.50), residues: 198 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 0.006 0.001 PHE B 279 TYR 0.018 0.001 TYR A 104 ARG 0.001 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 136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TRP cc_start: 0.8016 (t60) cc_final: 0.7446 (t60) REVERT: A 224 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8882 (mmmt) REVERT: A 238 ARG cc_start: 0.7715 (mpp-170) cc_final: 0.7292 (mtt-85) REVERT: A 246 GLU cc_start: 0.6257 (pp20) cc_final: 0.6020 (pp20) REVERT: B 119 TRP cc_start: 0.8014 (t60) cc_final: 0.7444 (t60) REVERT: B 224 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8843 (mmmt) REVERT: B 237 ASP cc_start: 0.6585 (m-30) cc_final: 0.5723 (p0) REVERT: B 238 ARG cc_start: 0.7579 (mpp-170) cc_final: 0.7232 (mtm-85) REVERT: B 246 GLU cc_start: 0.6333 (pp20) cc_final: 0.6105 (pp20) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 0.3721 time to fit residues: 66.4726 Evaluate side-chains 124 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.126053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094333 restraints weight = 10959.689| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.80 r_work: 0.3207 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3596 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 : 0.657 11.707 6831 Z= 0.292 Chirality : 0.041 0.163 766 Planarity : 0.004 0.036 859 Dihedral : 6.255 61.187 721 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.93 % Allowed : 23.17 % Favored : 74.90 % 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: -0.56 (0.35), residues: 594 helix: 0.42 (0.27), residues: 350 sheet: -2.99 (0.77), residues: 32 loop : -1.16 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 119 HIS 0.002 0.000 HIS B 74 PHE 0.003 0.001 PHE B 269 TYR 0.020 0.001 TYR B 104 ARG 0.006 0.000 ARG B 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 148 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TRP cc_start: 0.7998 (t60) cc_final: 0.7463 (t60) REVERT: A 150 LYS cc_start: 0.8713 (ttpp) cc_final: 0.8413 (ttpp) REVERT: A 224 LYS cc_start: 0.9115 (mmtt) cc_final: 0.8817 (mmmt) REVERT: A 238 ARG cc_start: 0.7720 (mpp-170) cc_final: 0.7447 (mtt-85) REVERT: A 271 MET cc_start: 0.8501 (mtp) cc_final: 0.8287 (mtp) REVERT: B 119 TRP cc_start: 0.7990 (t60) cc_final: 0.7449 (t60) REVERT: B 150 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8413 (ttpp) REVERT: B 224 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8797 (mmmt) REVERT: B 237 ASP cc_start: 0.6685 (m-30) cc_final: 0.5850 (p0) outliers start: 10 outliers final: 8 residues processed: 145 average time/residue: 0.2000 time to fit residues: 37.8993 Evaluate side-chains 126 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 261 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.123155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.091251 restraints weight = 11078.192| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.78 r_work: 0.3146 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5031 Z= 0.271 Angle : 0.729 11.258 6831 Z= 0.327 Chirality : 0.044 0.173 766 Planarity : 0.004 0.038 859 Dihedral : 6.369 60.934 721 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.67 % Allowed : 21.62 % Favored : 74.71 % 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: -0.34 (0.35), residues: 594 helix: 0.55 (0.27), residues: 350 sheet: -2.05 (0.73), residues: 46 loop : -0.99 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 34 HIS 0.002 0.001 HIS A 72 PHE 0.006 0.001 PHE A 279 TYR 0.015 0.001 TYR B 104 ARG 0.006 0.000 ARG A 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 140 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TRP cc_start: 0.8053 (t60) cc_final: 0.7521 (t60) REVERT: A 150 LYS cc_start: 0.8746 (ttpp) cc_final: 0.8455 (ttpp) REVERT: A 224 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8897 (mmmt) REVERT: A 238 ARG cc_start: 0.7741 (mpp-170) cc_final: 0.7502 (mtt-85) REVERT: B 119 TRP cc_start: 0.8046 (t60) cc_final: 0.7510 (t60) REVERT: B 150 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8424 (ttpp) REVERT: B 224 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8851 (mmmt) REVERT: B 237 ASP cc_start: 0.6694 (m-30) cc_final: 0.5894 (p0) REVERT: B 242 ASN cc_start: 0.9197 (m-40) cc_final: 0.8960 (m-40) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.1559 time to fit residues: 27.8949 Evaluate side-chains 130 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 A residue 194 VAL Chi-restraints excluded: chain A residue 239 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 Chi-restraints excluded: chain B residue 194 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.122109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091156 restraints weight = 10928.153| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.66 r_work: 0.3137 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5031 Z= 0.265 Angle : 0.735 11.044 6831 Z= 0.325 Chirality : 0.044 0.231 766 Planarity : 0.004 0.038 859 Dihedral : 6.438 61.226 721 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.28 % Allowed : 22.20 % Favored : 74.52 % 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: -0.34 (0.35), residues: 594 helix: 0.63 (0.27), residues: 350 sheet: -3.03 (0.77), residues: 32 loop : -1.09 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 34 HIS 0.001 0.001 HIS A 72 PHE 0.006 0.001 PHE A 279 TYR 0.014 0.001 TYR B 104 ARG 0.006 0.000 ARG A 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 135 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TRP cc_start: 0.8038 (t60) cc_final: 0.7536 (t60) REVERT: A 150 LYS cc_start: 0.8711 (ttpp) cc_final: 0.8437 (ttpp) REVERT: A 238 ARG cc_start: 0.7799 (mpp-170) cc_final: 0.7508 (mtt-85) REVERT: A 246 GLU cc_start: 0.6206 (pp20) cc_final: 0.5983 (pp20) REVERT: B 119 TRP cc_start: 0.8023 (t60) cc_final: 0.7521 (t60) REVERT: B 150 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8449 (ttpp) REVERT: B 224 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8856 (mmmt) REVERT: B 237 ASP cc_start: 0.6662 (m-30) cc_final: 0.6072 (p0) REVERT: B 242 ASN cc_start: 0.9239 (m-40) cc_final: 0.9000 (m-40) outliers start: 17 outliers final: 15 residues processed: 127 average time/residue: 0.1908 time to fit residues: 33.1256 Evaluate side-chains 129 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 73 ILE 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 A residue 239 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 73 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.123236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092324 restraints weight = 11072.516| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.69 r_work: 0.3161 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3744 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= 0.210 Angle : 0.715 11.165 6831 Z= 0.317 Chirality : 0.044 0.244 766 Planarity : 0.004 0.039 859 Dihedral : 6.335 60.871 721 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.12 % Allowed : 23.94 % Favored : 73.94 % 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: -0.22 (0.36), residues: 594 helix: 0.69 (0.27), residues: 354 sheet: -2.99 (0.77), residues: 32 loop : -1.00 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 161 HIS 0.001 0.001 HIS B 42 PHE 0.006 0.001 PHE B 279 TYR 0.014 0.001 TYR B 104 ARG 0.005 0.000 ARG A 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 131 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TRP cc_start: 0.8014 (t60) cc_final: 0.7528 (t60) REVERT: A 150 LYS cc_start: 0.8702 (ttpp) cc_final: 0.8427 (ttpp) REVERT: A 238 ARG cc_start: 0.7796 (mpp-170) cc_final: 0.7512 (mtt-85) REVERT: B 119 TRP cc_start: 0.7996 (t60) cc_final: 0.7510 (t60) REVERT: B 150 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8436 (ttpp) REVERT: B 224 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8869 (mmmt) REVERT: B 237 ASP cc_start: 0.6529 (m-30) cc_final: 0.6189 (p0) outliers start: 11 outliers final: 11 residues processed: 127 average time/residue: 0.1415 time to fit residues: 23.8930 Evaluate side-chains 128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 73 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 73 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 39 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.123134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092008 restraints weight = 10774.712| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.64 r_work: 0.3155 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5031 Z= 0.231 Angle : 0.749 11.325 6831 Z= 0.331 Chirality : 0.045 0.256 766 Planarity : 0.004 0.039 859 Dihedral : 6.334 60.965 721 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.12 % Allowed : 23.75 % Favored : 74.13 % 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: -0.21 (0.35), residues: 594 helix: 0.70 (0.27), residues: 354 sheet: -3.09 (0.77), residues: 32 loop : -0.99 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 161 HIS 0.001 0.001 HIS B 74 PHE 0.006 0.001 PHE B 279 TYR 0.013 0.001 TYR B 104 ARG 0.005 0.000 ARG A 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 128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TRP cc_start: 0.8048 (t60) cc_final: 0.7524 (t60) REVERT: A 150 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8406 (ttpp) REVERT: A 238 ARG cc_start: 0.7786 (mpp-170) cc_final: 0.7508 (mtt-85) REVERT: B 119 TRP cc_start: 0.8035 (t60) cc_final: 0.7508 (t60) REVERT: B 150 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8414 (ttpp) REVERT: B 224 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8870 (mmmt) REVERT: B 237 ASP cc_start: 0.6518 (m-30) cc_final: 0.6213 (p0) outliers start: 11 outliers final: 10 residues processed: 124 average time/residue: 0.2120 time to fit residues: 34.8516 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 : 0.561 ------------------------------------------------------------------------------- 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 73 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 73 ILE Chi-restraints excluded: chain B residue 136 LEU 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 46 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 0.0470 chunk 9 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.126504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095428 restraints weight = 10899.634| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.74 r_work: 0.3216 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5031 Z= 0.154 Angle : 0.729 11.720 6831 Z= 0.318 Chirality : 0.043 0.278 766 Planarity : 0.004 0.039 859 Dihedral : 6.070 59.913 721 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.32 % Allowed : 23.55 % Favored : 74.13 % 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: 0.04 (0.36), residues: 594 helix: 0.97 (0.28), residues: 350 sheet: -3.15 (0.78), residues: 32 loop : -0.94 (0.49), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 119 HIS 0.002 0.000 HIS B 42 PHE 0.005 0.001 PHE A 105 TYR 0.014 0.001 TYR B 104 ARG 0.005 0.000 ARG A 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: 12 poor density : 118 time to evaluate : 0.563 Fit side-chains REVERT: A 119 TRP cc_start: 0.8019 (t60) cc_final: 0.7522 (t60) REVERT: A 150 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8372 (ttpp) REVERT: A 238 ARG cc_start: 0.7739 (mpp-170) cc_final: 0.7483 (mtt-85) REVERT: B 119 TRP cc_start: 0.8009 (t60) cc_final: 0.7504 (t60) REVERT: B 150 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8386 (ttpp) REVERT: B 224 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8859 (mmmt) outliers start: 12 outliers final: 10 residues processed: 126 average time/residue: 0.1561 time to fit residues: 26.3273 Evaluate side-chains 123 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 33 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.3966 > 50: distance: 77 - 105: 23.647 distance: 83 - 88: 15.675 distance: 84 - 112: 20.087 distance: 88 - 89: 12.074 distance: 89 - 90: 16.641 distance: 89 - 92: 12.845 distance: 90 - 91: 15.817 distance: 90 - 96: 22.394 distance: 91 - 120: 23.736 distance: 92 - 93: 16.286 distance: 93 - 94: 18.391 distance: 93 - 95: 8.347 distance: 96 - 97: 9.574 distance: 97 - 98: 23.240 distance: 97 - 100: 21.616 distance: 98 - 99: 14.511 distance: 98 - 105: 18.319 distance: 99 - 131: 30.889 distance: 100 - 101: 21.121 distance: 101 - 102: 23.803 distance: 102 - 104: 55.848 distance: 105 - 106: 31.120 distance: 106 - 107: 28.539 distance: 106 - 109: 34.902 distance: 107 - 108: 17.479 distance: 107 - 112: 30.279 distance: 108 - 136: 23.062 distance: 109 - 110: 18.700 distance: 109 - 111: 18.369 distance: 112 - 113: 36.155 distance: 113 - 114: 50.236 distance: 113 - 116: 55.323 distance: 114 - 115: 35.453 distance: 114 - 120: 48.825 distance: 116 - 117: 12.154 distance: 117 - 118: 41.520 distance: 117 - 119: 42.030 distance: 120 - 121: 18.170 distance: 121 - 122: 12.045 distance: 121 - 124: 37.577 distance: 122 - 131: 39.732 distance: 123 - 150: 50.822 distance: 124 - 125: 10.731 distance: 125 - 126: 21.768 distance: 125 - 127: 10.058 distance: 127 - 129: 14.956 distance: 128 - 130: 23.339 distance: 132 - 133: 20.172 distance: 132 - 135: 28.561 distance: 133 - 134: 31.866 distance: 133 - 136: 10.876 distance: 134 - 159: 44.003 distance: 136 - 137: 19.790 distance: 137 - 138: 28.274 distance: 137 - 140: 19.416 distance: 138 - 139: 27.698 distance: 138 - 144: 10.571 distance: 140 - 141: 35.801 distance: 141 - 142: 5.603 distance: 142 - 143: 37.881 distance: 144 - 145: 29.166 distance: 145 - 146: 22.197 distance: 145 - 148: 30.600 distance: 146 - 147: 26.058 distance: 146 - 150: 16.926 distance: 148 - 149: 17.061 distance: 150 - 151: 9.263 distance: 151 - 152: 20.360 distance: 151 - 154: 44.121 distance: 152 - 153: 34.379 distance: 152 - 159: 49.064 distance: 154 - 155: 3.351 distance: 155 - 156: 18.813 distance: 156 - 157: 24.895 distance: 156 - 158: 42.492 distance: 159 - 160: 8.142 distance: 160 - 161: 13.051 distance: 160 - 163: 42.570 distance: 161 - 171: 34.953 distance: 164 - 165: 11.141 distance: 164 - 166: 3.101 distance: 165 - 167: 28.743 distance: 166 - 168: 24.668 distance: 167 - 169: 20.885 distance: 168 - 169: 16.872 distance: 169 - 170: 20.684