Starting phenix.real_space_refine on Tue Mar 3 12:52:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xpd_22285/03_2026/6xpd_22285.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xpd_22285/03_2026/6xpd_22285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xpd_22285/03_2026/6xpd_22285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xpd_22285/03_2026/6xpd_22285.map" model { file = "/net/cci-nas-00/data/ceres_data/6xpd_22285/03_2026/6xpd_22285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xpd_22285/03_2026/6xpd_22285.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 144 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 32 5.16 5 C 3010 2.51 5 N 754 2.21 5 O 822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4622 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2309 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2309 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2325 SG CYS A 53 42.422 21.767 23.908 1.00 88.16 S ATOM 2246 SG CYS B 361 39.757 15.017 23.922 1.00 99.56 S ATOM 2271 SG CYS B 364 39.570 17.025 26.950 1.00 81.28 S ATOM 16 SG CYS B 53 33.976 39.660 23.918 1.00 89.15 S ATOM 4555 SG CYS A 361 36.712 46.426 23.890 1.00100.58 S ATOM 4580 SG CYS A 364 36.887 44.419 26.919 1.00 82.53 S Time building chain proxies: 1.33, per 1000 atoms: 0.29 Number of scatterers: 4622 At special positions: 0 Unit cell: (77.19, 62.25, 102.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 32 16.00 O 822 8.00 N 754 7.00 C 3010 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: 0.35 Conformation dependent library (CDL) restraints added in 286.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 318 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 301 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 53 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 364 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS B 54 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 361 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS B 52 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 301 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 318 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 53 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 364 " pdb="ZN ZN B 402 " - pdb=" ND1 HIS A 54 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 361 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS A 52 " Number of angles added : 4 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: 1164 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 69.0% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 63 through 94 removed outlier: 3.844A pdb=" N TYR B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 126 removed outlier: 4.078A pdb=" N HIS B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 168 Processing helix chain 'B' and resid 176 through 196 removed outlier: 3.637A pdb=" N ILE B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 241 removed outlier: 3.688A pdb=" N ASN B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 275 removed outlier: 4.478A pdb=" N ILE B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 326 through 342 removed outlier: 3.983A pdb=" N VAL B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 365 removed outlier: 4.655A pdb=" N LEU B 362 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE B 363 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 94 removed outlier: 3.843A pdb=" N TYR A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 126 removed outlier: 4.036A pdb=" N HIS A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 168 Processing helix chain 'A' and resid 176 through 196 removed outlier: 3.637A pdb=" N ILE A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 182 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 241 removed outlier: 3.688A pdb=" N ASN A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 275 removed outlier: 4.478A pdb=" N ILE A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.983A pdb=" N VAL A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 365 removed outlier: 4.655A pdb=" N LEU A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE A 363 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 297 through 304 removed outlier: 5.680A pdb=" N VAL B 300 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA B 320 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER B 302 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B 318 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 315 " --> pdb=" O THR B 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 304 removed outlier: 5.679A pdb=" N VAL A 300 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA A 320 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER A 302 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS A 318 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 315 " --> pdb=" O THR A 348 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 894 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: 0.68 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1432 1.34 - 1.46: 1103 1.46 - 1.58: 2135 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 4714 Sorted by residual: bond pdb=" CA THR A 348 " pdb=" CB THR A 348 " ideal model delta sigma weight residual 1.527 1.498 0.029 2.48e-02 1.63e+03 1.38e+00 bond pdb=" C SER B 262 " pdb=" O SER B 262 " ideal model delta sigma weight residual 1.237 1.250 -0.014 1.17e-02 7.31e+03 1.36e+00 bond pdb=" CA THR B 348 " pdb=" CB THR B 348 " ideal model delta sigma weight residual 1.527 1.499 0.029 2.48e-02 1.63e+03 1.33e+00 bond pdb=" CG LEU B 308 " pdb=" CD1 LEU B 308 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU A 308 " pdb=" CD1 LEU A 308 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.16e+00 ... (remaining 4709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 5932 1.28 - 2.56: 369 2.56 - 3.85: 91 3.85 - 5.13: 22 5.13 - 6.41: 8 Bond angle restraints: 6422 Sorted by residual: angle pdb=" C SER B 353 " pdb=" N PRO B 354 " pdb=" CA PRO B 354 " ideal model delta sigma weight residual 119.05 122.88 -3.83 1.11e+00 8.12e-01 1.19e+01 angle pdb=" C SER A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.05 122.56 -3.51 1.11e+00 8.12e-01 9.98e+00 angle pdb=" C ASP B 356 " pdb=" N GLN B 357 " pdb=" CA GLN B 357 " ideal model delta sigma weight residual 122.41 117.98 4.43 1.41e+00 5.03e-01 9.86e+00 angle pdb=" C ASP A 356 " pdb=" N GLN A 357 " pdb=" CA GLN A 357 " ideal model delta sigma weight residual 122.16 118.05 4.11 1.50e+00 4.44e-01 7.51e+00 angle pdb=" N PRO B 354 " pdb=" CA PRO B 354 " pdb=" C PRO B 354 " ideal model delta sigma weight residual 113.53 110.13 3.40 1.39e+00 5.18e-01 6.00e+00 ... (remaining 6417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.92: 2330 12.92 - 25.83: 325 25.83 - 38.75: 94 38.75 - 51.67: 28 51.67 - 64.58: 11 Dihedral angle restraints: 2788 sinusoidal: 1008 harmonic: 1780 Sorted by residual: dihedral pdb=" CA LEU B 308 " pdb=" C LEU B 308 " pdb=" N THR B 309 " pdb=" CA THR B 309 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N THR A 309 " pdb=" CA THR A 309 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLU A 88 " pdb=" C GLU A 88 " pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 2785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 520 0.039 - 0.078: 232 0.078 - 0.118: 41 0.118 - 0.157: 5 0.157 - 0.196: 2 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA ASP A 356 " pdb=" N ASP A 356 " pdb=" C ASP A 356 " pdb=" CB ASP A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" CA ASP B 356 " pdb=" N ASP B 356 " pdb=" C ASP B 356 " pdb=" CB ASP B 356 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" CB ILE A 305 " pdb=" CA ILE A 305 " pdb=" CG1 ILE A 305 " pdb=" CG2 ILE A 305 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 797 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 220 " -0.010 2.00e-02 2.50e+03 1.21e-02 2.18e+00 pdb=" CG HIS B 220 " 0.026 2.00e-02 2.50e+03 pdb=" ND1 HIS B 220 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 220 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS B 220 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 220 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 220 " 0.011 2.00e-02 2.50e+03 1.20e-02 2.16e+00 pdb=" CG HIS A 220 " -0.026 2.00e-02 2.50e+03 pdb=" ND1 HIS A 220 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS A 220 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 220 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 220 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 365 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C GLU B 365 " -0.021 2.00e-02 2.50e+03 pdb=" O GLU B 365 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP B 366 " 0.007 2.00e-02 2.50e+03 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 3 2.15 - 2.84: 1695 2.84 - 3.52: 7055 3.52 - 4.21: 10088 4.21 - 4.90: 17725 Nonbonded interactions: 36566 Sorted by model distance: nonbonded pdb=" OE2 GLU A 352 " pdb="ZN ZN A 401 " model vdw 1.461 2.230 nonbonded pdb=" OE2 GLU B 352 " pdb="ZN ZN B 401 " model vdw 1.781 2.230 nonbonded pdb=" OG1 THR B 348 " pdb=" OG1 THR A 348 " model vdw 2.140 3.040 nonbonded pdb=" O GLN B 227 " pdb=" OG SER B 230 " model vdw 2.184 3.040 nonbonded pdb=" O GLN A 227 " pdb=" OG SER A 230 " model vdw 2.185 3.040 ... (remaining 36561 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.023 0.723 4728 Z= 0.699 Angle : 0.915 26.729 6426 Z= 0.439 Chirality : 0.043 0.196 800 Planarity : 0.003 0.022 776 Dihedral : 14.372 64.582 1624 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.20 % Allowed : 12.50 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.30), residues: 594 helix: -1.82 (0.22), residues: 384 sheet: -3.84 (0.69), residues: 46 loop : -3.48 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 331 TYR 0.011 0.002 TYR B 160 PHE 0.020 0.002 PHE A 82 TRP 0.016 0.002 TRP A 122 HIS 0.014 0.002 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 4714) covalent geometry : angle 0.76998 ( 6422) hydrogen bonds : bond 0.19814 ( 306) hydrogen bonds : angle 7.66761 ( 894) metal coordination : bond 0.40370 ( 14) metal coordination : angle 19.84357 ( 4) *********************** 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 135 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: B 71 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8312 (ttpp) REVERT: B 288 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8783 (ttmm) REVERT: B 295 ASP cc_start: 0.7659 (p0) cc_final: 0.7168 (p0) REVERT: A 71 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8300 (ttpp) REVERT: A 85 MET cc_start: 0.6314 (tmm) cc_final: 0.5953 (tmm) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.0894 time to fit residues: 14.4886 Evaluate side-chains 88 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN B 211 ASN B 224 ASN A 172 GLN A 211 ASN A 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093526 restraints weight = 8794.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.095909 restraints weight = 5244.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097491 restraints weight = 3795.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098415 restraints weight = 3096.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098730 restraints weight = 2757.897| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4728 Z= 0.180 Angle : 0.619 5.349 6426 Z= 0.319 Chirality : 0.040 0.112 800 Planarity : 0.004 0.032 776 Dihedral : 4.876 21.016 630 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.52 % Allowed : 17.38 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.36), residues: 594 helix: 0.78 (0.26), residues: 390 sheet: -3.94 (0.62), residues: 46 loop : -2.17 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 215 TYR 0.008 0.001 TYR A 160 PHE 0.016 0.001 PHE A 82 TRP 0.013 0.001 TRP B 122 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 4714) covalent geometry : angle 0.61809 ( 6422) hydrogen bonds : bond 0.05501 ( 306) hydrogen bonds : angle 4.02399 ( 894) metal coordination : bond 0.00677 ( 14) metal coordination : angle 1.78005 ( 4) *********************** 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 133 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.177 Fit side-chains REVERT: B 151 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8783 (mm) REVERT: B 229 ILE cc_start: 0.9204 (pt) cc_final: 0.8959 (mt) REVERT: A 85 MET cc_start: 0.6332 (tmm) cc_final: 0.5973 (tmm) REVERT: A 151 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8797 (mm) REVERT: A 344 MET cc_start: 0.8010 (mmm) cc_final: 0.7673 (mmm) outliers start: 18 outliers final: 11 residues processed: 121 average time/residue: 0.0407 time to fit residues: 7.1742 Evaluate side-chains 103 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 305 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 54 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN A 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098839 restraints weight = 8564.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101324 restraints weight = 5097.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.102952 restraints weight = 3668.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104047 restraints weight = 2985.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104598 restraints weight = 2618.542| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4728 Z= 0.119 Angle : 0.619 14.588 6426 Z= 0.286 Chirality : 0.037 0.107 800 Planarity : 0.003 0.033 776 Dihedral : 4.263 19.467 630 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.93 % Allowed : 22.07 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.37), residues: 594 helix: 1.83 (0.26), residues: 392 sheet: -3.70 (0.70), residues: 40 loop : -1.77 (0.55), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 215 TYR 0.004 0.001 TYR A 160 PHE 0.011 0.001 PHE A 82 TRP 0.009 0.001 TRP B 122 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 4714) covalent geometry : angle 0.56057 ( 6422) hydrogen bonds : bond 0.04456 ( 306) hydrogen bonds : angle 3.31331 ( 894) metal coordination : bond 0.01256 ( 14) metal coordination : angle 10.50411 ( 4) *********************** 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 119 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.175 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 112 average time/residue: 0.0474 time to fit residues: 7.5962 Evaluate side-chains 101 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain A residue 72 TRP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 353 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 15 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.120079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099549 restraints weight = 8836.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102054 restraints weight = 5198.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103753 restraints weight = 3718.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104654 restraints weight = 3016.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105358 restraints weight = 2681.902| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4728 Z= 0.118 Angle : 0.580 10.653 6426 Z= 0.278 Chirality : 0.037 0.112 800 Planarity : 0.004 0.034 776 Dihedral : 4.018 17.164 630 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.71 % Allowed : 23.44 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.37), residues: 594 helix: 2.06 (0.26), residues: 392 sheet: -3.42 (0.73), residues: 40 loop : -1.54 (0.55), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 325 TYR 0.020 0.001 TYR B 67 PHE 0.026 0.001 PHE B 240 TRP 0.008 0.001 TRP B 122 HIS 0.007 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 4714) covalent geometry : angle 0.54850 ( 6422) hydrogen bonds : bond 0.04278 ( 306) hydrogen bonds : angle 3.21573 ( 894) metal coordination : bond 0.00932 ( 14) metal coordination : angle 7.58319 ( 4) *********************** 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 106 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.172 Fit side-chains REVERT: B 151 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8793 (mm) REVERT: A 151 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8773 (mm) outliers start: 19 outliers final: 15 residues processed: 96 average time/residue: 0.0428 time to fit residues: 6.1725 Evaluate side-chains 103 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain A residue 72 TRP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 353 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.118413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098035 restraints weight = 8896.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100511 restraints weight = 5211.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102181 restraints weight = 3723.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103065 restraints weight = 3016.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103534 restraints weight = 2676.866| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4728 Z= 0.142 Angle : 0.595 9.441 6426 Z= 0.287 Chirality : 0.039 0.151 800 Planarity : 0.004 0.037 776 Dihedral : 4.063 18.067 630 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.49 % Allowed : 24.22 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.37), residues: 594 helix: 2.07 (0.26), residues: 392 sheet: -3.29 (0.74), residues: 40 loop : -1.52 (0.55), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 215 TYR 0.019 0.001 TYR B 67 PHE 0.020 0.001 PHE B 240 TRP 0.009 0.001 TRP B 122 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4714) covalent geometry : angle 0.57358 ( 6422) hydrogen bonds : bond 0.04364 ( 306) hydrogen bonds : angle 3.33479 ( 894) metal coordination : bond 0.00717 ( 14) metal coordination : angle 6.38598 ( 4) *********************** 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 123 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.179 Fit side-chains REVERT: B 151 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8785 (mm) REVERT: B 215 ARG cc_start: 0.8005 (ttt-90) cc_final: 0.7624 (ttp-170) REVERT: B 269 ASP cc_start: 0.8419 (t0) cc_final: 0.8199 (t0) REVERT: A 151 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8739 (mm) outliers start: 23 outliers final: 17 residues processed: 112 average time/residue: 0.0479 time to fit residues: 7.7112 Evaluate side-chains 106 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain A residue 72 TRP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 353 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098558 restraints weight = 8981.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101038 restraints weight = 5289.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.102697 restraints weight = 3775.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103534 restraints weight = 3054.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104236 restraints weight = 2717.918| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4728 Z= 0.136 Angle : 0.634 10.254 6426 Z= 0.295 Chirality : 0.039 0.131 800 Planarity : 0.003 0.035 776 Dihedral : 4.008 17.840 630 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.10 % Allowed : 25.78 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.37), residues: 594 helix: 2.08 (0.26), residues: 392 sheet: -3.16 (0.76), residues: 40 loop : -1.54 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 215 TYR 0.020 0.001 TYR B 67 PHE 0.016 0.001 PHE B 240 TRP 0.009 0.001 TRP A 122 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4714) covalent geometry : angle 0.61994 ( 6422) hydrogen bonds : bond 0.04316 ( 306) hydrogen bonds : angle 3.30036 ( 894) metal coordination : bond 0.00621 ( 14) metal coordination : angle 5.43869 ( 4) *********************** 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 119 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.181 Fit side-chains REVERT: B 151 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8768 (mm) REVERT: B 348 THR cc_start: 0.8069 (p) cc_final: 0.7706 (p) REVERT: A 110 ASN cc_start: 0.7774 (m-40) cc_final: 0.7370 (m-40) REVERT: A 348 THR cc_start: 0.8113 (p) cc_final: 0.7752 (p) outliers start: 21 outliers final: 18 residues processed: 107 average time/residue: 0.0441 time to fit residues: 7.0203 Evaluate side-chains 111 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain A residue 72 TRP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 353 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098085 restraints weight = 8878.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100506 restraints weight = 5254.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102209 restraints weight = 3767.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103111 restraints weight = 3033.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103877 restraints weight = 2671.867| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4728 Z= 0.154 Angle : 0.645 10.513 6426 Z= 0.310 Chirality : 0.039 0.125 800 Planarity : 0.004 0.036 776 Dihedral : 4.128 22.709 630 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.08 % Allowed : 26.17 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.36), residues: 594 helix: 1.97 (0.25), residues: 392 sheet: -3.11 (0.84), residues: 34 loop : -1.59 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 215 TYR 0.020 0.001 TYR B 67 PHE 0.032 0.002 PHE A 240 TRP 0.010 0.001 TRP B 122 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4714) covalent geometry : angle 0.63134 ( 6422) hydrogen bonds : bond 0.04522 ( 306) hydrogen bonds : angle 3.34873 ( 894) metal coordination : bond 0.00580 ( 14) metal coordination : angle 5.23562 ( 4) *********************** 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 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.183 Fit side-chains REVERT: B 174 GLN cc_start: 0.6117 (OUTLIER) cc_final: 0.5728 (pm20) REVERT: B 215 ARG cc_start: 0.7922 (ttt-90) cc_final: 0.7691 (ttp-170) REVERT: A 215 ARG cc_start: 0.7950 (ttt-90) cc_final: 0.7738 (ttp-170) outliers start: 26 outliers final: 21 residues processed: 117 average time/residue: 0.0506 time to fit residues: 8.3275 Evaluate side-chains 116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain A residue 72 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 353 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 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 174 GLN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100649 restraints weight = 8898.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103118 restraints weight = 5215.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.104815 restraints weight = 3730.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105773 restraints weight = 2972.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106246 restraints weight = 2594.904| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4728 Z= 0.132 Angle : 0.640 10.799 6426 Z= 0.308 Chirality : 0.038 0.113 800 Planarity : 0.004 0.037 776 Dihedral : 4.056 25.273 630 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.49 % Allowed : 28.12 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.36), residues: 594 helix: 1.97 (0.25), residues: 392 sheet: -2.72 (1.01), residues: 28 loop : -1.53 (0.51), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 215 TYR 0.021 0.001 TYR B 67 PHE 0.028 0.001 PHE A 240 TRP 0.037 0.002 TRP A 152 HIS 0.012 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4714) covalent geometry : angle 0.63052 ( 6422) hydrogen bonds : bond 0.04370 ( 306) hydrogen bonds : angle 3.30931 ( 894) metal coordination : bond 0.00591 ( 14) metal coordination : angle 4.40039 ( 4) *********************** 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 125 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.183 Fit side-chains REVERT: B 110 ASN cc_start: 0.7666 (m-40) cc_final: 0.7239 (m-40) REVERT: B 174 GLN cc_start: 0.5977 (OUTLIER) cc_final: 0.5729 (pm20) outliers start: 23 outliers final: 19 residues processed: 114 average time/residue: 0.0436 time to fit residues: 7.3367 Evaluate side-chains 115 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain A residue 72 TRP Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 353 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN B 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098763 restraints weight = 8967.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.101216 restraints weight = 5374.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102660 restraints weight = 3851.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103762 restraints weight = 3147.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104229 restraints weight = 2743.379| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4728 Z= 0.168 Angle : 0.671 9.429 6426 Z= 0.329 Chirality : 0.040 0.150 800 Planarity : 0.004 0.037 776 Dihedral : 4.200 23.449 630 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.69 % Allowed : 28.12 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.36), residues: 594 helix: 1.83 (0.25), residues: 392 sheet: -3.16 (0.82), residues: 34 loop : -1.46 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 215 TYR 0.020 0.001 TYR B 67 PHE 0.027 0.002 PHE A 240 TRP 0.045 0.003 TRP A 152 HIS 0.021 0.002 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4714) covalent geometry : angle 0.65987 ( 6422) hydrogen bonds : bond 0.04702 ( 306) hydrogen bonds : angle 3.51940 ( 894) metal coordination : bond 0.00613 ( 14) metal coordination : angle 5.02346 ( 4) *********************** 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 122 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.180 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 110 average time/residue: 0.0510 time to fit residues: 7.9368 Evaluate side-chains 111 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain A residue 72 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 353 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 33 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097609 restraints weight = 9073.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.099890 restraints weight = 5428.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101471 restraints weight = 3923.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102448 restraints weight = 3188.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103006 restraints weight = 2794.415| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4728 Z= 0.188 Angle : 0.719 9.600 6426 Z= 0.351 Chirality : 0.040 0.144 800 Planarity : 0.004 0.037 776 Dihedral : 4.382 19.764 630 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.10 % Allowed : 29.30 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.36), residues: 594 helix: 1.67 (0.25), residues: 388 sheet: -3.18 (0.81), residues: 34 loop : -1.36 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 215 TYR 0.020 0.002 TYR B 67 PHE 0.025 0.002 PHE A 240 TRP 0.037 0.003 TRP B 152 HIS 0.023 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 4714) covalent geometry : angle 0.70766 ( 6422) hydrogen bonds : bond 0.04912 ( 306) hydrogen bonds : angle 3.63627 ( 894) metal coordination : bond 0.00693 ( 14) metal coordination : angle 5.20081 ( 4) ********************** 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 118 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8018 (ttt-90) cc_final: 0.7691 (ttp80) outliers start: 21 outliers final: 20 residues processed: 108 average time/residue: 0.0515 time to fit residues: 7.9404 Evaluate side-chains 113 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain A residue 72 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 353 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 0.0570 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 0.0370 chunk 44 optimal weight: 0.0570 chunk 54 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106240 restraints weight = 8739.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108685 restraints weight = 5017.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110330 restraints weight = 3517.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110934 restraints weight = 2804.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111911 restraints weight = 2525.656| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4728 Z= 0.123 Angle : 0.657 9.427 6426 Z= 0.312 Chirality : 0.038 0.113 800 Planarity : 0.004 0.038 776 Dihedral : 4.043 20.545 630 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.56 % Allowed : 32.42 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.35), residues: 594 helix: 1.86 (0.25), residues: 390 sheet: -2.71 (0.99), residues: 28 loop : -1.47 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 215 TYR 0.021 0.001 TYR A 67 PHE 0.023 0.001 PHE A 240 TRP 0.021 0.002 TRP B 152 HIS 0.017 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4714) covalent geometry : angle 0.65262 ( 6422) hydrogen bonds : bond 0.04143 ( 306) hydrogen bonds : angle 3.40147 ( 894) metal coordination : bond 0.00679 ( 14) metal coordination : angle 3.06729 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 829.34 seconds wall clock time: 15 minutes 1.16 seconds (901.16 seconds total)