Starting phenix.real_space_refine on Tue Feb 11 07:18:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xpd_22285/02_2025/6xpd_22285.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xpd_22285/02_2025/6xpd_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_22285/02_2025/6xpd_22285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xpd_22285/02_2025/6xpd_22285.map" model { file = "/net/cci-nas-00/data/ceres_data/6xpd_22285/02_2025/6xpd_22285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xpd_22285/02_2025/6xpd_22285.cif" } resolution = 3.8 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= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.32, per 1000 atoms: 0.72 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: 1.22 Conformation dependent library (CDL) restraints added in 545.8 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: 0.41 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: 1.19 Time building geometry restraints manager: 1.40 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: 0.02 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.700 Find NCS groups from input model: 0.150 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.320 ------------------------------------------------------------------------------- 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 : 0.007 0.036 4714 Z= 0.456 Angle : 0.770 6.410 6422 Z= 0.430 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 : 13.89 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 (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: -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 TRP 0.016 0.002 TRP A 122 HIS 0.014 0.002 HIS B 220 PHE 0.020 0.002 PHE A 82 TYR 0.011 0.002 TYR B 160 ARG 0.001 0.000 ARG A 331 *********************** 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 : 0.534 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: 0.2039 time to fit residues: 32.8928 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 : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 A 106 HIS A 172 GLN A 211 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097431 restraints weight = 8688.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099878 restraints weight = 5123.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101535 restraints weight = 3683.277| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4714 Z= 0.178 Angle : 0.566 5.306 6422 Z= 0.295 Chirality : 0.038 0.111 800 Planarity : 0.004 0.032 776 Dihedral : 4.616 21.033 630 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.54 % Allowed : 14.45 % Favored : 83.01 % 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: -0.31 (0.36), residues: 594 helix: 0.97 (0.26), residues: 390 sheet: -3.75 (0.73), residues: 40 loop : -2.06 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 122 HIS 0.006 0.001 HIS A 197 PHE 0.016 0.001 PHE A 82 TYR 0.006 0.001 TYR A 160 ARG 0.002 0.000 ARG B 325 *********************** 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 135 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.439 Fit side-chains REVERT: B 72 TRP cc_start: 0.7178 (m100) cc_final: 0.6562 (t-100) REVERT: A 72 TRP cc_start: 0.7052 (m100) cc_final: 0.6656 (t-100) REVERT: A 85 MET cc_start: 0.6303 (tmm) cc_final: 0.5900 (tmm) outliers start: 13 outliers final: 10 residues processed: 127 average time/residue: 0.1071 time to fit residues: 19.2515 Evaluate side-chains 98 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 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 A residue 151 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 50 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 30.0000 chunk 4 optimal weight: 0.0670 overall best weight: 1.7924 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.117668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.097017 restraints weight = 8779.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099485 restraints weight = 5181.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100989 restraints weight = 3722.125| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4714 Z= 0.192 Angle : 0.578 7.591 6422 Z= 0.291 Chirality : 0.038 0.138 800 Planarity : 0.004 0.032 776 Dihedral : 4.367 21.053 630 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.10 % Allowed : 20.90 % 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 (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: 0.69 (0.37), residues: 594 helix: 1.85 (0.26), residues: 384 sheet: -3.79 (0.68), residues: 40 loop : -1.73 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 122 HIS 0.004 0.001 HIS A 197 PHE 0.012 0.001 PHE A 82 TYR 0.018 0.001 TYR B 67 ARG 0.001 0.000 ARG B 331 *********************** 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 116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.541 Fit side-chains REVERT: B 72 TRP cc_start: 0.7215 (m100) cc_final: 0.6474 (t-100) REVERT: B 224 ASN cc_start: 0.7858 (m110) cc_final: 0.7520 (m-40) REVERT: A 72 TRP cc_start: 0.7179 (m100) cc_final: 0.6598 (t-100) REVERT: A 85 MET cc_start: 0.6332 (tmm) cc_final: 0.5924 (tmm) outliers start: 21 outliers final: 21 residues processed: 107 average time/residue: 0.1112 time to fit residues: 16.8190 Evaluate side-chains 112 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 LEU 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 B residue 353 SER Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.118379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097517 restraints weight = 8839.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099874 restraints weight = 5234.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101616 restraints weight = 3786.005| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4714 Z= 0.189 Angle : 0.562 6.042 6422 Z= 0.281 Chirality : 0.038 0.109 800 Planarity : 0.004 0.034 776 Dihedral : 4.202 20.111 630 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.49 % Allowed : 22.27 % Favored : 73.24 % 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: 1.01 (0.37), residues: 594 helix: 2.07 (0.26), residues: 384 sheet: -3.60 (0.63), residues: 46 loop : -1.46 (0.55), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 122 HIS 0.008 0.001 HIS B 220 PHE 0.010 0.001 PHE A 82 TYR 0.019 0.001 TYR B 67 ARG 0.001 0.000 ARG A 215 *********************** 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 116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.601 Fit side-chains REVERT: B 151 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8829 (mm) outliers start: 23 outliers final: 19 residues processed: 107 average time/residue: 0.0999 time to fit residues: 15.4002 Evaluate side-chains 103 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 167 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 LEU 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 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 236 LEU 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 353 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3541 r_free = 0.3541 target = 0.118064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.097462 restraints weight = 8835.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099922 restraints weight = 5253.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101593 restraints weight = 3769.311| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4714 Z= 0.204 Angle : 0.569 6.518 6422 Z= 0.289 Chirality : 0.038 0.116 800 Planarity : 0.004 0.034 776 Dihedral : 4.162 20.013 630 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.08 % Allowed : 24.41 % Favored : 70.51 % 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: 1.03 (0.36), residues: 594 helix: 2.07 (0.26), residues: 384 sheet: -3.42 (0.65), residues: 46 loop : -1.45 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 122 HIS 0.011 0.001 HIS A 220 PHE 0.030 0.001 PHE B 240 TYR 0.020 0.001 TYR B 67 ARG 0.001 0.000 ARG B 215 *********************** 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 127 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.479 Fit side-chains REVERT: B 151 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8788 (mm) REVERT: A 215 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7694 (ttp-170) outliers start: 26 outliers final: 20 residues processed: 113 average time/residue: 0.1068 time to fit residues: 16.9374 Evaluate side-chains 105 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 236 LEU 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 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 236 LEU 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 30 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 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 = 0.3554 r_free = 0.3554 target = 0.119041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098557 restraints weight = 8852.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101020 restraints weight = 5259.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102707 restraints weight = 3780.405| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4714 Z= 0.193 Angle : 0.599 7.310 6422 Z= 0.299 Chirality : 0.038 0.127 800 Planarity : 0.004 0.035 776 Dihedral : 4.144 19.618 630 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.88 % Allowed : 26.37 % 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 (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: 1.14 (0.36), residues: 594 helix: 2.09 (0.26), residues: 384 sheet: -3.06 (0.86), residues: 34 loop : -1.50 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 122 HIS 0.011 0.001 HIS A 220 PHE 0.024 0.001 PHE B 240 TYR 0.020 0.001 TYR B 67 ARG 0.001 0.000 ARG A 215 *********************** 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 121 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.649 Fit side-chains outliers start: 25 outliers final: 21 residues processed: 110 average time/residue: 0.1045 time to fit residues: 16.5015 Evaluate side-chains 110 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 167 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 LEU 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 236 LEU 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 5 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3547 r_free = 0.3547 target = 0.118705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098520 restraints weight = 8892.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100984 restraints weight = 5297.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102631 restraints weight = 3798.724| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4714 Z= 0.215 Angle : 0.606 7.943 6422 Z= 0.304 Chirality : 0.039 0.144 800 Planarity : 0.004 0.035 776 Dihedral : 4.161 19.241 630 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.69 % Allowed : 27.15 % Favored : 68.16 % 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: 1.14 (0.36), residues: 594 helix: 2.04 (0.26), residues: 384 sheet: -2.98 (0.88), residues: 34 loop : -1.41 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 152 HIS 0.018 0.001 HIS A 220 PHE 0.032 0.002 PHE A 240 TYR 0.019 0.001 TYR B 67 ARG 0.001 0.000 ARG A 215 *********************** 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 116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.485 Fit side-chains outliers start: 24 outliers final: 21 residues processed: 105 average time/residue: 0.1010 time to fit residues: 15.1580 Evaluate side-chains 108 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 LEU 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 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 236 LEU 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 8 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 26 optimal weight: 0.0970 chunk 50 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- 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** B 174 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.3528 r_free = 0.3528 target = 0.117104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.097113 restraints weight = 8795.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099523 restraints weight = 5231.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101120 restraints weight = 3756.311| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4714 Z= 0.266 Angle : 0.664 8.395 6422 Z= 0.330 Chirality : 0.040 0.127 800 Planarity : 0.004 0.036 776 Dihedral : 4.392 24.345 630 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.47 % Allowed : 27.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.36), residues: 594 helix: 1.76 (0.26), residues: 390 sheet: -3.07 (0.85), residues: 34 loop : -1.31 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 152 HIS 0.019 0.002 HIS A 220 PHE 0.029 0.002 PHE A 240 TYR 0.020 0.002 TYR B 67 ARG 0.001 0.000 ARG A 215 *********************** 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 123 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.536 Fit side-chains REVERT: B 174 GLN cc_start: 0.6240 (OUTLIER) cc_final: 0.5818 (pm20) REVERT: B 215 ARG cc_start: 0.8033 (ttt-90) cc_final: 0.7694 (ttp-170) outliers start: 28 outliers final: 21 residues processed: 114 average time/residue: 0.1123 time to fit residues: 17.8786 Evaluate side-chains 111 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 174 GLN Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 LEU 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 150 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 236 LEU 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 34 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN ** A 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 = 0.3516 r_free = 0.3516 target = 0.116326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096208 restraints weight = 9065.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098591 restraints weight = 5392.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100224 restraints weight = 3878.262| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4714 Z= 0.304 Angle : 0.693 9.534 6422 Z= 0.349 Chirality : 0.041 0.135 800 Planarity : 0.004 0.036 776 Dihedral : 4.548 25.846 630 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.08 % Allowed : 27.73 % 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 (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: 0.79 (0.36), residues: 594 helix: 1.69 (0.25), residues: 390 sheet: -3.16 (0.83), residues: 34 loop : -1.41 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 152 HIS 0.024 0.002 HIS A 220 PHE 0.027 0.002 PHE A 240 TYR 0.019 0.002 TYR B 67 ARG 0.001 0.000 ARG A 215 *********************** 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 121 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.510 Fit side-chains REVERT: B 174 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.5667 (pm20) REVERT: B 215 ARG cc_start: 0.8036 (ttt-90) cc_final: 0.7655 (ttp-170) outliers start: 26 outliers final: 24 residues processed: 111 average time/residue: 0.1253 time to fit residues: 19.0789 Evaluate side-chains 115 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 167 LEU Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 LEU 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 150 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 236 LEU 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 17 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 0.0040 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN A 174 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.101171 restraints weight = 8733.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103651 restraints weight = 5059.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105257 restraints weight = 3570.651| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4714 Z= 0.197 Angle : 0.663 9.853 6422 Z= 0.326 Chirality : 0.039 0.136 800 Planarity : 0.004 0.036 776 Dihedral : 4.405 24.977 630 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.93 % Allowed : 30.66 % Favored : 66.41 % 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: 1.04 (0.36), residues: 594 helix: 1.96 (0.26), residues: 384 sheet: -3.03 (0.86), residues: 34 loop : -1.43 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 152 HIS 0.028 0.002 HIS B 220 PHE 0.025 0.001 PHE A 240 TYR 0.021 0.001 TYR B 67 ARG 0.001 0.000 ARG A 215 ********************** 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 108 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.490 Fit side-chains REVERT: B 174 GLN cc_start: 0.6003 (OUTLIER) cc_final: 0.5417 (mt0) REVERT: A 174 GLN cc_start: 0.6096 (OUTLIER) cc_final: 0.5713 (pm20) REVERT: A 264 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7110 (mm) outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.1066 time to fit residues: 15.3225 Evaluate side-chains 104 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain A residue 72 TRP Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 236 LEU 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 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 31 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.120639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100651 restraints weight = 8880.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103117 restraints weight = 5298.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104782 restraints weight = 3796.858| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 4714 Z= 0.323 Angle : 1.310 59.199 6422 Z= 0.791 Chirality : 0.054 0.905 800 Planarity : 0.008 0.192 776 Dihedral : 4.508 29.808 630 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.73 % Allowed : 31.05 % Favored : 66.21 % Cbeta Deviations : 0.17 % 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: 1.02 (0.36), residues: 594 helix: 1.97 (0.26), residues: 384 sheet: -3.04 (0.86), residues: 34 loop : -1.49 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 152 HIS 0.027 0.002 HIS B 220 PHE 0.024 0.001 PHE A 240 TYR 0.020 0.001 TYR B 67 ARG 0.001 0.000 ARG A 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.44 seconds wall clock time: 27 minutes 5.68 seconds (1625.68 seconds total)