Starting phenix.real_space_refine on Thu Feb 13 22:47:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oz1_13118/02_2025/7oz1_13118.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oz1_13118/02_2025/7oz1_13118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oz1_13118/02_2025/7oz1_13118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oz1_13118/02_2025/7oz1_13118.map" model { file = "/net/cci-nas-00/data/ceres_data/7oz1_13118/02_2025/7oz1_13118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oz1_13118/02_2025/7oz1_13118.cif" } resolution = 4.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 68 5.16 5 C 5864 2.51 5 N 1414 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8942 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4257 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 19, 'TRANS': 524} Chain breaks: 2 Chain: "B" Number of atoms: 4257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4257 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 19, 'TRANS': 524} Chain breaks: 2 Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 214 Unusual residues: {'ATP': 1, 'PEE': 1, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 214 Unusual residues: {'ATP': 1, 'PEE': 1, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 5.08, per 1000 atoms: 0.57 Number of scatterers: 8942 At special positions: 0 Unit cell: (78.54, 104.94, 123.42, 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) S 68 16.00 P 8 15.00 O 1588 8.00 N 1414 7.00 C 5864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS A 617 " distance=2.04 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS B 617 " distance=2.04 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: 2.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 60.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.748A pdb=" N LYS A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.924A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.633A pdb=" N ALA A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 211 " --> pdb=" O SER A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' Processing helix chain 'A' and resid 218 through 232 removed outlier: 4.046A pdb=" N GLU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.857A pdb=" N ASP A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 3.607A pdb=" N SER A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.673A pdb=" N ARG A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 439 through 475 removed outlier: 3.887A pdb=" N MET A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Proline residue: A 460 - end of helix Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 482 through 513 removed outlier: 3.628A pdb=" N TYR A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Proline residue: A 496 - end of helix Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 518 through 547 removed outlier: 4.322A pdb=" N PHE A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 Proline residue: A 558 - end of helix Processing helix chain 'A' and resid 560 through 567 removed outlier: 4.139A pdb=" N VAL A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.697A pdb=" N SER A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 586' Processing helix chain 'A' and resid 588 through 602 removed outlier: 3.779A pdb=" N TYR A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 636 through 664 removed outlier: 3.740A pdb=" N PHE A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.748A pdb=" N LYS B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 205 removed outlier: 3.924A pdb=" N GLU B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.632A pdb=" N ALA B 210 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 207 through 211' Processing helix chain 'B' and resid 218 through 232 removed outlier: 4.046A pdb=" N GLU B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.857A pdb=" N ASP B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.607A pdb=" N SER B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 4.673A pdb=" N ARG B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 439 through 475 removed outlier: 3.887A pdb=" N MET B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Proline residue: B 460 - end of helix Proline residue: B 466 - end of helix Processing helix chain 'B' and resid 482 through 513 removed outlier: 3.628A pdb=" N TYR B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Proline residue: B 496 - end of helix Proline residue: B 502 - end of helix Processing helix chain 'B' and resid 518 through 547 removed outlier: 4.322A pdb=" N PHE B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 560 Proline residue: B 558 - end of helix Processing helix chain 'B' and resid 560 through 567 removed outlier: 4.139A pdb=" N VAL B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.696A pdb=" N SER B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 586 " --> pdb=" O GLN B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 586' Processing helix chain 'B' and resid 588 through 602 removed outlier: 3.779A pdb=" N TYR B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 636 through 664 removed outlier: 3.741A pdb=" N PHE B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 99 removed outlier: 5.219A pdb=" N ILE A 104 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 removed outlier: 4.209A pdb=" N LEU A 82 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS A 140 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 161 removed outlier: 6.752A pdb=" N CYS A 160 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN A 286 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 291 removed outlier: 7.006A pdb=" N VAL A 289 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 99 removed outlier: 5.219A pdb=" N ILE B 104 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 99 removed outlier: 4.209A pdb=" N LEU B 82 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 140 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 removed outlier: 6.751A pdb=" N CYS B 160 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B 286 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 291 removed outlier: 7.007A pdb=" N VAL B 289 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1397 1.32 - 1.45: 2380 1.45 - 1.57: 5245 1.57 - 1.70: 14 1.70 - 1.83: 110 Bond restraints: 9146 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.89e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C5 ATP B 701 " pdb=" C6 ATP B 701 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C8 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.20e+01 ... (remaining 9141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 12322 3.66 - 7.33: 72 7.33 - 10.99: 8 10.99 - 14.65: 0 14.65 - 18.31: 6 Bond angle restraints: 12408 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 123.04 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 123.04 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 120.56 16.27 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 120.59 16.24 1.00e+00 1.00e+00 2.64e+02 angle pdb=" N PRO A 276 " pdb=" CA PRO A 276 " pdb=" C PRO A 276 " ideal model delta sigma weight residual 112.47 94.16 18.31 2.06e+00 2.36e-01 7.90e+01 ... (remaining 12403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 5712 34.15 - 68.30: 156 68.30 - 102.46: 14 102.46 - 136.61: 0 136.61 - 170.76: 6 Dihedral angle restraints: 5888 sinusoidal: 2746 harmonic: 3142 Sorted by residual: dihedral pdb=" CB CYS A 611 " pdb=" SG CYS A 611 " pdb=" SG CYS A 617 " pdb=" CB CYS A 617 " ideal model delta sinusoidal sigma weight residual -86.00 -45.47 -40.53 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CB CYS B 611 " pdb=" SG CYS B 611 " pdb=" SG CYS B 617 " pdb=" CB CYS B 617 " ideal model delta sinusoidal sigma weight residual -86.00 -45.49 -40.51 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" C4 PEE B 706 " pdb=" O4P PEE B 706 " pdb=" P PEE B 706 " pdb=" O2P PEE B 706 " ideal model delta sinusoidal sigma weight residual 284.22 113.46 170.76 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1238 0.070 - 0.140: 167 0.140 - 0.210: 19 0.210 - 0.280: 4 0.280 - 0.350: 2 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA PRO A 276 " pdb=" N PRO A 276 " pdb=" C PRO A 276 " pdb=" CB PRO A 276 " both_signs ideal model delta sigma weight residual False 2.72 3.07 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA PRO B 276 " pdb=" N PRO B 276 " pdb=" C PRO B 276 " pdb=" CB PRO B 276 " both_signs ideal model delta sigma weight residual False 2.72 3.07 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CBE Y01 B 702 " pdb=" CAP Y01 B 702 " pdb=" CBB Y01 B 702 " pdb=" CBI Y01 B 702 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1427 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 277 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C SER B 277 " -0.061 2.00e-02 2.50e+03 pdb=" O SER B 277 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA B 278 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 277 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C SER A 277 " 0.060 2.00e-02 2.50e+03 pdb=" O SER A 277 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA A 278 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 459 " 0.034 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO A 460 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " 0.029 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 119 2.67 - 3.23: 8739 3.23 - 3.78: 13178 3.78 - 4.34: 17986 4.34 - 4.90: 28954 Nonbonded interactions: 68976 Sorted by model distance: nonbonded pdb=" OG SER B 125 " pdb=" O1B ATP B 701 " model vdw 2.109 3.040 nonbonded pdb=" OG SER A 125 " pdb=" O1B ATP A 701 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR B 297 " pdb=" O LYS B 300 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR A 297 " pdb=" O LYS A 300 " model vdw 2.160 3.040 nonbonded pdb=" O LEU B 550 " pdb=" OG1 THR B 554 " model vdw 2.251 3.040 ... (remaining 68971 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 664 or resid 701 through 704)) selection = (chain 'B' and (resid 74 through 664 or resid 701 through 704)) } 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: 9.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.670 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.006 0.083 9146 Z= 0.401 Angle : 0.916 18.314 12408 Z= 0.584 Chirality : 0.051 0.350 1430 Planarity : 0.004 0.051 1490 Dihedral : 16.761 170.761 3870 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.21 % Allowed : 7.51 % Favored : 92.27 % 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: -3.23 (0.23), residues: 1076 helix: -1.39 (0.18), residues: 602 sheet: -1.84 (0.63), residues: 74 loop : -3.31 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 480 HIS 0.002 0.001 HIS A 171 PHE 0.012 0.002 PHE B 646 TYR 0.009 0.001 TYR B 481 ARG 0.003 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8493 (tpp) cc_final: 0.8029 (tpt) REVERT: A 259 MET cc_start: 0.8671 (ttm) cc_final: 0.8359 (ttm) REVERT: A 492 MET cc_start: 0.7730 (mmm) cc_final: 0.7334 (mtp) REVERT: A 511 TRP cc_start: 0.8125 (m100) cc_final: 0.7833 (m-10) REVERT: A 609 LEU cc_start: 0.8598 (tp) cc_final: 0.8385 (tp) REVERT: B 179 MET cc_start: 0.8477 (tpp) cc_final: 0.7954 (tpt) REVERT: B 259 MET cc_start: 0.8654 (ttm) cc_final: 0.8327 (ttm) REVERT: B 492 MET cc_start: 0.7721 (mmm) cc_final: 0.7368 (mtp) REVERT: B 511 TRP cc_start: 0.8110 (m100) cc_final: 0.7852 (m-10) REVERT: B 609 LEU cc_start: 0.8582 (tp) cc_final: 0.8366 (tp) outliers start: 2 outliers final: 0 residues processed: 201 average time/residue: 0.2441 time to fit residues: 65.1750 Evaluate side-chains 142 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 336 GLN A 418 HIS B 175 GLN B 418 HIS B 633 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121063 restraints weight = 12369.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123476 restraints weight = 8153.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125259 restraints weight = 5930.327| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9146 Z= 0.178 Angle : 0.632 5.791 12408 Z= 0.312 Chirality : 0.041 0.170 1430 Planarity : 0.004 0.034 1490 Dihedral : 14.859 176.243 1896 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.29 % Allowed : 15.45 % Favored : 83.26 % 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: -1.74 (0.25), residues: 1076 helix: -0.05 (0.21), residues: 612 sheet: -1.66 (0.58), residues: 74 loop : -2.85 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.004 0.001 HIS A 319 PHE 0.014 0.002 PHE B 281 TYR 0.007 0.001 TYR B 510 ARG 0.007 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.035 Fit side-chains REVERT: A 178 MET cc_start: 0.7968 (mmm) cc_final: 0.7406 (mmm) REVERT: A 179 MET cc_start: 0.8650 (tpp) cc_final: 0.8299 (tpt) REVERT: A 298 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7838 (tmm-80) REVERT: A 404 ILE cc_start: 0.8032 (tt) cc_final: 0.7669 (mt) REVERT: A 407 ASP cc_start: 0.8208 (t0) cc_final: 0.7974 (t0) REVERT: A 446 LEU cc_start: 0.8243 (tp) cc_final: 0.7903 (tp) REVERT: A 492 MET cc_start: 0.7736 (mmm) cc_final: 0.7248 (mtp) REVERT: A 511 TRP cc_start: 0.7962 (m100) cc_final: 0.7640 (m-10) REVERT: A 609 LEU cc_start: 0.8513 (tp) cc_final: 0.8197 (tp) REVERT: B 178 MET cc_start: 0.7960 (mmm) cc_final: 0.7366 (mmm) REVERT: B 179 MET cc_start: 0.8613 (tpp) cc_final: 0.8151 (tpt) REVERT: B 298 ARG cc_start: 0.8435 (tmm-80) cc_final: 0.8228 (ttt180) REVERT: B 404 ILE cc_start: 0.8036 (tt) cc_final: 0.7678 (mt) REVERT: B 407 ASP cc_start: 0.8159 (t0) cc_final: 0.7944 (t0) REVERT: B 446 LEU cc_start: 0.8220 (tp) cc_final: 0.7856 (tp) REVERT: B 492 MET cc_start: 0.7751 (mmm) cc_final: 0.7285 (mtp) REVERT: B 511 TRP cc_start: 0.7925 (m100) cc_final: 0.7566 (m-10) REVERT: B 609 LEU cc_start: 0.8501 (tp) cc_final: 0.8174 (tp) outliers start: 12 outliers final: 8 residues processed: 159 average time/residue: 0.2086 time to fit residues: 46.4928 Evaluate side-chains 142 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 467 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 82 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN A 418 HIS B 418 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117755 restraints weight = 12898.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120344 restraints weight = 8270.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122167 restraints weight = 5933.547| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9146 Z= 0.238 Angle : 0.609 5.703 12408 Z= 0.302 Chirality : 0.041 0.146 1430 Planarity : 0.004 0.033 1490 Dihedral : 14.018 173.506 1896 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.04 % Allowed : 18.67 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.26), residues: 1076 helix: 0.31 (0.21), residues: 622 sheet: -1.61 (0.57), residues: 74 loop : -2.71 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 583 HIS 0.012 0.001 HIS B 418 PHE 0.008 0.001 PHE B 646 TYR 0.009 0.001 TYR B 288 ARG 0.005 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.115 Fit side-chains REVERT: A 179 MET cc_start: 0.8624 (tpp) cc_final: 0.8319 (tpt) REVERT: A 404 ILE cc_start: 0.8070 (tt) cc_final: 0.7726 (mt) REVERT: A 407 ASP cc_start: 0.8234 (t0) cc_final: 0.8023 (t0) REVERT: A 492 MET cc_start: 0.7656 (mmm) cc_final: 0.7214 (mtp) REVERT: A 511 TRP cc_start: 0.7975 (m100) cc_final: 0.7681 (m-10) REVERT: B 179 MET cc_start: 0.8578 (tpp) cc_final: 0.8157 (tpt) REVERT: B 298 ARG cc_start: 0.8385 (tmm-80) cc_final: 0.8182 (ttt180) REVERT: B 404 ILE cc_start: 0.8073 (tt) cc_final: 0.7727 (mt) REVERT: B 492 MET cc_start: 0.7708 (mmm) cc_final: 0.7280 (mtp) REVERT: B 511 TRP cc_start: 0.7934 (m100) cc_final: 0.7661 (m-10) outliers start: 19 outliers final: 15 residues processed: 153 average time/residue: 0.2137 time to fit residues: 47.1758 Evaluate side-chains 148 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 657 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS B 418 HIS B 582 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120142 restraints weight = 12551.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122618 restraints weight = 8251.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124357 restraints weight = 5967.997| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9146 Z= 0.166 Angle : 0.580 6.320 12408 Z= 0.282 Chirality : 0.040 0.139 1430 Planarity : 0.004 0.032 1490 Dihedral : 13.153 169.055 1896 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.47 % Allowed : 19.31 % Favored : 78.22 % 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: -0.86 (0.26), residues: 1076 helix: 0.66 (0.22), residues: 624 sheet: -1.45 (0.57), residues: 74 loop : -2.52 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 583 HIS 0.007 0.001 HIS B 171 PHE 0.017 0.001 PHE B 281 TYR 0.006 0.001 TYR A 510 ARG 0.003 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.020 Fit side-chains REVERT: A 179 MET cc_start: 0.8617 (tpp) cc_final: 0.8400 (tpt) REVERT: A 404 ILE cc_start: 0.8014 (tt) cc_final: 0.7721 (mt) REVERT: A 492 MET cc_start: 0.7617 (mmm) cc_final: 0.7180 (mtp) REVERT: A 511 TRP cc_start: 0.7924 (m100) cc_final: 0.7542 (m-10) REVERT: B 178 MET cc_start: 0.7953 (mmm) cc_final: 0.7337 (mmm) REVERT: B 179 MET cc_start: 0.8595 (tpp) cc_final: 0.8210 (tpt) REVERT: B 404 ILE cc_start: 0.7960 (tt) cc_final: 0.7668 (mt) REVERT: B 407 ASP cc_start: 0.8484 (t0) cc_final: 0.8068 (m-30) REVERT: B 492 MET cc_start: 0.7697 (mmm) cc_final: 0.7286 (mtp) REVERT: B 511 TRP cc_start: 0.7907 (m100) cc_final: 0.7572 (m-10) outliers start: 23 outliers final: 19 residues processed: 157 average time/residue: 0.1867 time to fit residues: 42.4159 Evaluate side-chains 155 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 0.0060 chunk 51 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 418 HIS B 171 HIS B 264 GLN B 418 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133002 restraints weight = 11923.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135783 restraints weight = 7159.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137798 restraints weight = 4886.669| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9146 Z= 0.239 Angle : 0.597 5.383 12408 Z= 0.292 Chirality : 0.041 0.138 1430 Planarity : 0.004 0.034 1490 Dihedral : 12.735 170.074 1896 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.90 % Allowed : 20.06 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.26), residues: 1076 helix: 0.64 (0.21), residues: 636 sheet: -1.45 (0.56), residues: 74 loop : -2.64 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 583 HIS 0.009 0.002 HIS A 171 PHE 0.014 0.001 PHE A 281 TYR 0.025 0.001 TYR B 297 ARG 0.006 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.025 Fit side-chains REVERT: A 171 HIS cc_start: 0.8245 (m-70) cc_final: 0.8022 (m-70) REVERT: A 178 MET cc_start: 0.8066 (mmm) cc_final: 0.7505 (mmm) REVERT: A 179 MET cc_start: 0.8618 (tpp) cc_final: 0.8399 (tpt) REVERT: A 404 ILE cc_start: 0.7977 (tt) cc_final: 0.7705 (mt) REVERT: A 407 ASP cc_start: 0.8557 (t0) cc_final: 0.8330 (m-30) REVERT: A 492 MET cc_start: 0.7691 (mmm) cc_final: 0.7299 (mtp) REVERT: A 500 MET cc_start: 0.7072 (mmt) cc_final: 0.6415 (mtm) REVERT: A 511 TRP cc_start: 0.8005 (m100) cc_final: 0.7529 (m-10) REVERT: B 179 MET cc_start: 0.8598 (tpp) cc_final: 0.8179 (tpt) REVERT: B 404 ILE cc_start: 0.7956 (tt) cc_final: 0.7698 (mt) REVERT: B 405 MET cc_start: 0.8321 (tmm) cc_final: 0.7859 (tmm) REVERT: B 492 MET cc_start: 0.7687 (mmm) cc_final: 0.7262 (mtp) REVERT: B 511 TRP cc_start: 0.7972 (m100) cc_final: 0.7525 (m-10) outliers start: 27 outliers final: 20 residues processed: 151 average time/residue: 0.1708 time to fit residues: 38.9032 Evaluate side-chains 146 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132612 restraints weight = 11986.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134473 restraints weight = 8071.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135874 restraints weight = 5943.893| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9146 Z= 0.231 Angle : 0.606 7.994 12408 Z= 0.294 Chirality : 0.040 0.138 1430 Planarity : 0.004 0.035 1490 Dihedral : 12.495 168.842 1896 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.58 % Allowed : 20.17 % Favored : 77.25 % 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: -0.78 (0.26), residues: 1076 helix: 0.76 (0.21), residues: 634 sheet: -1.44 (0.57), residues: 74 loop : -2.64 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 583 HIS 0.007 0.001 HIS B 171 PHE 0.012 0.001 PHE A 281 TYR 0.016 0.001 TYR B 297 ARG 0.002 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.573 Fit side-chains REVERT: A 171 HIS cc_start: 0.8232 (m-70) cc_final: 0.7916 (m170) REVERT: A 404 ILE cc_start: 0.7993 (tt) cc_final: 0.7711 (mt) REVERT: A 405 MET cc_start: 0.8295 (tmm) cc_final: 0.7870 (tmm) REVERT: A 407 ASP cc_start: 0.8492 (t0) cc_final: 0.8039 (m-30) REVERT: A 492 MET cc_start: 0.7685 (mmm) cc_final: 0.7312 (mtp) REVERT: A 511 TRP cc_start: 0.7965 (m100) cc_final: 0.7607 (m-10) REVERT: B 179 MET cc_start: 0.8601 (tpp) cc_final: 0.8202 (tpt) REVERT: B 405 MET cc_start: 0.8286 (tmm) cc_final: 0.7811 (tmm) REVERT: B 407 ASP cc_start: 0.8238 (t0) cc_final: 0.7942 (m-30) REVERT: B 492 MET cc_start: 0.7702 (mmm) cc_final: 0.7311 (mtp) REVERT: B 500 MET cc_start: 0.6982 (mmt) cc_final: 0.6422 (mtm) REVERT: B 511 TRP cc_start: 0.7911 (m100) cc_final: 0.7506 (m-10) outliers start: 24 outliers final: 18 residues processed: 152 average time/residue: 0.1701 time to fit residues: 38.7680 Evaluate side-chains 147 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 0.0770 chunk 86 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS A 618 HIS B 418 HIS B 618 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121524 restraints weight = 12524.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123808 restraints weight = 8118.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125562 restraints weight = 5864.765| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9146 Z= 0.155 Angle : 0.577 7.285 12408 Z= 0.278 Chirality : 0.039 0.152 1430 Planarity : 0.003 0.034 1490 Dihedral : 12.205 163.878 1896 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.47 % Allowed : 21.14 % Favored : 76.39 % 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: -0.62 (0.26), residues: 1076 helix: 0.88 (0.21), residues: 644 sheet: -1.29 (0.58), residues: 74 loop : -2.67 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 583 HIS 0.004 0.001 HIS A 418 PHE 0.012 0.001 PHE A 281 TYR 0.012 0.001 TYR B 297 ARG 0.006 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.016 Fit side-chains REVERT: A 178 MET cc_start: 0.7883 (mmm) cc_final: 0.7328 (mmm) REVERT: A 404 ILE cc_start: 0.7930 (tt) cc_final: 0.7704 (mt) REVERT: A 405 MET cc_start: 0.8256 (tmm) cc_final: 0.7826 (tmm) REVERT: A 407 ASP cc_start: 0.8488 (t0) cc_final: 0.8191 (m-30) REVERT: A 492 MET cc_start: 0.7622 (mmm) cc_final: 0.7281 (mtp) REVERT: A 500 MET cc_start: 0.7042 (mmt) cc_final: 0.6393 (mtm) REVERT: A 511 TRP cc_start: 0.7861 (m100) cc_final: 0.7513 (m-10) REVERT: A 660 TYR cc_start: 0.7922 (t80) cc_final: 0.7504 (t80) REVERT: B 179 MET cc_start: 0.8599 (tpp) cc_final: 0.8290 (tpt) REVERT: B 405 MET cc_start: 0.8418 (tmm) cc_final: 0.7905 (tmm) REVERT: B 407 ASP cc_start: 0.8224 (t0) cc_final: 0.7978 (m-30) REVERT: B 492 MET cc_start: 0.7637 (mmm) cc_final: 0.7264 (mtp) REVERT: B 500 MET cc_start: 0.6963 (mmt) cc_final: 0.6411 (mtm) REVERT: B 511 TRP cc_start: 0.7837 (m100) cc_final: 0.7492 (m-10) REVERT: B 660 TYR cc_start: 0.7922 (t80) cc_final: 0.7505 (t80) outliers start: 23 outliers final: 18 residues processed: 165 average time/residue: 0.1728 time to fit residues: 42.3321 Evaluate side-chains 153 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124303 restraints weight = 12573.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126628 restraints weight = 8005.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128378 restraints weight = 5750.353| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9146 Z= 0.209 Angle : 0.584 6.049 12408 Z= 0.285 Chirality : 0.041 0.222 1430 Planarity : 0.004 0.036 1490 Dihedral : 12.084 158.926 1896 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.58 % Allowed : 21.24 % Favored : 76.18 % 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: -0.61 (0.26), residues: 1076 helix: 0.92 (0.21), residues: 642 sheet: -1.38 (0.58), residues: 74 loop : -2.69 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 583 HIS 0.003 0.001 HIS A 171 PHE 0.013 0.001 PHE A 281 TYR 0.010 0.001 TYR A 297 ARG 0.002 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.962 Fit side-chains REVERT: A 178 MET cc_start: 0.7915 (mmm) cc_final: 0.7604 (mmm) REVERT: A 404 ILE cc_start: 0.7962 (tt) cc_final: 0.7740 (mt) REVERT: A 405 MET cc_start: 0.8273 (tmm) cc_final: 0.7841 (tmm) REVERT: A 407 ASP cc_start: 0.8490 (t0) cc_final: 0.8199 (m-30) REVERT: A 492 MET cc_start: 0.7654 (mmm) cc_final: 0.7316 (mtp) REVERT: A 500 MET cc_start: 0.6964 (mmt) cc_final: 0.6383 (mtm) REVERT: A 511 TRP cc_start: 0.8020 (m100) cc_final: 0.7543 (m-10) REVERT: A 660 TYR cc_start: 0.7945 (t80) cc_final: 0.7534 (t80) REVERT: B 178 MET cc_start: 0.7956 (mmm) cc_final: 0.7427 (mmm) REVERT: B 179 MET cc_start: 0.8579 (tpp) cc_final: 0.8174 (tpt) REVERT: B 405 MET cc_start: 0.8461 (tmm) cc_final: 0.7947 (tmm) REVERT: B 407 ASP cc_start: 0.8220 (t0) cc_final: 0.7949 (m-30) REVERT: B 492 MET cc_start: 0.7666 (mmm) cc_final: 0.7308 (mtp) REVERT: B 500 MET cc_start: 0.6920 (mmt) cc_final: 0.6380 (mtm) REVERT: B 511 TRP cc_start: 0.8002 (m100) cc_final: 0.7518 (m-10) REVERT: B 660 TYR cc_start: 0.7937 (t80) cc_final: 0.7525 (t80) outliers start: 24 outliers final: 20 residues processed: 157 average time/residue: 0.1741 time to fit residues: 40.7905 Evaluate side-chains 154 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132671 restraints weight = 12109.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135005 restraints weight = 7681.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136727 restraints weight = 5488.969| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9146 Z= 0.290 Angle : 0.625 5.520 12408 Z= 0.307 Chirality : 0.042 0.139 1430 Planarity : 0.004 0.036 1490 Dihedral : 12.160 155.640 1896 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.79 % Allowed : 21.24 % Favored : 75.97 % 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: -0.59 (0.26), residues: 1076 helix: 0.88 (0.21), residues: 638 sheet: -1.51 (0.57), residues: 74 loop : -2.49 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 583 HIS 0.004 0.001 HIS B 418 PHE 0.015 0.002 PHE A 501 TYR 0.010 0.001 TYR A 288 ARG 0.002 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.071 Fit side-chains REVERT: A 178 MET cc_start: 0.7985 (mmm) cc_final: 0.7398 (mmm) REVERT: A 404 ILE cc_start: 0.8010 (tt) cc_final: 0.7794 (mt) REVERT: A 405 MET cc_start: 0.8292 (tmm) cc_final: 0.7855 (tmm) REVERT: A 407 ASP cc_start: 0.8490 (t0) cc_final: 0.8186 (m-30) REVERT: A 492 MET cc_start: 0.7657 (mmm) cc_final: 0.7298 (mtp) REVERT: A 500 MET cc_start: 0.6981 (mmt) cc_final: 0.6490 (mtm) REVERT: A 511 TRP cc_start: 0.8115 (m100) cc_final: 0.7605 (m-10) REVERT: B 179 MET cc_start: 0.8562 (tpp) cc_final: 0.8048 (tpt) REVERT: B 405 MET cc_start: 0.8483 (tmm) cc_final: 0.7952 (tmm) REVERT: B 492 MET cc_start: 0.7709 (mmm) cc_final: 0.7310 (mtp) REVERT: B 511 TRP cc_start: 0.8101 (m100) cc_final: 0.7615 (m-10) outliers start: 26 outliers final: 22 residues processed: 160 average time/residue: 0.1793 time to fit residues: 42.2611 Evaluate side-chains 152 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136293 restraints weight = 11943.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138717 restraints weight = 7535.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140477 restraints weight = 5318.847| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9146 Z= 0.173 Angle : 0.580 7.518 12408 Z= 0.283 Chirality : 0.040 0.232 1430 Planarity : 0.004 0.034 1490 Dihedral : 11.942 149.319 1896 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.47 % Allowed : 21.57 % Favored : 75.97 % 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: -0.50 (0.26), residues: 1076 helix: 1.01 (0.22), residues: 640 sheet: -1.37 (0.58), residues: 74 loop : -2.62 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 583 HIS 0.003 0.001 HIS A 418 PHE 0.038 0.002 PHE B 522 TYR 0.010 0.001 TYR A 297 ARG 0.002 0.000 ARG B 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.933 Fit side-chains REVERT: A 178 MET cc_start: 0.7942 (mmm) cc_final: 0.7351 (mmm) REVERT: A 404 ILE cc_start: 0.7954 (tt) cc_final: 0.7726 (mt) REVERT: A 405 MET cc_start: 0.8240 (tmm) cc_final: 0.7847 (tmm) REVERT: A 492 MET cc_start: 0.7639 (mmm) cc_final: 0.7293 (mtp) REVERT: A 511 TRP cc_start: 0.7958 (m100) cc_final: 0.7495 (m-10) REVERT: A 660 TYR cc_start: 0.7951 (t80) cc_final: 0.7541 (t80) REVERT: B 178 MET cc_start: 0.7990 (mmm) cc_final: 0.7430 (mmm) REVERT: B 179 MET cc_start: 0.8559 (tpp) cc_final: 0.8124 (tpt) REVERT: B 405 MET cc_start: 0.8412 (tmm) cc_final: 0.7939 (tmm) REVERT: B 492 MET cc_start: 0.7678 (mmm) cc_final: 0.7279 (mtp) REVERT: B 511 TRP cc_start: 0.7970 (m100) cc_final: 0.7465 (m-10) REVERT: B 660 TYR cc_start: 0.7936 (t80) cc_final: 0.7529 (t80) outliers start: 23 outliers final: 20 residues processed: 167 average time/residue: 0.1688 time to fit residues: 42.0870 Evaluate side-chains 162 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 49 optimal weight: 0.0170 chunk 88 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 103 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138243 restraints weight = 11760.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140192 restraints weight = 7735.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141724 restraints weight = 5626.435| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9146 Z= 0.150 Angle : 0.580 8.169 12408 Z= 0.280 Chirality : 0.040 0.253 1430 Planarity : 0.003 0.035 1490 Dihedral : 11.750 142.763 1896 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.93 % Allowed : 22.75 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.27), residues: 1076 helix: 1.12 (0.22), residues: 640 sheet: -1.25 (0.59), residues: 74 loop : -2.58 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 583 HIS 0.005 0.001 HIS A 171 PHE 0.034 0.001 PHE B 522 TYR 0.010 0.001 TYR A 297 ARG 0.004 0.000 ARG B 651 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.27 seconds wall clock time: 47 minutes 59.05 seconds (2879.05 seconds total)