Starting phenix.real_space_refine on Sat Oct 24 13:23:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y73_72642/10_2026/9y73_72642.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y73_72642/10_2026/9y73_72642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y73_72642/10_2026/9y73_72642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y73_72642/10_2026/9y73_72642.map" model { file = "/net/cci-nas-00/data/ceres_data/9y73_72642/10_2026/9y73_72642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y73_72642/10_2026/9y73_72642.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8732 2.51 5 N 2096 2.21 5 O 2372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13280 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3293 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 4, 'TRANS': 402} Chain breaks: 3 Chain: "C" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3293 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 4, 'TRANS': 402} Chain breaks: 3 Chain: "B" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3293 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 4, 'TRANS': 402} Chain breaks: 3 Chain: "D" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3293 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 4, 'TRANS': 402} Chain breaks: 3 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'AQV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.12, per 1000 atoms: 0.23 Number of scatterers: 13280 At special positions: 0 Unit cell: (102.837, 102.837, 108.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2372 8.00 N 2096 7.00 C 8732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 190 " distance=2.03 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 243 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 190 " distance=2.03 Simple disulfide: pdb=" SG CYS D 243 " - pdb=" SG CYS D 274 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 418.5 milliseconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 66.3% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 66 through 106 Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 291 through 322 Processing helix chain 'A' and resid 344 through 371 removed outlier: 4.014A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 392 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 400 through 440 removed outlier: 4.304A pdb=" N LEU A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 443 through 447 removed outlier: 4.098A pdb=" N GLU A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 removed outlier: 3.618A pdb=" N ASN A 461 " --> pdb=" O PHE A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 476 through 515 Processing helix chain 'C' and resid 66 through 106 Processing helix chain 'C' and resid 123 through 140 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 291 through 322 Processing helix chain 'C' and resid 344 through 371 removed outlier: 4.014A pdb=" N VAL C 348 " --> pdb=" O ASN C 344 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 349 " --> pdb=" O GLY C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 392 Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 400 through 440 removed outlier: 4.305A pdb=" N LEU C 408 " --> pdb=" O ASN C 404 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 413 " --> pdb=" O THR C 409 " (cutoff:3.500A) Proline residue: C 415 - end of helix Processing helix chain 'C' and resid 443 through 447 removed outlier: 4.095A pdb=" N GLU C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 461 removed outlier: 3.620A pdb=" N ASN C 461 " --> pdb=" O PHE C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 476 through 515 Processing helix chain 'B' and resid 66 through 106 Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 291 through 322 Processing helix chain 'B' and resid 344 through 371 removed outlier: 4.015A pdb=" N VAL B 348 " --> pdb=" O ASN B 344 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 392 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 400 through 440 removed outlier: 4.304A pdb=" N LEU B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 413 " --> pdb=" O THR B 409 " (cutoff:3.500A) Proline residue: B 415 - end of helix Processing helix chain 'B' and resid 443 through 447 removed outlier: 4.097A pdb=" N GLU B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 461 removed outlier: 3.620A pdb=" N ASN B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 476 through 515 Processing helix chain 'D' and resid 66 through 106 Processing helix chain 'D' and resid 123 through 140 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 232 through 238 Processing helix chain 'D' and resid 291 through 322 Processing helix chain 'D' and resid 344 through 371 removed outlier: 4.014A pdb=" N VAL D 348 " --> pdb=" O ASN D 344 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 349 " --> pdb=" O GLY D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 392 Processing helix chain 'D' and resid 393 through 398 Processing helix chain 'D' and resid 400 through 440 removed outlier: 4.304A pdb=" N LEU D 408 " --> pdb=" O ASN D 404 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 413 " --> pdb=" O THR D 409 " (cutoff:3.500A) Proline residue: D 415 - end of helix Processing helix chain 'D' and resid 443 through 447 removed outlier: 4.105A pdb=" N GLU D 447 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 461 removed outlier: 3.621A pdb=" N ASN D 461 " --> pdb=" O PHE D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 476 through 515 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.664A pdb=" N GLN A 220 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA A 226 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY A 160 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AA4, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.672A pdb=" N GLN C 220 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA C 226 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY C 160 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.665A pdb=" N GLN B 220 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA B 226 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY B 160 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.672A pdb=" N GLN D 220 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA D 226 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY D 160 " --> pdb=" O ALA D 226 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 3096 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: 2.25 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2700 1.33 - 1.45: 3191 1.45 - 1.57: 7553 1.57 - 1.69: 4 1.69 - 1.81: 112 Bond restraints: 13560 Sorted by residual: bond pdb=" C10 AQV C 601 " pdb=" N2 AQV C 601 " ideal model delta sigma weight residual 1.367 1.458 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C10 AQV B 601 " pdb=" N2 AQV B 601 " ideal model delta sigma weight residual 1.367 1.457 -0.090 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C10 AQV A 602 " pdb=" N2 AQV A 602 " ideal model delta sigma weight residual 1.367 1.457 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C10 AQV A 601 " pdb=" N2 AQV A 601 " ideal model delta sigma weight residual 1.367 1.457 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C11 AQV B 601 " pdb=" N2 AQV B 601 " ideal model delta sigma weight residual 1.513 1.577 -0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 13555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 18163 1.84 - 3.67: 157 3.67 - 5.51: 44 5.51 - 7.34: 4 7.34 - 9.18: 8 Bond angle restraints: 18376 Sorted by residual: angle pdb=" C9 AQV B 601 " pdb=" C10 AQV B 601 " pdb=" N2 AQV B 601 " ideal model delta sigma weight residual 119.50 128.68 -9.18 3.00e+00 1.11e-01 9.36e+00 angle pdb=" C9 AQV A 602 " pdb=" C10 AQV A 602 " pdb=" N2 AQV A 602 " ideal model delta sigma weight residual 119.50 128.67 -9.17 3.00e+00 1.11e-01 9.35e+00 angle pdb=" C9 AQV C 601 " pdb=" C10 AQV C 601 " pdb=" N2 AQV C 601 " ideal model delta sigma weight residual 119.50 128.64 -9.14 3.00e+00 1.11e-01 9.29e+00 angle pdb=" C9 AQV A 601 " pdb=" C10 AQV A 601 " pdb=" N2 AQV A 601 " ideal model delta sigma weight residual 119.50 128.64 -9.14 3.00e+00 1.11e-01 9.29e+00 angle pdb=" C9 AQV A 602 " pdb=" C10 AQV A 602 " pdb=" O1 AQV A 602 " ideal model delta sigma weight residual 116.83 108.94 7.89 3.00e+00 1.11e-01 6.91e+00 ... (remaining 18371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.19: 7563 26.19 - 52.39: 396 52.39 - 78.58: 17 78.58 - 104.78: 4 104.78 - 130.97: 24 Dihedral angle restraints: 8004 sinusoidal: 3204 harmonic: 4800 Sorted by residual: dihedral pdb=" C10 AQV A 602 " pdb=" C11 AQV A 602 " pdb=" N2 AQV A 602 " pdb=" C21 AQV A 602 " ideal model delta sinusoidal sigma weight residual 45.18 -85.79 130.97 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C10 AQV C 601 " pdb=" C11 AQV C 601 " pdb=" N2 AQV C 601 " pdb=" C21 AQV C 601 " ideal model delta sinusoidal sigma weight residual 45.18 -85.79 130.97 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C10 AQV B 601 " pdb=" C11 AQV B 601 " pdb=" N2 AQV B 601 " pdb=" C21 AQV B 601 " ideal model delta sinusoidal sigma weight residual 45.18 -85.76 130.94 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 8001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1443 0.033 - 0.066: 563 0.066 - 0.099: 95 0.099 - 0.132: 48 0.132 - 0.165: 7 Chirality restraints: 2156 Sorted by residual: chirality pdb=" CG LEU B 501 " pdb=" CB LEU B 501 " pdb=" CD1 LEU B 501 " pdb=" CD2 LEU B 501 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CG LEU A 501 " pdb=" CB LEU A 501 " pdb=" CD1 LEU A 501 " pdb=" CD2 LEU A 501 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CG LEU C 501 " pdb=" CB LEU C 501 " pdb=" CD1 LEU C 501 " pdb=" CD2 LEU C 501 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 2153 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 296 " 0.009 2.00e-02 2.50e+03 8.25e-03 1.19e+00 pdb=" CG PHE D 296 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE D 296 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE D 296 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 296 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 296 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 296 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 296 " -0.009 2.00e-02 2.50e+03 8.19e-03 1.17e+00 pdb=" CG PHE A 296 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 296 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 296 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 296 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 296 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 296 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 296 " -0.009 2.00e-02 2.50e+03 8.11e-03 1.15e+00 pdb=" CG PHE B 296 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE B 296 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 296 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 296 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 296 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 296 " -0.000 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 234 2.70 - 3.25: 13099 3.25 - 3.80: 20892 3.80 - 4.35: 26240 4.35 - 4.90: 45634 Nonbonded interactions: 106099 Sorted by model distance: nonbonded pdb=" OH TYR C 428 " pdb=" O ALA C 453 " model vdw 2.156 3.040 nonbonded pdb=" OH TYR B 428 " pdb=" O ALA B 453 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR A 428 " pdb=" O ALA A 453 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR D 428 " pdb=" O ALA D 453 " model vdw 2.158 3.040 nonbonded pdb=" O GLN A 196 " pdb=" OG1 THR A 200 " model vdw 2.214 3.040 ... (remaining 106094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 65 through 515) selection = (chain 'B' and resid 65 through 515) selection = (chain 'C' and resid 65 through 515) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.550 Find NCS groups from input model: 0.290 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.005 0.091 13568 Z= 0.207 Angle : 0.553 9.177 18392 Z= 0.282 Chirality : 0.038 0.165 2156 Planarity : 0.002 0.023 2220 Dihedral : 16.569 130.971 4876 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.20), residues: 1596 helix: 2.41 (0.16), residues: 964 sheet: 1.05 (0.35), residues: 208 loop : -2.05 (0.22), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.011 0.001 TYR B 403 PHE 0.019 0.002 PHE D 296 TRP 0.004 0.001 TRP A 480 HIS 0.003 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (13560) covalent geometry : angle 0.55277 / 0.28 (18376) SS BOND : bond 0.00132 / 0.07 ( 8) SS BOND : angle 0.22691 / 0.11 ( 16) hydrogen bonds : bond 0.15068 / 10.02 ( 988) hydrogen bonds : angle 6.60448 / 4.85 ( 3096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.352 Fit side-chains REVERT: A 497 MET cc_start: 0.8140 (mtp) cc_final: 0.7933 (mtt) REVERT: C 497 MET cc_start: 0.8124 (mtp) cc_final: 0.7872 (mtt) REVERT: D 239 GLU cc_start: 0.6251 (mp0) cc_final: 0.6006 (mp0) REVERT: D 242 ASP cc_start: 0.7641 (m-30) cc_final: 0.7382 (m-30) REVERT: D 371 LYS cc_start: 0.7504 (mttt) cc_final: 0.6704 (pttt) REVERT: D 497 MET cc_start: 0.8005 (mtp) cc_final: 0.7490 (mtm) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1018 time to fit residues: 28.3371 Evaluate side-chains 146 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 443 HIS B 471 GLN D 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.198210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152759 restraints weight = 13845.939| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.32 r_work: 0.3391 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13568 Z= 0.190 Angle : 0.565 8.019 18392 Z= 0.298 Chirality : 0.039 0.149 2156 Planarity : 0.003 0.025 2220 Dihedral : 14.648 133.361 1840 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.17 % Allowed : 5.69 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.20), residues: 1596 helix: 2.33 (0.16), residues: 984 sheet: 0.95 (0.34), residues: 208 loop : -2.25 (0.22), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 395 TYR 0.014 0.001 TYR C 486 PHE 0.018 0.002 PHE D 293 TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (13560) covalent geometry : angle 0.55697 / 0.29 (18376) SS BOND : bond 0.00752 / 0.41 ( 8) SS BOND : angle 3.21778 / 1.65 ( 16) hydrogen bonds : bond 0.04863 / 3.23 ( 988) hydrogen bonds : angle 4.43639 / 3.20 ( 3096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.448 Fit side-chains REVERT: A 471 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.6717 (mp-120) REVERT: A 494 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.5220 (t80) REVERT: A 497 MET cc_start: 0.7978 (mtp) cc_final: 0.7761 (mtt) REVERT: C 471 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: C 497 MET cc_start: 0.8147 (mtp) cc_final: 0.7820 (mtt) REVERT: B 471 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: B 494 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5037 (t80) REVERT: B 502 PHE cc_start: 0.7952 (t80) cc_final: 0.7640 (t80) REVERT: D 239 GLU cc_start: 0.6697 (mp0) cc_final: 0.5941 (mp0) REVERT: D 471 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: D 490 PHE cc_start: 0.8172 (t80) cc_final: 0.7918 (t80) REVERT: D 497 MET cc_start: 0.8000 (mtp) cc_final: 0.7628 (mtt) outliers start: 32 outliers final: 19 residues processed: 169 average time/residue: 0.1100 time to fit residues: 27.6993 Evaluate side-chains 164 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 471 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [53, 48, 57, 22, 70, 137, 4, 19, 15, 35, 79] chunk 53 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 471 GLN D 471 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.200643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155809 restraints weight = 13896.248| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.31 r_work: 0.3459 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13568 Z= 0.137 Angle : 0.631 16.450 18392 Z= 0.325 Chirality : 0.037 0.142 2156 Planarity : 0.003 0.023 2220 Dihedral : 14.668 134.158 1840 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.96 % Allowed : 9.62 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1596 helix: 2.50 (0.16), residues: 984 sheet: 0.57 (0.34), residues: 208 loop : -2.17 (0.23), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 395 TYR 0.013 0.001 TYR C 486 PHE 0.012 0.001 PHE D 293 TRP 0.006 0.001 TRP D 436 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (13560) covalent geometry : angle 0.59605 / 0.31 (18376) SS BOND : bond 0.00498 / 0.29 ( 8) SS BOND : angle 7.06672 / 3.58 ( 16) hydrogen bonds : bond 0.04313 / 2.86 ( 988) hydrogen bonds : angle 4.18777 / 3.02 ( 3096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.491 Fit side-chains REVERT: A 471 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.6768 (mp-120) REVERT: A 494 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.5581 (t80) REVERT: A 497 MET cc_start: 0.7899 (mtp) cc_final: 0.7692 (mtt) REVERT: C 371 LYS cc_start: 0.7301 (mtpt) cc_final: 0.6250 (pttt) REVERT: C 471 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.6752 (mp-120) REVERT: C 497 MET cc_start: 0.8092 (mtp) cc_final: 0.7803 (mtt) REVERT: B 471 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: B 494 PHE cc_start: 0.6314 (OUTLIER) cc_final: 0.5261 (t80) REVERT: B 497 MET cc_start: 0.8255 (mtt) cc_final: 0.7870 (mtp) REVERT: D 471 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: D 474 GLN cc_start: 0.7295 (mp10) cc_final: 0.6409 (tt0) REVERT: D 497 MET cc_start: 0.7964 (mtp) cc_final: 0.7633 (mtt) outliers start: 29 outliers final: 19 residues processed: 174 average time/residue: 0.1025 time to fit residues: 26.7268 Evaluate side-chains 163 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 471 GLN Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [17, 77, 141, 40, 123, 159, 100, 28, 129, 138, 152] chunk 17 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 129 optimal weight: 0.1980 chunk 138 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 167 HIS B 233 GLN B 471 GLN D 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.199574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154682 restraints weight = 13900.962| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.29 r_work: 0.3452 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13568 Z= 0.149 Angle : 0.619 15.237 18392 Z= 0.319 Chirality : 0.037 0.141 2156 Planarity : 0.003 0.023 2220 Dihedral : 14.687 138.859 1840 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.71 % Allowed : 12.20 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1596 helix: 2.52 (0.16), residues: 984 sheet: 0.54 (0.35), residues: 208 loop : -2.22 (0.23), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 395 TYR 0.014 0.001 TYR D 486 PHE 0.011 0.001 PHE A 494 TRP 0.005 0.001 TRP D 436 HIS 0.003 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13560) covalent geometry : angle 0.58461 / 0.30 (18376) SS BOND : bond 0.00327 / 0.19 ( 8) SS BOND : angle 6.90123 / 3.50 ( 16) hydrogen bonds : bond 0.04374 / 2.90 ( 988) hydrogen bonds : angle 4.12931 / 2.99 ( 3096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.446 Fit side-chains REVERT: A 239 GLU cc_start: 0.6657 (mp0) cc_final: 0.5873 (mp0) REVERT: A 471 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.6854 (mp-120) REVERT: A 494 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.5277 (t80) REVERT: A 497 MET cc_start: 0.7966 (mtp) cc_final: 0.7725 (mtt) REVERT: C 115 ASP cc_start: 0.8762 (t70) cc_final: 0.8533 (t70) REVERT: C 471 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.6773 (mp-120) REVERT: C 497 MET cc_start: 0.8075 (mtp) cc_final: 0.7773 (mtt) REVERT: C 502 PHE cc_start: 0.8048 (t80) cc_final: 0.7734 (t80) REVERT: B 233 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.6721 (tp40) REVERT: B 471 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7677 (mp10) REVERT: B 474 GLN cc_start: 0.7277 (mp10) cc_final: 0.6460 (tt0) REVERT: B 494 PHE cc_start: 0.6250 (OUTLIER) cc_final: 0.5119 (t80) REVERT: B 497 MET cc_start: 0.8007 (mtt) cc_final: 0.7712 (mtp) REVERT: D 471 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: D 497 MET cc_start: 0.7990 (mtp) cc_final: 0.7637 (mtt) outliers start: 40 outliers final: 26 residues processed: 179 average time/residue: 0.1032 time to fit residues: 27.7288 Evaluate side-chains 184 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 471 GLN Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [93, 107, 151, 147, 20, 10, 21, 79, 76, 143, 90] chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 167 HIS B 167 HIS B 471 GLN D 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.199277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154739 restraints weight = 13911.788| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.25 r_work: 0.3454 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13568 Z= 0.148 Angle : 0.610 14.756 18392 Z= 0.315 Chirality : 0.037 0.139 2156 Planarity : 0.003 0.023 2220 Dihedral : 14.678 139.177 1840 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.05 % Allowed : 14.09 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.20), residues: 1596 helix: 2.54 (0.16), residues: 984 sheet: 0.72 (0.36), residues: 192 loop : -2.30 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 395 TYR 0.013 0.001 TYR B 486 PHE 0.011 0.001 PHE A 494 TRP 0.005 0.001 TRP B 436 HIS 0.004 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (13560) covalent geometry : angle 0.57591 / 0.30 (18376) SS BOND : bond 0.00278 / 0.15 ( 8) SS BOND : angle 6.80028 / 3.46 ( 16) hydrogen bonds : bond 0.04340 / 2.88 ( 988) hydrogen bonds : angle 4.10745 / 2.97 ( 3096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 0.451 Fit side-chains REVERT: A 115 ASP cc_start: 0.8696 (t70) cc_final: 0.8438 (t70) REVERT: A 239 GLU cc_start: 0.6795 (mp0) cc_final: 0.6006 (mp0) REVERT: A 371 LYS cc_start: 0.7501 (mtpp) cc_final: 0.7300 (mttt) REVERT: A 471 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6848 (mp-120) REVERT: A 494 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.5344 (t80) REVERT: A 497 MET cc_start: 0.7962 (mtp) cc_final: 0.7729 (mtt) REVERT: C 471 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.6692 (mp-120) REVERT: C 497 MET cc_start: 0.8090 (mtp) cc_final: 0.7792 (mtt) REVERT: B 471 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: B 474 GLN cc_start: 0.7428 (mp10) cc_final: 0.6561 (tt0) REVERT: D 497 MET cc_start: 0.8033 (mtp) cc_final: 0.7690 (mtt) REVERT: D 502 PHE cc_start: 0.7868 (t80) cc_final: 0.7553 (t80) outliers start: 45 outliers final: 31 residues processed: 185 average time/residue: 0.1019 time to fit residues: 28.6106 Evaluate side-chains 185 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [147, 152, 100, 46, 87, 61, 24, 135, 96, 139, 81] chunk 147 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 HIS C 167 HIS D 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.199608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155232 restraints weight = 13788.692| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.24 r_work: 0.3462 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13568 Z= 0.143 Angle : 0.606 14.366 18392 Z= 0.313 Chirality : 0.037 0.138 2156 Planarity : 0.002 0.023 2220 Dihedral : 14.663 138.784 1840 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.39 % Allowed : 14.57 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1596 helix: 2.54 (0.16), residues: 984 sheet: 0.69 (0.36), residues: 192 loop : -2.26 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 395 TYR 0.013 0.001 TYR C 486 PHE 0.011 0.001 PHE A 494 TRP 0.005 0.001 TRP B 480 HIS 0.004 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13560) covalent geometry : angle 0.57323 / 0.30 (18376) SS BOND : bond 0.00240 / 0.13 ( 8) SS BOND : angle 6.71791 / 3.42 ( 16) hydrogen bonds : bond 0.04280 / 2.84 ( 988) hydrogen bonds : angle 4.10469 / 2.97 ( 3096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 471 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.6834 (mp-120) REVERT: A 494 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.5307 (t80) REVERT: A 497 MET cc_start: 0.7941 (mtp) cc_final: 0.7712 (mtt) REVERT: C 271 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8379 (mm) REVERT: C 371 LYS cc_start: 0.7334 (mtpp) cc_final: 0.6302 (pttt) REVERT: C 471 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: C 474 GLN cc_start: 0.7124 (mp10) cc_final: 0.5581 (tm-30) REVERT: C 497 MET cc_start: 0.8077 (mtp) cc_final: 0.7770 (mtt) REVERT: B 271 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8303 (mm) REVERT: B 494 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.5335 (t80) REVERT: D 474 GLN cc_start: 0.7271 (mp10) cc_final: 0.5788 (tm-30) REVERT: D 497 MET cc_start: 0.8023 (mtp) cc_final: 0.7680 (mtt) REVERT: D 502 PHE cc_start: 0.7908 (t80) cc_final: 0.7620 (t80) outliers start: 50 outliers final: 33 residues processed: 192 average time/residue: 0.1053 time to fit residues: 30.4135 Evaluate side-chains 182 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [159, 105, 35, 94, 151, 129, 24, 87, 81, 82, 84] chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.200851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156802 restraints weight = 13874.472| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.24 r_work: 0.3475 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13568 Z= 0.131 Angle : 0.595 14.149 18392 Z= 0.307 Chirality : 0.037 0.137 2156 Planarity : 0.002 0.023 2220 Dihedral : 14.647 138.650 1840 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.85 % Allowed : 15.38 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.20), residues: 1596 helix: 2.59 (0.16), residues: 984 sheet: 0.68 (0.36), residues: 192 loop : -2.22 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 419 TYR 0.013 0.001 TYR B 486 PHE 0.011 0.001 PHE A 494 TRP 0.005 0.001 TRP B 480 HIS 0.005 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (13560) covalent geometry : angle 0.56319 / 0.29 (18376) SS BOND : bond 0.00203 / 0.11 ( 8) SS BOND : angle 6.57303 / 3.34 ( 16) hydrogen bonds : bond 0.04154 / 2.75 ( 988) hydrogen bonds : angle 4.07674 / 2.95 ( 3096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.489 Fit side-chains REVERT: A 471 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.6828 (mp-120) REVERT: A 494 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5329 (t80) REVERT: A 497 MET cc_start: 0.7922 (mtp) cc_final: 0.7694 (mtt) REVERT: C 371 LYS cc_start: 0.7300 (mtpp) cc_final: 0.6298 (pttt) REVERT: C 471 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7553 (mp10) REVERT: C 497 MET cc_start: 0.8060 (mtp) cc_final: 0.7754 (mtt) REVERT: B 271 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8284 (mm) REVERT: B 471 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: B 494 PHE cc_start: 0.6419 (OUTLIER) cc_final: 0.5299 (t80) REVERT: B 497 MET cc_start: 0.8246 (mtt) cc_final: 0.8036 (mtt) REVERT: D 497 MET cc_start: 0.7983 (mtp) cc_final: 0.7640 (mtt) REVERT: D 502 PHE cc_start: 0.7811 (t80) cc_final: 0.7522 (t80) outliers start: 42 outliers final: 31 residues processed: 182 average time/residue: 0.1036 time to fit residues: 28.2080 Evaluate side-chains 183 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [95, 65, 100, 132, 134, 114, 90, 98, 15, 122, 120] chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 167 HIS B 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.200201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156218 restraints weight = 13744.709| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.28 r_work: 0.3462 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13568 Z= 0.141 Angle : 0.606 14.037 18392 Z= 0.312 Chirality : 0.037 0.135 2156 Planarity : 0.002 0.023 2220 Dihedral : 14.646 138.736 1840 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.18 % Allowed : 15.58 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.20), residues: 1596 helix: 2.57 (0.16), residues: 984 sheet: 0.70 (0.36), residues: 192 loop : -2.21 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 419 TYR 0.014 0.001 TYR B 486 PHE 0.011 0.001 PHE B 420 TRP 0.005 0.001 TRP B 480 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13560) covalent geometry : angle 0.57371 / 0.30 (18376) SS BOND : bond 0.00208 / 0.11 ( 8) SS BOND : angle 6.60580 / 3.36 ( 16) hydrogen bonds : bond 0.04215 / 2.79 ( 988) hydrogen bonds : angle 4.07358 / 2.95 ( 3096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.499 Fit side-chains REVERT: A 471 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6821 (mp-120) REVERT: A 494 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5274 (t80) REVERT: A 497 MET cc_start: 0.7926 (mtp) cc_final: 0.7697 (mtt) REVERT: C 371 LYS cc_start: 0.7373 (mtpp) cc_final: 0.6422 (pttt) REVERT: C 471 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: C 474 GLN cc_start: 0.7106 (mp10) cc_final: 0.5597 (tm-30) REVERT: C 497 MET cc_start: 0.8073 (mtp) cc_final: 0.7767 (mtt) REVERT: B 271 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8307 (mm) REVERT: B 471 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: B 494 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.5325 (t80) REVERT: D 474 GLN cc_start: 0.7255 (mp10) cc_final: 0.5955 (tm-30) REVERT: D 497 MET cc_start: 0.7990 (mtp) cc_final: 0.7646 (mtt) outliers start: 47 outliers final: 36 residues processed: 178 average time/residue: 0.1059 time to fit residues: 28.5550 Evaluate side-chains 187 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [27, 41, 16, 8, 36, 76, 136, 71, 12, 6, 81] chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 136 optimal weight: 0.1980 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 81 optimal weight: 0.1980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 HIS C 167 HIS B 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.203596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159246 restraints weight = 13859.410| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.31 r_work: 0.3467 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13568 Z= 0.116 Angle : 0.581 13.206 18392 Z= 0.300 Chirality : 0.036 0.151 2156 Planarity : 0.002 0.023 2220 Dihedral : 14.626 138.641 1840 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.98 % Allowed : 16.19 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.20), residues: 1596 helix: 2.72 (0.16), residues: 984 sheet: 0.70 (0.36), residues: 192 loop : -2.12 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.013 0.001 TYR A 486 PHE 0.013 0.001 PHE D 502 TRP 0.006 0.001 TRP B 480 HIS 0.008 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (13560) covalent geometry : angle 0.55084 / 0.29 (18376) SS BOND : bond 0.00141 / 0.07 ( 8) SS BOND : angle 6.27956 / 3.20 ( 16) hydrogen bonds : bond 0.03908 / 2.59 ( 988) hydrogen bonds : angle 4.00526 / 2.90 ( 3096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.504 Fit side-chains REVERT: A 143 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7768 (t0) REVERT: A 471 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7619 (mt0) REVERT: A 494 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5238 (t80) REVERT: A 497 MET cc_start: 0.7984 (mtp) cc_final: 0.7705 (mtt) REVERT: C 143 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7776 (t0) REVERT: C 371 LYS cc_start: 0.7321 (mtpp) cc_final: 0.6406 (pttt) REVERT: C 471 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: C 474 GLN cc_start: 0.7083 (mp10) cc_final: 0.5555 (tm-30) REVERT: C 497 MET cc_start: 0.7967 (mtp) cc_final: 0.7640 (mtt) REVERT: B 143 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7850 (t0) REVERT: B 271 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8278 (mm) REVERT: B 371 LYS cc_start: 0.7366 (mtpp) cc_final: 0.6336 (pttt) REVERT: B 471 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: D 143 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7765 (t0) REVERT: D 474 GLN cc_start: 0.7268 (mp10) cc_final: 0.5715 (tm-30) REVERT: D 497 MET cc_start: 0.8037 (mtp) cc_final: 0.7668 (mtt) outliers start: 44 outliers final: 29 residues processed: 190 average time/residue: 0.0988 time to fit residues: 28.6457 Evaluate side-chains 197 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [56, 105, 151, 89, 35, 135, 17, 131, 88, 119, 77] chunk 56 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.201863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.161986 restraints weight = 13831.353| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.14 r_work: 0.3434 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13568 Z= 0.133 Angle : 0.594 13.460 18392 Z= 0.307 Chirality : 0.037 0.164 2156 Planarity : 0.002 0.023 2220 Dihedral : 14.658 138.603 1840 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.57 % Allowed : 16.67 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.20), residues: 1596 helix: 2.67 (0.16), residues: 984 sheet: 0.70 (0.36), residues: 192 loop : -2.11 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.014 0.001 TYR B 486 PHE 0.013 0.001 PHE B 494 TRP 0.005 0.001 TRP B 480 HIS 0.004 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13560) covalent geometry : angle 0.56326 / 0.29 (18376) SS BOND : bond 0.00166 / 0.09 ( 8) SS BOND : angle 6.42017 / 3.27 ( 16) hydrogen bonds : bond 0.04048 / 2.68 ( 988) hydrogen bonds : angle 4.01411 / 2.91 ( 3096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.426 Fit side-chains REVERT: A 143 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7831 (t0) REVERT: A 471 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: A 494 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.5216 (t80) REVERT: A 497 MET cc_start: 0.7912 (mtp) cc_final: 0.7620 (mtt) REVERT: C 143 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7828 (t0) REVERT: C 371 LYS cc_start: 0.7315 (mtpp) cc_final: 0.6387 (pttt) REVERT: C 471 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: C 474 GLN cc_start: 0.7080 (mp10) cc_final: 0.5546 (tm-30) REVERT: C 497 MET cc_start: 0.7962 (mtp) cc_final: 0.7649 (mtt) REVERT: B 143 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7870 (t0) REVERT: B 271 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8292 (mm) REVERT: B 471 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: D 143 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7811 (t0) REVERT: D 474 GLN cc_start: 0.7209 (mp10) cc_final: 0.5677 (tm-30) REVERT: D 497 MET cc_start: 0.8055 (mtp) cc_final: 0.7699 (mtt) outliers start: 38 outliers final: 27 residues processed: 181 average time/residue: 0.1002 time to fit residues: 27.4727 Evaluate side-chains 190 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [107, 157, 9, 78, 142, 54, 29, 74, 154, 1, 49] chunk 107 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 154 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 HIS C 167 HIS B 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.201216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.157250 restraints weight = 13866.167| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.27 r_work: 0.3476 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13568 Z= 0.138 Angle : 0.599 13.583 18392 Z= 0.309 Chirality : 0.037 0.172 2156 Planarity : 0.002 0.023 2220 Dihedral : 14.663 138.938 1840 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.78 % Allowed : 16.60 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.20), residues: 1596 helix: 2.65 (0.16), residues: 984 sheet: 0.68 (0.36), residues: 192 loop : -2.13 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.014 0.001 TYR B 486 PHE 0.013 0.001 PHE B 420 TRP 0.005 0.001 TRP B 480 HIS 0.004 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (13560) covalent geometry : angle 0.56804 / 0.30 (18376) SS BOND : bond 0.00183 / 0.10 ( 8) SS BOND : angle 6.47662 / 3.30 ( 16) hydrogen bonds : bond 0.04123 / 2.73 ( 988) hydrogen bonds : angle 4.02703 / 2.92 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2710.91 seconds wall clock time: 47 minutes 24.60 seconds (2844.60 seconds total)