Starting phenix.real_space_refine on Tue Aug 4 17:18:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vvm_64067/08_2026/9vvm_64067.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vvm_64067/08_2026/9vvm_64067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vvm_64067/08_2026/9vvm_64067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vvm_64067/08_2026/9vvm_64067.map" model { file = "/net/cci-nas-00/data/ceres_data/9vvm_64067/08_2026/9vvm_64067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vvm_64067/08_2026/9vvm_64067.cif" } resolution = 3.38 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= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 29 5.16 5 C 3434 2.51 5 N 850 2.21 5 O 935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5250 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5206 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 24, 'TRANS': 632} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.35, per 1000 atoms: 0.26 Number of scatterers: 5250 At special positions: 0 Unit cell: (82.29, 87.565, 124.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 2 15.00 O 935 8.00 N 850 7.00 C 3434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 188.9 milliseconds 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1234 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 59.7% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 41 through 46 removed outlier: 4.187A pdb=" N ILE A 46 " --> pdb=" O TYR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 66 removed outlier: 4.111A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 78 through 109 removed outlier: 3.743A pdb=" N THR A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 3.788A pdb=" N ALA A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 133 removed outlier: 3.517A pdb=" N LEU A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 172 Proline residue: A 162 - end of helix removed outlier: 4.659A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 209 Proline residue: A 203 - end of helix removed outlier: 3.761A pdb=" N VAL A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 238 removed outlier: 4.035A pdb=" N ALA A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) Proline residue: A 224 - end of helix Processing helix chain 'A' and resid 250 through 270 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 289 through 304 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 308 through 317 removed outlier: 4.203A pdb=" N PHE A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 4.065A pdb=" N ARG A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 362 Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 377 through 405 Processing helix chain 'A' and resid 607 through 610 Processing helix chain 'A' and resid 611 through 637 removed outlier: 4.293A pdb=" N VAL A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THR A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 667 removed outlier: 3.867A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 695 removed outlier: 3.993A pdb=" N TYR A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 456 removed outlier: 7.472A pdb=" N GLU A 413 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N TYR A 487 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 415 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 489 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN A 417 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A 491 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 419 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLU A 493 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 456 removed outlier: 7.472A pdb=" N GLU A 413 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N TYR A 487 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 415 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 489 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN A 417 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A 491 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 419 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLU A 493 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443 Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 545 removed outlier: 3.815A pdb=" N GLY A 544 " --> pdb=" O ASN A 521 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 521 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545 removed outlier: 3.815A pdb=" N GLY A 544 " --> pdb=" O ASN A 521 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 521 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR A 516 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE A 583 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG A 518 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE A 585 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL A 520 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN A 587 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA A 580 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 600 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 582 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 598 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 584 " --> pdb=" O TRP A 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.667A pdb=" N VAL A 527 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 removed outlier: 4.010A pdb=" N GLY A 554 " --> pdb=" O LEU A 575 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 817 1.31 - 1.43: 1512 1.43 - 1.56: 3001 1.56 - 1.68: 9 1.68 - 1.81: 47 Bond restraints: 5386 Sorted by residual: bond pdb=" C3D NAD A 801 " pdb=" C4D NAD A 801 " ideal model delta sigma weight residual 1.531 1.291 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C4D NAD A 801 " pdb=" O4D NAD A 801 " ideal model delta sigma weight residual 1.445 1.682 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1B NAD A 801 " pdb=" O4B NAD A 801 " ideal model delta sigma weight residual 1.402 1.589 -0.187 2.00e-02 2.50e+03 8.74e+01 bond pdb=" C2B NAD A 801 " pdb=" C3B NAD A 801 " ideal model delta sigma weight residual 1.524 1.339 0.185 2.00e-02 2.50e+03 8.52e+01 bond pdb=" C6A NAD A 801 " pdb=" N6A NAD A 801 " ideal model delta sigma weight residual 1.334 1.471 -0.137 2.00e-02 2.50e+03 4.67e+01 ... (remaining 5381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 7245 2.62 - 5.24: 68 5.24 - 7.87: 10 7.87 - 10.49: 3 10.49 - 13.11: 3 Bond angle restraints: 7329 Sorted by residual: angle pdb=" O1A NAD A 801 " pdb=" PA NAD A 801 " pdb=" O2A NAD A 801 " ideal model delta sigma weight residual 122.64 109.53 13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" O3 NAD A 801 " pdb=" PN NAD A 801 " pdb=" O5D NAD A 801 " ideal model delta sigma weight residual 98.00 109.90 -11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O1N NAD A 801 " pdb=" PN NAD A 801 " pdb=" O2N NAD A 801 " ideal model delta sigma weight residual 120.02 109.47 10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C2A NAD A 801 " pdb=" N3A NAD A 801 " pdb=" C4A NAD A 801 " ideal model delta sigma weight residual 111.69 120.96 -9.27 3.00e+00 1.11e-01 9.56e+00 angle pdb=" O3 NAD A 801 " pdb=" PA NAD A 801 " pdb=" O5B NAD A 801 " ideal model delta sigma weight residual 101.67 110.27 -8.60 3.00e+00 1.11e-01 8.22e+00 ... (remaining 7324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 2776 17.72 - 35.44: 301 35.44 - 53.16: 80 53.16 - 70.88: 15 70.88 - 88.60: 9 Dihedral angle restraints: 3181 sinusoidal: 1262 harmonic: 1919 Sorted by residual: dihedral pdb=" CA PHE A 625 " pdb=" C PHE A 625 " pdb=" N SER A 626 " pdb=" CA SER A 626 " ideal model delta harmonic sigma weight residual 180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG A 332 " pdb=" CD ARG A 332 " pdb=" NE ARG A 332 " pdb=" CZ ARG A 332 " ideal model delta sinusoidal sigma weight residual -180.00 -135.66 -44.34 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 365 " pdb=" CD ARG A 365 " pdb=" NE ARG A 365 " pdb=" CZ ARG A 365 " ideal model delta sinusoidal sigma weight residual -90.00 -47.87 -42.13 2 1.50e+01 4.44e-03 9.60e+00 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 742 0.066 - 0.132: 93 0.132 - 0.198: 1 0.198 - 0.263: 1 0.263 - 0.329: 1 Chirality restraints: 838 Sorted by residual: chirality pdb=" C3D NAD A 801 " pdb=" C2D NAD A 801 " pdb=" C4D NAD A 801 " pdb=" O3D NAD A 801 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3B NAD A 801 " pdb=" C2B NAD A 801 " pdb=" C4B NAD A 801 " pdb=" O3B NAD A 801 " both_signs ideal model delta sigma weight residual False -2.71 -2.50 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1B NAD A 801 " pdb=" C2B NAD A 801 " pdb=" N9A NAD A 801 " pdb=" O4B NAD A 801 " both_signs ideal model delta sigma weight residual False 2.35 2.52 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 835 not shown) Planarity restraints: 906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 274 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 275 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 275 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 275 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 121 " -0.017 2.00e-02 2.50e+03 1.33e-02 3.54e+00 pdb=" CG TYR A 121 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 121 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 121 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 121 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 121 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 121 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 121 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 202 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 203 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " 0.019 5.00e-02 4.00e+02 ... (remaining 903 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1419 2.80 - 3.33: 5061 3.33 - 3.85: 8891 3.85 - 4.38: 9977 4.38 - 4.90: 17561 Nonbonded interactions: 42909 Sorted by model distance: nonbonded pdb=" OE2 GLU A 507 " pdb=" OG1 THR A 510 " model vdw 2.280 3.040 nonbonded pdb=" OE1 GLN A 326 " pdb=" NE2 GLN A 611 " model vdw 2.289 3.120 nonbonded pdb=" OH TYR A 70 " pdb=" OG SER A 146 " model vdw 2.302 3.040 nonbonded pdb=" OG SER A 59 " pdb=" O PRO A 224 " model vdw 2.309 3.040 nonbonded pdb=" OD1 ASP A 317 " pdb=" O3D NAD A 801 " model vdw 2.312 3.040 ... (remaining 42904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.240 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.370 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 : 0.008 0.240 5386 Z= 0.405 Angle : 0.699 13.112 7329 Z= 0.334 Chirality : 0.043 0.329 838 Planarity : 0.004 0.048 906 Dihedral : 16.359 88.604 1947 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.18 % Allowed : 20.56 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.33), residues: 655 helix: 1.61 (0.27), residues: 355 sheet: 0.46 (0.48), residues: 103 loop : -1.21 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 365 TYR 0.033 0.001 TYR A 121 PHE 0.010 0.001 PHE A 577 TRP 0.021 0.001 TRP A 280 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.40 ( 5386) covalent geometry : angle 0.69939 / 0.33 ( 7329) hydrogen bonds : bond 0.12709 / 8.67 ( 325) hydrogen bonds : angle 6.42114 / 4.48 ( 957) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.203 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0445 time to fit residues: 2.4576 Evaluate side-chains 35 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.226793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.168213 restraints weight = 4914.676| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.08 r_work: 0.3342 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5386 Z= 0.143 Angle : 0.543 7.829 7329 Z= 0.278 Chirality : 0.041 0.132 838 Planarity : 0.004 0.032 906 Dihedral : 10.354 82.735 759 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.93 % Allowed : 19.16 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.33), residues: 655 helix: 1.61 (0.27), residues: 356 sheet: 0.77 (0.52), residues: 90 loop : -1.28 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 365 TYR 0.027 0.001 TYR A 121 PHE 0.010 0.001 PHE A 167 TRP 0.013 0.001 TRP A 280 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 5386) covalent geometry : angle 0.54255 / 0.28 ( 7329) hydrogen bonds : bond 0.04344 / 2.75 ( 325) hydrogen bonds : angle 5.10699 / 3.62 ( 957) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.107 Fit side-chains REVERT: A 317 ASP cc_start: 0.7917 (m-30) cc_final: 0.7497 (m-30) outliers start: 11 outliers final: 6 residues processed: 44 average time/residue: 0.0463 time to fit residues: 3.0210 Evaluate side-chains 41 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.216424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.159884 restraints weight = 4948.255| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.65 r_work: 0.3145 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5386 Z= 0.178 Angle : 0.576 8.874 7329 Z= 0.294 Chirality : 0.042 0.134 838 Planarity : 0.004 0.036 906 Dihedral : 9.255 75.596 759 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.16 % Allowed : 18.98 % Favored : 77.86 % 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: 0.76 (0.33), residues: 655 helix: 1.36 (0.27), residues: 359 sheet: 0.68 (0.48), residues: 102 loop : -1.16 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 365 TYR 0.028 0.002 TYR A 121 PHE 0.015 0.002 PHE A 58 TRP 0.015 0.002 TRP A 280 HIS 0.006 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 5386) covalent geometry : angle 0.57600 / 0.29 ( 7329) hydrogen bonds : bond 0.04508 / 2.95 ( 325) hydrogen bonds : angle 4.76361 / 3.41 ( 957) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.251 Fit side-chains REVERT: A 105 ASP cc_start: 0.6528 (OUTLIER) cc_final: 0.5618 (t0) REVERT: A 127 ILE cc_start: 0.8077 (mm) cc_final: 0.7805 (mt) REVERT: A 212 PHE cc_start: 0.5012 (OUTLIER) cc_final: 0.3862 (p90) REVERT: A 317 ASP cc_start: 0.7765 (m-30) cc_final: 0.7377 (m-30) REVERT: A 694 TYR cc_start: 0.7709 (t80) cc_final: 0.7439 (t80) outliers start: 18 outliers final: 11 residues processed: 53 average time/residue: 0.0517 time to fit residues: 4.0271 Evaluate side-chains 50 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 697 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 45 optimal weight: 8.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.219342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3778 r_free = 0.3778 target = 0.159811 restraints weight = 4926.949| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.31 r_work: 0.3208 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5386 Z= 0.130 Angle : 0.513 8.055 7329 Z= 0.261 Chirality : 0.040 0.131 838 Planarity : 0.003 0.036 906 Dihedral : 8.210 73.280 759 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.34 % Allowed : 20.04 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.33), residues: 655 helix: 1.61 (0.28), residues: 357 sheet: 0.59 (0.48), residues: 105 loop : -1.08 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.017 0.001 TYR A 121 PHE 0.010 0.001 PHE A 312 TRP 0.015 0.001 TRP A 280 HIS 0.006 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 5386) covalent geometry : angle 0.51285 / 0.26 ( 7329) hydrogen bonds : bond 0.03847 / 2.47 ( 325) hydrogen bonds : angle 4.53863 / 3.26 ( 957) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.6220 (t0) REVERT: A 127 ILE cc_start: 0.8075 (mm) cc_final: 0.7792 (mt) REVERT: A 212 PHE cc_start: 0.5298 (OUTLIER) cc_final: 0.3992 (p90) REVERT: A 299 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6990 (tp) REVERT: A 302 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.8110 (p) REVERT: A 317 ASP cc_start: 0.7911 (m-30) cc_final: 0.7590 (m-30) REVERT: A 581 TYR cc_start: 0.7004 (m-80) cc_final: 0.6493 (m-80) REVERT: A 606 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6061 (ttm) REVERT: A 694 TYR cc_start: 0.7697 (t80) cc_final: 0.7462 (t80) outliers start: 19 outliers final: 10 residues processed: 54 average time/residue: 0.0551 time to fit residues: 4.2048 Evaluate side-chains 56 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 692 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.218356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161352 restraints weight = 5064.470| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.33 r_work: 0.3215 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5386 Z= 0.139 Angle : 0.520 8.153 7329 Z= 0.263 Chirality : 0.041 0.130 838 Planarity : 0.003 0.037 906 Dihedral : 6.997 73.032 759 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.22 % Allowed : 19.33 % Favored : 76.45 % 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: 1.08 (0.33), residues: 655 helix: 1.62 (0.27), residues: 358 sheet: 0.68 (0.47), residues: 107 loop : -0.97 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 365 TYR 0.018 0.001 TYR A 121 PHE 0.011 0.001 PHE A 312 TRP 0.015 0.001 TRP A 280 HIS 0.006 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5386) covalent geometry : angle 0.51997 / 0.26 ( 7329) hydrogen bonds : bond 0.03908 / 2.53 ( 325) hydrogen bonds : angle 4.42952 / 3.19 ( 957) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6226 (t0) REVERT: A 127 ILE cc_start: 0.8143 (mm) cc_final: 0.7849 (mt) REVERT: A 212 PHE cc_start: 0.5285 (OUTLIER) cc_final: 0.3882 (p90) REVERT: A 302 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8136 (p) REVERT: A 317 ASP cc_start: 0.7800 (m-30) cc_final: 0.7468 (m-30) REVERT: A 330 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.9111 (mtm) REVERT: A 502 MET cc_start: 0.7623 (tpt) cc_final: 0.7330 (tpt) REVERT: A 581 TYR cc_start: 0.7207 (m-80) cc_final: 0.6678 (m-80) REVERT: A 694 TYR cc_start: 0.7757 (t80) cc_final: 0.7549 (t80) outliers start: 24 outliers final: 13 residues processed: 56 average time/residue: 0.0398 time to fit residues: 3.3593 Evaluate side-chains 57 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 692 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.216766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.159764 restraints weight = 5017.514| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.68 r_work: 0.3145 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5386 Z= 0.154 Angle : 0.531 8.300 7329 Z= 0.268 Chirality : 0.041 0.137 838 Planarity : 0.003 0.037 906 Dihedral : 6.864 73.984 759 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.87 % Allowed : 19.51 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.02 (0.33), residues: 655 helix: 1.54 (0.27), residues: 358 sheet: 0.64 (0.45), residues: 107 loop : -0.91 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 365 TYR 0.017 0.001 TYR A 121 PHE 0.011 0.001 PHE A 58 TRP 0.016 0.001 TRP A 280 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.15 ( 5386) covalent geometry : angle 0.53102 / 0.27 ( 7329) hydrogen bonds : bond 0.03991 / 2.59 ( 325) hydrogen bonds : angle 4.41389 / 3.19 ( 957) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6323 (t0) REVERT: A 127 ILE cc_start: 0.8191 (mm) cc_final: 0.7989 (mt) REVERT: A 317 ASP cc_start: 0.7634 (m-30) cc_final: 0.7249 (m-30) REVERT: A 502 MET cc_start: 0.7785 (tpt) cc_final: 0.7516 (tpt) outliers start: 22 outliers final: 12 residues processed: 55 average time/residue: 0.0676 time to fit residues: 5.1478 Evaluate side-chains 52 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 692 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 34 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.217051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.160624 restraints weight = 5010.492| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.51 r_work: 0.3177 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5386 Z= 0.144 Angle : 0.525 8.216 7329 Z= 0.266 Chirality : 0.041 0.131 838 Planarity : 0.003 0.038 906 Dihedral : 6.801 73.087 759 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.34 % Allowed : 19.51 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.33), residues: 655 helix: 1.58 (0.27), residues: 358 sheet: 0.73 (0.46), residues: 107 loop : -0.90 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.015 0.001 TYR A 121 PHE 0.011 0.001 PHE A 312 TRP 0.015 0.001 TRP A 280 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 5386) covalent geometry : angle 0.52517 / 0.27 ( 7329) hydrogen bonds : bond 0.03939 / 2.54 ( 325) hydrogen bonds : angle 4.36407 / 3.16 ( 957) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 127 ILE cc_start: 0.8202 (mm) cc_final: 0.7985 (mt) REVERT: A 317 ASP cc_start: 0.7581 (m-30) cc_final: 0.7183 (m-30) REVERT: A 560 HIS cc_start: 0.5263 (OUTLIER) cc_final: 0.4713 (t-90) REVERT: A 606 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6121 (ttm) REVERT: A 641 MET cc_start: 0.7769 (mmm) cc_final: 0.7418 (mtp) outliers start: 19 outliers final: 13 residues processed: 52 average time/residue: 0.0511 time to fit residues: 3.8444 Evaluate side-chains 55 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.217739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.161137 restraints weight = 4924.748| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.37 r_work: 0.3201 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5386 Z= 0.131 Angle : 0.510 8.004 7329 Z= 0.261 Chirality : 0.040 0.130 838 Planarity : 0.003 0.038 906 Dihedral : 6.732 70.837 759 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.34 % Allowed : 19.51 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.33), residues: 655 helix: 1.63 (0.27), residues: 358 sheet: 0.74 (0.46), residues: 107 loop : -0.88 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.014 0.001 TYR A 121 PHE 0.013 0.001 PHE A 312 TRP 0.015 0.001 TRP A 280 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 5386) covalent geometry : angle 0.50954 / 0.26 ( 7329) hydrogen bonds : bond 0.03833 / 2.46 ( 325) hydrogen bonds : angle 4.33116 / 3.13 ( 957) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 127 ILE cc_start: 0.8170 (mm) cc_final: 0.7945 (mt) REVERT: A 317 ASP cc_start: 0.7615 (m-30) cc_final: 0.7234 (m-30) REVERT: A 560 HIS cc_start: 0.5415 (OUTLIER) cc_final: 0.4827 (t-90) REVERT: A 606 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6072 (ttm) REVERT: A 641 MET cc_start: 0.7684 (mmm) cc_final: 0.7339 (mtp) outliers start: 19 outliers final: 15 residues processed: 51 average time/residue: 0.0564 time to fit residues: 4.0789 Evaluate side-chains 56 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN ** A 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.208400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126239 restraints weight = 5080.995| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.43 r_work: 0.3136 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 5386 Z= 0.363 Angle : 0.750 11.469 7329 Z= 0.377 Chirality : 0.048 0.160 838 Planarity : 0.004 0.039 906 Dihedral : 7.399 80.988 759 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.99 % Allowed : 20.04 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.33), residues: 655 helix: 0.81 (0.27), residues: 360 sheet: 0.70 (0.45), residues: 111 loop : -0.87 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 180 TYR 0.023 0.003 TYR A 121 PHE 0.022 0.002 PHE A 58 TRP 0.022 0.002 TRP A 280 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00926 / 0.36 ( 5386) covalent geometry : angle 0.74966 / 0.38 ( 7329) hydrogen bonds : bond 0.05837 / 3.85 ( 325) hydrogen bonds : angle 4.87490 / 3.55 ( 957) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7813 (m-30) cc_final: 0.7221 (m-30) REVERT: A 361 PHE cc_start: 0.8119 (m-10) cc_final: 0.7859 (m-80) REVERT: A 502 MET cc_start: 0.7368 (tpp) cc_final: 0.6696 (tpp) REVERT: A 560 HIS cc_start: 0.5465 (OUTLIER) cc_final: 0.4837 (t-90) REVERT: A 694 TYR cc_start: 0.7953 (t80) cc_final: 0.7736 (t80) outliers start: 17 outliers final: 10 residues processed: 54 average time/residue: 0.0507 time to fit residues: 3.8462 Evaluate side-chains 49 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 624 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.214701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157956 restraints weight = 5005.189| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.66 r_work: 0.3106 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5386 Z= 0.164 Angle : 0.572 8.855 7329 Z= 0.290 Chirality : 0.041 0.133 838 Planarity : 0.004 0.040 906 Dihedral : 7.049 78.431 759 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.11 % Allowed : 21.44 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.33), residues: 655 helix: 1.25 (0.27), residues: 361 sheet: 0.70 (0.46), residues: 109 loop : -0.91 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.016 0.001 TYR A 121 PHE 0.012 0.001 PHE A 58 TRP 0.009 0.001 TRP A 260 HIS 0.006 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 ( 5386) covalent geometry : angle 0.57246 / 0.29 ( 7329) hydrogen bonds : bond 0.04253 / 2.74 ( 325) hydrogen bonds : angle 4.50481 / 3.26 ( 957) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7650 (m-30) cc_final: 0.7155 (m-30) REVERT: A 641 MET cc_start: 0.7872 (mmm) cc_final: 0.7313 (mtp) REVERT: A 694 TYR cc_start: 0.7825 (t80) cc_final: 0.7541 (t80) outliers start: 12 outliers final: 11 residues processed: 46 average time/residue: 0.0460 time to fit residues: 3.0122 Evaluate side-chains 49 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 624 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.0010 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.214641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.157269 restraints weight = 4984.365| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.73 r_work: 0.3106 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 5386 Z= 0.279 Angle : 1.073 59.199 7329 Z= 0.648 Chirality : 0.046 0.569 838 Planarity : 0.004 0.040 906 Dihedral : 7.055 78.407 759 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.11 % Allowed : 21.97 % Favored : 75.92 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.33), residues: 655 helix: 1.25 (0.27), residues: 361 sheet: 0.69 (0.46), residues: 109 loop : -0.92 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.015 0.001 TYR A 121 PHE 0.011 0.001 PHE A 58 TRP 0.008 0.001 TRP A 280 HIS 0.006 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.28 ( 5386) covalent geometry : angle 1.07331 / 0.65 ( 7329) hydrogen bonds : bond 0.04277 / 2.74 ( 325) hydrogen bonds : angle 4.55672 / 3.30 ( 957) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1211.17 seconds wall clock time: 21 minutes 23.56 seconds (1283.56 seconds total)