Starting phenix.real_space_refine on Tue Feb 3 16:10:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kkl_62391/02_2026/9kkl_62391.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kkl_62391/02_2026/9kkl_62391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kkl_62391/02_2026/9kkl_62391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kkl_62391/02_2026/9kkl_62391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kkl_62391/02_2026/9kkl_62391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kkl_62391/02_2026/9kkl_62391.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 20 5.16 5 C 2982 2.51 5 N 764 2.21 5 O 934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4700 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2314 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 26, 'TRANS': 276} Chain breaks: 1 Chain: "A" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2314 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 26, 'TRANS': 276} Chain breaks: 1 Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'A2G': 1, 'FUC': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'A2G': 1, 'FUC': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.13, per 1000 atoms: 0.24 Number of scatterers: 4700 At special positions: 0 Unit cell: (75.4, 75.4, 78, 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 20 16.00 O 934 8.00 N 764 7.00 C 2982 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 Links applied ALPHA1-3 " GLA C 1 " - " A2G C 3 " " GLA D 1 " - " A2G D 3 " BETA1-2 " GLA C 1 " - " FUC C 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " GLA D 1 " - " FUC D 2 " Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 242.5 milliseconds 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1088 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 11 sheets defined 8.9% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.545A pdb=" N MET B 221 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 4.004A pdb=" N ASP B 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'B' and resid 448 through 453 removed outlier: 3.926A pdb=" N ILE B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.555A pdb=" N MET A 221 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 448 through 453 removed outlier: 3.780A pdb=" N ILE A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.527A pdb=" N VAL A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AA2, first strand: chain 'B' and resid 250 through 251 removed outlier: 3.513A pdb=" N GLY B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 438 through 439 removed outlier: 4.837A pdb=" N ALA B 385 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N MET B 345 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 429 " --> pdb=" O TYR B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 438 through 439 removed outlier: 4.837A pdb=" N ALA B 385 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG B 377 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 329 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 383 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL B 325 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA B 385 " --> pdb=" O HIS B 323 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N HIS B 323 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N GLN B 322 " --> pdb=" O TYR B 348 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N TYR B 348 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 330 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP B 340 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 429 " --> pdb=" O TYR B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 416 through 418 removed outlier: 5.248A pdb=" N ASN B 492 " --> pdb=" O GLN B 480 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N GLN B 480 " --> pdb=" O ASN B 492 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 477 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 465 " --> pdb=" O TRP B 513 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TRP B 513 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 467 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 423 through 425 Processing sheet with id=AA7, first strand: chain 'B' and resid 427 through 429 removed outlier: 6.230A pdb=" N ALA B 427 " --> pdb=" O TYR A 338 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASP A 340 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N SER B 429 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASP A 342 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP A 340 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL A 330 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N TYR A 348 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N GLN A 322 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS A 323 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 427 through 429 removed outlier: 6.230A pdb=" N ALA B 427 " --> pdb=" O TYR A 338 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASP A 340 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N SER B 429 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASP A 342 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET A 345 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TRP A 285 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLY A 277 " --> pdb=" O TRP A 285 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 287 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 275 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ARG A 377 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 329 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS A 323 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AB1, first strand: chain 'A' and resid 416 through 418 removed outlier: 4.999A pdb=" N ASN A 492 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLN A 480 " --> pdb=" O ASN A 492 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 512 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP A 469 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N PHE A 510 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 471 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 508 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 425 108 hydrogen bonds defined for protein. 279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.41 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 762 1.30 - 1.43: 1368 1.43 - 1.56: 2686 1.56 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4848 Sorted by residual: bond pdb=" C7 A2G C 3 " pdb=" N2 A2G C 3 " ideal model delta sigma weight residual 1.349 1.475 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C7 A2G D 3 " pdb=" N2 A2G D 3 " ideal model delta sigma weight residual 1.349 1.474 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C5 A2G D 3 " pdb=" C6 A2G D 3 " ideal model delta sigma weight residual 1.520 1.403 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C5 A2G C 3 " pdb=" C6 A2G C 3 " ideal model delta sigma weight residual 1.520 1.405 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C5 A2G C 3 " pdb=" O5 A2G C 3 " ideal model delta sigma weight residual 1.419 1.533 -0.114 2.00e-02 2.50e+03 3.26e+01 ... (remaining 4843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 6336 2.32 - 4.64: 267 4.64 - 6.97: 34 6.97 - 9.29: 7 9.29 - 11.61: 2 Bond angle restraints: 6646 Sorted by residual: angle pdb=" N ALA B 320 " pdb=" CA ALA B 320 " pdb=" C ALA B 320 " ideal model delta sigma weight residual 112.92 104.92 8.00 1.23e+00 6.61e-01 4.23e+01 angle pdb=" O ASN B 295 " pdb=" C ASN B 295 " pdb=" N PRO B 296 " ideal model delta sigma weight residual 121.42 117.48 3.94 9.10e-01 1.21e+00 1.88e+01 angle pdb=" N ASN B 295 " pdb=" CA ASN B 295 " pdb=" C ASN B 295 " ideal model delta sigma weight residual 108.97 101.49 7.48 1.82e+00 3.02e-01 1.69e+01 angle pdb=" N PRO B 503 " pdb=" CA PRO B 503 " pdb=" C PRO B 503 " ideal model delta sigma weight residual 110.70 115.69 -4.99 1.22e+00 6.72e-01 1.67e+01 angle pdb=" CA ASN B 295 " pdb=" C ASN B 295 " pdb=" N PRO B 296 " ideal model delta sigma weight residual 117.73 121.86 -4.13 1.04e+00 9.25e-01 1.58e+01 ... (remaining 6641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 2635 15.06 - 30.11: 179 30.11 - 45.17: 44 45.17 - 60.22: 23 60.22 - 75.28: 3 Dihedral angle restraints: 2884 sinusoidal: 1160 harmonic: 1724 Sorted by residual: dihedral pdb=" CD ARG B 321 " pdb=" NE ARG B 321 " pdb=" CZ ARG B 321 " pdb=" NH1 ARG B 321 " ideal model delta sinusoidal sigma weight residual 0.00 -63.11 63.11 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CD ARG A 321 " pdb=" NE ARG A 321 " pdb=" CZ ARG A 321 " pdb=" NH1 ARG A 321 " ideal model delta sinusoidal sigma weight residual 0.00 34.46 -34.46 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CA VAL B 419 " pdb=" C VAL B 419 " pdb=" N TRP B 420 " pdb=" CA TRP B 420 " ideal model delta harmonic sigma weight residual -180.00 -161.00 -19.00 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 2881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 517 0.056 - 0.111: 139 0.111 - 0.167: 47 0.167 - 0.222: 19 0.222 - 0.278: 4 Chirality restraints: 726 Sorted by residual: chirality pdb=" C1 FUC D 2 " pdb=" O2 GLA D 1 " pdb=" C2 FUC D 2 " pdb=" O5 FUC D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.74e+02 chirality pdb=" C1 A2G D 3 " pdb=" O3 GLA D 1 " pdb=" C2 A2G D 3 " pdb=" O5 A2G D 3 " both_signs ideal model delta sigma weight residual False 2.40 2.66 -0.26 2.00e-02 2.50e+03 1.64e+02 chirality pdb=" C1 A2G C 3 " pdb=" O3 GLA C 1 " pdb=" C2 A2G C 3 " pdb=" O5 A2G C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.62 -0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 723 not shown) Planarity restraints: 858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 321 " 0.959 9.50e-02 1.11e+02 4.30e-01 1.12e+02 pdb=" NE ARG B 321 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG B 321 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 321 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 321 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 321 " -0.619 9.50e-02 1.11e+02 2.77e-01 4.70e+01 pdb=" NE ARG A 321 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 321 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 321 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 321 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 422 " 0.514 9.50e-02 1.11e+02 2.31e-01 3.25e+01 pdb=" NE ARG A 422 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 422 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 422 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 422 " 0.017 2.00e-02 2.50e+03 ... (remaining 855 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 7 2.17 - 2.85: 1737 2.85 - 3.53: 5479 3.53 - 4.22: 10125 4.22 - 4.90: 17577 Nonbonded interactions: 34925 Sorted by model distance: nonbonded pdb=" O SER A 314 " pdb=" NE2 GLN A 322 " model vdw 1.485 3.120 nonbonded pdb=" O ASP B 333 " pdb=" OD1 ASN B 334 " model vdw 1.515 3.040 nonbonded pdb=" CD1 LEU B 472 " pdb=" O ASP B 505 " model vdw 1.836 3.460 nonbonded pdb=" C ASP B 333 " pdb=" OD1 ASN B 334 " model vdw 1.871 3.270 nonbonded pdb=" O ASN A 437 " pdb=" OD1 ASN A 437 " model vdw 1.879 3.040 ... (remaining 34920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.840 Find NCS groups from input model: 0.050 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.010 0.126 4852 Z= 0.643 Angle : 1.061 12.937 6658 Z= 0.640 Chirality : 0.066 0.278 726 Planarity : 0.020 0.430 858 Dihedral : 12.137 75.277 1796 Min Nonbonded Distance : 1.485 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.35 % Favored : 94.15 % Rotamer: Outliers : 5.36 % Allowed : 9.72 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.30), residues: 598 helix: -2.27 (0.96), residues: 24 sheet: -1.84 (0.40), residues: 166 loop : -2.24 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 321 TYR 0.023 0.002 TYR A 473 PHE 0.015 0.001 PHE A 508 TRP 0.008 0.001 TRP B 404 HIS 0.001 0.000 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.01041 ( 4848) covalent geometry : angle 1.02504 ( 6646) hydrogen bonds : bond 0.23189 ( 104) hydrogen bonds : angle 9.34619 ( 279) link_ALPHA1-3 : bond 0.00434 ( 2) link_ALPHA1-3 : angle 9.01476 ( 6) link_BETA1-2 : bond 0.03165 ( 2) link_BETA1-2 : angle 2.16393 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.188 Fit side-chains REVERT: B 289 MET cc_start: 0.7911 (mtp) cc_final: 0.7685 (mtt) REVERT: B 295 ASN cc_start: 0.8676 (t0) cc_final: 0.8207 (t0) REVERT: B 438 SER cc_start: 0.8971 (p) cc_final: 0.8692 (p) REVERT: A 512 SER cc_start: 0.8282 (t) cc_final: 0.8070 (m) outliers start: 27 outliers final: 5 residues processed: 111 average time/residue: 0.0549 time to fit residues: 8.2628 Evaluate side-chains 52 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 0.0050 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN A 334 ASN A 363 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.142652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.121695 restraints weight = 5638.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.124800 restraints weight = 3582.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.126994 restraints weight = 2672.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.128448 restraints weight = 2204.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.129166 restraints weight = 1916.156| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4852 Z= 0.113 Angle : 0.657 10.228 6658 Z= 0.313 Chirality : 0.048 0.232 726 Planarity : 0.005 0.032 858 Dihedral : 7.315 58.718 788 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.58 % Allowed : 12.90 % Favored : 84.52 % 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: -2.70 (0.30), residues: 598 helix: -3.15 (0.72), residues: 26 sheet: -1.38 (0.40), residues: 168 loop : -1.98 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 422 TYR 0.013 0.001 TYR B 378 PHE 0.011 0.001 PHE A 327 TRP 0.011 0.001 TRP B 346 HIS 0.007 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4848) covalent geometry : angle 0.60625 ( 6646) hydrogen bonds : bond 0.04243 ( 104) hydrogen bonds : angle 7.14453 ( 279) link_ALPHA1-3 : bond 0.00315 ( 2) link_ALPHA1-3 : angle 8.36325 ( 6) link_BETA1-2 : bond 0.01485 ( 2) link_BETA1-2 : angle 1.18224 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.175 Fit side-chains REVERT: B 289 MET cc_start: 0.7914 (mtp) cc_final: 0.7683 (mtt) REVERT: A 244 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8778 (p0) outliers start: 13 outliers final: 6 residues processed: 59 average time/residue: 0.0546 time to fit residues: 4.5973 Evaluate side-chains 48 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.126807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.105507 restraints weight = 5923.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.108360 restraints weight = 3770.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.110355 restraints weight = 2855.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.111571 restraints weight = 2389.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.112414 restraints weight = 2120.766| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 : 0.004 0.033 4852 Z= 0.180 Angle : 0.682 9.195 6658 Z= 0.334 Chirality : 0.049 0.159 726 Planarity : 0.005 0.038 858 Dihedral : 7.121 54.827 784 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.77 % Allowed : 12.50 % Favored : 83.73 % 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: -2.60 (0.30), residues: 598 helix: -2.87 (0.85), residues: 26 sheet: -1.44 (0.42), residues: 150 loop : -1.86 (0.25), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 422 TYR 0.016 0.002 TYR B 365 PHE 0.018 0.002 PHE A 421 TRP 0.013 0.001 TRP A 420 HIS 0.005 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 4848) covalent geometry : angle 0.64255 ( 6646) hydrogen bonds : bond 0.04265 ( 104) hydrogen bonds : angle 6.54070 ( 279) link_ALPHA1-3 : bond 0.00445 ( 2) link_ALPHA1-3 : angle 7.43227 ( 6) link_BETA1-2 : bond 0.00956 ( 2) link_BETA1-2 : angle 1.69118 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: B 289 MET cc_start: 0.8116 (mtp) cc_final: 0.7763 (mtt) REVERT: A 244 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8750 (p0) outliers start: 19 outliers final: 13 residues processed: 63 average time/residue: 0.0593 time to fit residues: 5.1842 Evaluate side-chains 57 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.125955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.104540 restraints weight = 5837.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.107471 restraints weight = 3679.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.109541 restraints weight = 2770.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.110789 restraints weight = 2288.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.111805 restraints weight = 2022.985| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4852 Z= 0.103 Angle : 0.589 8.363 6658 Z= 0.284 Chirality : 0.045 0.142 726 Planarity : 0.004 0.033 858 Dihedral : 6.659 53.420 782 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.17 % Allowed : 14.48 % Favored : 82.34 % 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: -2.48 (0.31), residues: 598 helix: -2.72 (0.89), residues: 26 sheet: -1.64 (0.40), residues: 162 loop : -1.64 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.011 0.001 TYR B 235 PHE 0.011 0.001 PHE A 272 TRP 0.007 0.001 TRP B 346 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 4848) covalent geometry : angle 0.55271 ( 6646) hydrogen bonds : bond 0.03170 ( 104) hydrogen bonds : angle 6.21657 ( 279) link_ALPHA1-3 : bond 0.00391 ( 2) link_ALPHA1-3 : angle 6.67311 ( 6) link_BETA1-2 : bond 0.01048 ( 2) link_BETA1-2 : angle 1.33968 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: B 289 MET cc_start: 0.8064 (mtp) cc_final: 0.7731 (mtt) outliers start: 16 outliers final: 12 residues processed: 58 average time/residue: 0.0599 time to fit residues: 4.8613 Evaluate side-chains 54 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 512 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 49 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.137160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.116549 restraints weight = 5845.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.119531 restraints weight = 3734.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.121598 restraints weight = 2816.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.122772 restraints weight = 2344.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.123410 restraints weight = 2087.448| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4852 Z= 0.088 Angle : 0.542 7.418 6658 Z= 0.261 Chirality : 0.044 0.141 726 Planarity : 0.004 0.031 858 Dihedral : 6.164 55.240 782 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.57 % Allowed : 14.88 % Favored : 81.55 % 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: -2.14 (0.31), residues: 598 helix: -2.45 (0.95), residues: 26 sheet: -1.17 (0.43), residues: 146 loop : -1.52 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.010 0.001 TYR A 365 PHE 0.010 0.001 PHE A 272 TRP 0.005 0.000 TRP B 346 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 4848) covalent geometry : angle 0.51115 ( 6646) hydrogen bonds : bond 0.02774 ( 104) hydrogen bonds : angle 5.85694 ( 279) link_ALPHA1-3 : bond 0.00406 ( 2) link_ALPHA1-3 : angle 5.86687 ( 6) link_BETA1-2 : bond 0.00890 ( 2) link_BETA1-2 : angle 1.39257 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.180 Fit side-chains REVERT: B 437 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8641 (p0) REVERT: A 244 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8797 (p0) outliers start: 18 outliers final: 13 residues processed: 64 average time/residue: 0.0594 time to fit residues: 5.2669 Evaluate side-chains 59 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.121863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.100299 restraints weight = 6034.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.103085 restraints weight = 3752.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.105087 restraints weight = 2823.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.106454 restraints weight = 2343.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.107097 restraints weight = 2069.816| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4852 Z= 0.143 Angle : 0.607 7.431 6658 Z= 0.298 Chirality : 0.047 0.162 726 Planarity : 0.005 0.035 858 Dihedral : 6.135 59.982 780 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.98 % Allowed : 15.87 % Favored : 81.15 % 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: -2.15 (0.32), residues: 598 helix: -2.63 (0.95), residues: 26 sheet: -1.16 (0.43), residues: 148 loop : -1.52 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.014 0.002 TYR B 365 PHE 0.015 0.002 PHE A 272 TRP 0.011 0.001 TRP B 404 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4848) covalent geometry : angle 0.57861 ( 6646) hydrogen bonds : bond 0.03634 ( 104) hydrogen bonds : angle 5.96264 ( 279) link_ALPHA1-3 : bond 0.00325 ( 2) link_ALPHA1-3 : angle 5.95941 ( 6) link_BETA1-2 : bond 0.00787 ( 2) link_BETA1-2 : angle 1.69167 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.104 Fit side-chains REVERT: B 289 MET cc_start: 0.8151 (mtp) cc_final: 0.7766 (mtt) REVERT: B 464 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8496 (mmmm) REVERT: A 244 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8769 (p0) outliers start: 15 outliers final: 11 residues processed: 57 average time/residue: 0.0685 time to fit residues: 5.2520 Evaluate side-chains 55 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 512 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.123110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.101715 restraints weight = 5945.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.104509 restraints weight = 3736.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.106539 restraints weight = 2817.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.107775 restraints weight = 2351.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.108638 restraints weight = 2083.433| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4852 Z= 0.104 Angle : 0.558 7.279 6658 Z= 0.271 Chirality : 0.045 0.131 726 Planarity : 0.004 0.032 858 Dihedral : 5.864 58.726 780 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.58 % Allowed : 15.28 % Favored : 82.14 % 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: -2.04 (0.32), residues: 598 helix: -2.50 (0.96), residues: 26 sheet: -1.04 (0.43), residues: 146 loop : -1.47 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.012 0.001 TYR A 365 PHE 0.011 0.001 PHE A 272 TRP 0.007 0.001 TRP B 404 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4848) covalent geometry : angle 0.53002 ( 6646) hydrogen bonds : bond 0.03085 ( 104) hydrogen bonds : angle 5.85318 ( 279) link_ALPHA1-3 : bond 0.00319 ( 2) link_ALPHA1-3 : angle 5.67259 ( 6) link_BETA1-2 : bond 0.00869 ( 2) link_BETA1-2 : angle 1.43858 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.174 Fit side-chains REVERT: B 289 MET cc_start: 0.8124 (mtp) cc_final: 0.7755 (mtt) REVERT: B 464 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8504 (mmmm) REVERT: A 244 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8769 (p0) REVERT: A 249 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7274 (mtp180) outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 0.0800 time to fit residues: 5.8319 Evaluate side-chains 55 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 512 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.121220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.099844 restraints weight = 6068.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.102669 restraints weight = 3810.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.104628 restraints weight = 2864.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.105848 restraints weight = 2397.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.106631 restraints weight = 2125.249| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4852 Z= 0.133 Angle : 0.587 7.183 6658 Z= 0.289 Chirality : 0.046 0.139 726 Planarity : 0.004 0.034 858 Dihedral : 5.669 50.806 780 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.78 % Allowed : 14.88 % Favored : 82.34 % 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: -2.01 (0.32), residues: 598 helix: -2.61 (0.96), residues: 26 sheet: -1.00 (0.44), residues: 146 loop : -1.44 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.013 0.002 TYR B 365 PHE 0.012 0.002 PHE A 421 TRP 0.009 0.001 TRP B 404 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4848) covalent geometry : angle 0.56069 ( 6646) hydrogen bonds : bond 0.03447 ( 104) hydrogen bonds : angle 5.89362 ( 279) link_ALPHA1-3 : bond 0.00256 ( 2) link_ALPHA1-3 : angle 5.63421 ( 6) link_BETA1-2 : bond 0.00784 ( 2) link_BETA1-2 : angle 1.67252 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.172 Fit side-chains REVERT: B 289 MET cc_start: 0.8160 (mtp) cc_final: 0.7778 (mtt) REVERT: A 244 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8775 (p0) REVERT: A 249 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7301 (mtp180) outliers start: 14 outliers final: 9 residues processed: 56 average time/residue: 0.0776 time to fit residues: 5.6647 Evaluate side-chains 54 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 512 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.124232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.102982 restraints weight = 5853.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.105902 restraints weight = 3695.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.107806 restraints weight = 2792.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.109026 restraints weight = 2328.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.109975 restraints weight = 2065.934| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4852 Z= 0.088 Angle : 0.535 6.762 6658 Z= 0.259 Chirality : 0.044 0.127 726 Planarity : 0.004 0.032 858 Dihedral : 5.055 43.912 778 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.79 % Allowed : 15.87 % Favored : 82.34 % 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: -1.99 (0.32), residues: 598 helix: -2.38 (0.97), residues: 26 sheet: -1.17 (0.42), residues: 158 loop : -1.36 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.011 0.001 TYR A 365 PHE 0.011 0.001 PHE A 272 TRP 0.005 0.000 TRP B 404 HIS 0.003 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 4848) covalent geometry : angle 0.51022 ( 6646) hydrogen bonds : bond 0.02798 ( 104) hydrogen bonds : angle 5.71549 ( 279) link_ALPHA1-3 : bond 0.00288 ( 2) link_ALPHA1-3 : angle 5.17903 ( 6) link_BETA1-2 : bond 0.00894 ( 2) link_BETA1-2 : angle 1.37466 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.120 Fit side-chains REVERT: B 289 MET cc_start: 0.8093 (mtp) cc_final: 0.7734 (mtt) REVERT: A 244 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8787 (p0) REVERT: A 317 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7572 (ttmt) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.0515 time to fit residues: 3.3521 Evaluate side-chains 50 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 46 optimal weight: 0.0870 chunk 14 optimal weight: 0.0270 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.124572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.103359 restraints weight = 5946.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.106329 restraints weight = 3743.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.108323 restraints weight = 2801.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.109508 restraints weight = 2320.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.110410 restraints weight = 2062.732| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4852 Z= 0.092 Angle : 0.534 6.456 6658 Z= 0.260 Chirality : 0.044 0.161 726 Planarity : 0.004 0.032 858 Dihedral : 4.654 32.249 778 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.39 % Allowed : 16.27 % Favored : 82.34 % 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: -1.92 (0.33), residues: 598 helix: -2.33 (0.98), residues: 26 sheet: -1.12 (0.42), residues: 158 loop : -1.30 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.011 0.001 TYR A 365 PHE 0.010 0.001 PHE A 272 TRP 0.007 0.000 TRP B 404 HIS 0.003 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 4848) covalent geometry : angle 0.51104 ( 6646) hydrogen bonds : bond 0.02738 ( 104) hydrogen bonds : angle 5.60810 ( 279) link_ALPHA1-3 : bond 0.00230 ( 2) link_ALPHA1-3 : angle 4.97571 ( 6) link_BETA1-2 : bond 0.00836 ( 2) link_BETA1-2 : angle 1.52315 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.174 Fit side-chains REVERT: B 289 MET cc_start: 0.8074 (mtp) cc_final: 0.7731 (mtt) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.0673 time to fit residues: 4.4799 Evaluate side-chains 49 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 59 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.120758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.099349 restraints weight = 6001.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.102201 restraints weight = 3789.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.103971 restraints weight = 2859.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.105220 restraints weight = 2405.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.105222 restraints weight = 2150.212| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4852 Z= 0.160 Angle : 0.610 6.877 6658 Z= 0.303 Chirality : 0.047 0.141 726 Planarity : 0.005 0.034 858 Dihedral : 4.893 26.956 778 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.79 % Allowed : 16.27 % Favored : 81.94 % 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: -2.07 (0.32), residues: 598 helix: -2.53 (0.97), residues: 26 sheet: -1.19 (0.42), residues: 158 loop : -1.42 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.014 0.002 TYR A 365 PHE 0.012 0.002 PHE A 421 TRP 0.012 0.001 TRP B 404 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 4848) covalent geometry : angle 0.58657 ( 6646) hydrogen bonds : bond 0.03613 ( 104) hydrogen bonds : angle 5.83527 ( 279) link_ALPHA1-3 : bond 0.00187 ( 2) link_ALPHA1-3 : angle 5.36390 ( 6) link_BETA1-2 : bond 0.00753 ( 2) link_BETA1-2 : angle 1.75150 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 872.19 seconds wall clock time: 15 minutes 52.29 seconds (952.29 seconds total)