Starting phenix.real_space_refine on Fri Jul 3 08:41:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pvo_71894/07_2026/9pvo_71894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pvo_71894/07_2026/9pvo_71894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pvo_71894/07_2026/9pvo_71894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pvo_71894/07_2026/9pvo_71894.map" model { file = "/net/cci-nas-00/data/ceres_data/9pvo_71894/07_2026/9pvo_71894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pvo_71894/07_2026/9pvo_71894.cif" } resolution = 3.89 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= 0.007 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 S 51 5.16 5 C 4091 2.51 5 N 1104 2.21 5 O 1197 1.98 5 H 6254 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12697 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4591 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 21, 'TRANS': 263} Chain breaks: 6 Chain: "B" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 7019 Classifications: {'peptide': 443} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain breaks: 2 Chain: "Q" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 664 Classifications: {'peptide': 46} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "R" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 423 Classifications: {'peptide': 27} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 26} Time building chain proxies: 2.62, per 1000 atoms: 0.21 Number of scatterers: 12697 At special positions: 0 Unit cell: (93.28, 102.82, 118.72, 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 51 16.00 O 1197 8.00 N 1104 7.00 C 4091 6.00 H 6254 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 872 " distance=2.03 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 6 " - pdb=" SG CYS Q 11 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 7 " - pdb=" SG CYS R 7 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 20 " - pdb=" SG CYS R 19 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 472.6 milliseconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 14 sheets defined 20.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 638 through 643 Processing helix chain 'A' and resid 706 through 714 removed outlier: 4.815A pdb=" N ASN A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 712 " --> pdb=" O TYR A 708 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.674A pdb=" N ASP A 825 " --> pdb=" O LYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 882 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.620A pdb=" N PHE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 removed outlier: 4.037A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 193 through 200 removed outlier: 6.523A pdb=" N SER B 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 200 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.536A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.302A pdb=" N PHE B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 448 through 452 removed outlier: 4.160A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 12 through 18 Processing helix chain 'Q' and resid 32 through 45 Processing helix chain 'R' and resid 8 through 20 removed outlier: 4.087A pdb=" N VAL R 12 " --> pdb=" O GLY R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 23 No H-bonds generated for 'chain 'R' and resid 21 through 23' Processing sheet with id=AA1, first strand: chain 'A' and resid 475 through 479 Processing sheet with id=AA2, first strand: chain 'A' and resid 532 through 533 removed outlier: 4.572A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 607 removed outlier: 6.274A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 771 through 775 removed outlier: 3.516A pdb=" N GLU A 633 " --> pdb=" O ARG A 792 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 873 through 874 removed outlier: 7.268A pdb=" N THR A 901 " --> pdb=" O VAL A 855 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 8 removed outlier: 6.076A pdb=" N GLU B 6 " --> pdb=" O CYS B 26 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 28 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 56 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 14 Processing sheet with id=AA8, first strand: chain 'B' and resid 212 through 216 removed outlier: 5.468A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AB1, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AB2, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AB4, first strand: chain 'B' and resid 319 through 321 removed outlier: 8.344A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 335 through 336 160 hydrogen bonds defined for protein. 399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6253 1.03 - 1.23: 99 1.23 - 1.43: 2718 1.43 - 1.62: 3716 1.62 - 1.82: 61 Bond restraints: 12847 Sorted by residual: bond pdb=" CB PRO A 618 " pdb=" CG PRO A 618 " ideal model delta sigma weight residual 1.492 1.609 -0.117 5.00e-02 4.00e+02 5.51e+00 bond pdb=" N PHE A 705 " pdb=" CA PHE A 705 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" CG PRO A 618 " pdb=" CD PRO A 618 " ideal model delta sigma weight residual 1.503 1.444 0.059 3.40e-02 8.65e+02 3.00e+00 bond pdb=" N PHE A 705 " pdb=" H PHE A 705 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" CA PHE B 51 " pdb=" CB PHE B 51 " ideal model delta sigma weight residual 1.522 1.532 -0.010 7.00e-03 2.04e+04 1.95e+00 ... (remaining 12842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 22789 1.59 - 3.18: 345 3.18 - 4.77: 33 4.77 - 6.37: 7 6.37 - 7.96: 4 Bond angle restraints: 23178 Sorted by residual: angle pdb=" CA PRO A 618 " pdb=" N PRO A 618 " pdb=" CD PRO A 618 " ideal model delta sigma weight residual 112.00 104.04 7.96 1.40e+00 5.10e-01 3.23e+01 angle pdb=" N PRO A 618 " pdb=" CD PRO A 618 " pdb=" CG PRO A 618 " ideal model delta sigma weight residual 103.20 97.37 5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C SER Q 31 " pdb=" N LEU Q 32 " pdb=" CA LEU Q 32 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.86e+00 angle pdb=" CB MET B 38 " pdb=" CG MET B 38 " pdb=" SD MET B 38 " ideal model delta sigma weight residual 112.70 120.26 -7.56 3.00e+00 1.11e-01 6.35e+00 angle pdb=" N VAL Q 3 " pdb=" CA VAL Q 3 " pdb=" C VAL Q 3 " ideal model delta sigma weight residual 112.98 110.03 2.95 1.25e+00 6.40e-01 5.57e+00 ... (remaining 23173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 5410 17.05 - 34.10: 502 34.10 - 51.15: 137 51.15 - 68.20: 38 68.20 - 85.25: 19 Dihedral angle restraints: 6106 sinusoidal: 3311 harmonic: 2795 Sorted by residual: dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 182 " pdb=" CB CYS B 182 " ideal model delta sinusoidal sigma weight residual -86.00 -3.49 -82.51 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS B 259 " pdb=" SG CYS B 259 " pdb=" SG CYS B 284 " pdb=" CB CYS B 284 " ideal model delta sinusoidal sigma weight residual -86.00 -137.41 51.41 1 1.00e+01 1.00e-02 3.61e+01 dihedral pdb=" CA SER Q 9 " pdb=" C SER Q 9 " pdb=" N ILE Q 10 " pdb=" CA ILE Q 10 " ideal model delta harmonic sigma weight residual -180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 6103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 563 0.027 - 0.054: 261 0.054 - 0.080: 61 0.080 - 0.107: 49 0.107 - 0.134: 35 Chirality restraints: 969 Sorted by residual: chirality pdb=" CA ILE B 82 " pdb=" N ILE B 82 " pdb=" C ILE B 82 " pdb=" CB ILE B 82 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE B 285 " pdb=" N ILE B 285 " pdb=" C ILE B 285 " pdb=" CB ILE B 285 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL B 278 " pdb=" N VAL B 278 " pdb=" C VAL B 278 " pdb=" CB VAL B 278 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 966 not shown) Planarity restraints: 1900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 617 " 0.063 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO A 618 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO A 618 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 618 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 100 " -0.011 2.00e-02 2.50e+03 1.01e-02 2.27e+00 pdb=" CG HIS B 100 " 0.026 2.00e-02 2.50e+03 pdb=" ND1 HIS B 100 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS B 100 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 100 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 100 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS B 100 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS B 100 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 HIS B 100 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 597 " 0.019 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO A 598 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " 0.016 5.00e-02 4.00e+02 ... (remaining 1897 not shown) Histogram of nonbonded interaction distances: 1.31 - 1.97: 128 1.97 - 2.63: 16326 2.63 - 3.29: 37514 3.29 - 3.94: 47171 3.94 - 4.60: 73350 Nonbonded interactions: 174489 Sorted by model distance: nonbonded pdb=" O ASN B 343 " pdb="HD21 ASN B 343 " model vdw 1.313 2.450 nonbonded pdb=" OE1 GLU A 637 " pdb=" H GLU A 637 " model vdw 1.533 2.450 nonbonded pdb=" O ALA A 900 " pdb=" H GLY A 907 " model vdw 1.566 2.450 nonbonded pdb=" O PRO B 52 " pdb="HD21 ASN B 78 " model vdw 1.586 2.450 nonbonded pdb=" OE1 GLU B 204 " pdb=" H GLU B 204 " model vdw 1.588 2.450 ... (remaining 174484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 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: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.050 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.004 0.117 6611 Z= 0.155 Angle : 0.592 7.958 8961 Z= 0.308 Chirality : 0.042 0.134 969 Planarity : 0.004 0.091 1151 Dihedral : 14.913 83.938 2436 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.52 % Favored : 90.35 % Rotamer: Outliers : 0.14 % Allowed : 15.75 % Favored : 84.12 % 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: -1.44 (0.31), residues: 777 helix: -0.71 (0.55), residues: 99 sheet: -1.20 (0.42), residues: 147 loop : -0.94 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.010 0.001 TYR A 507 PHE 0.014 0.001 PHE B 51 TRP 0.005 0.001 TRP A 489 HIS 0.015 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 6593) covalent geometry : angle 0.59154 / 0.31 ( 8925) SS BOND : bond 0.00273 / 0.13 ( 18) SS BOND : angle 0.60727 / 0.38 ( 36) hydrogen bonds : bond 0.22315 / 13.74 ( 160) hydrogen bonds : angle 9.93082 / 6.58 ( 399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.1073 time to fit residues: 10.0553 Evaluate side-chains 59 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.134033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.100114 restraints weight = 40682.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103571 restraints weight = 24457.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.105893 restraints weight = 17515.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107390 restraints weight = 13943.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.108408 restraints weight = 11937.853| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6611 Z= 0.113 Angle : 0.574 5.971 8961 Z= 0.304 Chirality : 0.043 0.159 969 Planarity : 0.004 0.028 1151 Dihedral : 4.980 27.515 866 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.24 % Favored : 91.63 % Rotamer: Outliers : 0.69 % Allowed : 15.33 % Favored : 83.98 % 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: -1.46 (0.31), residues: 777 helix: -0.98 (0.51), residues: 96 sheet: -0.97 (0.43), residues: 148 loop : -0.98 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.011 0.001 TYR A 507 PHE 0.020 0.001 PHE A 497 TRP 0.003 0.001 TRP A 489 HIS 0.008 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 6593) covalent geometry : angle 0.57331 / 0.30 ( 8925) SS BOND : bond 0.00263 / 0.11 ( 18) SS BOND : angle 0.72353 / 0.40 ( 36) hydrogen bonds : bond 0.05576 / 3.39 ( 160) hydrogen bonds : angle 7.76738 / 5.18 ( 399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 GLU cc_start: 0.7425 (mp0) cc_final: 0.7148 (mp0) REVERT: B 404 ASP cc_start: 0.8298 (t0) cc_final: 0.8028 (t0) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.1131 time to fit residues: 10.7934 Evaluate side-chains 60 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 0.0670 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 635 GLN B 260 GLN B 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.134394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.100431 restraints weight = 40623.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103948 restraints weight = 23984.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.106374 restraints weight = 17020.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.107859 restraints weight = 13396.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.109044 restraints weight = 11433.522| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6611 Z= 0.104 Angle : 0.538 5.999 8961 Z= 0.279 Chirality : 0.042 0.161 969 Planarity : 0.003 0.029 1151 Dihedral : 4.840 27.328 866 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.27 % Favored : 90.60 % Rotamer: Outliers : 0.97 % Allowed : 15.19 % Favored : 83.84 % 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: -1.54 (0.31), residues: 777 helix: -1.06 (0.51), residues: 96 sheet: -1.11 (0.45), residues: 133 loop : -1.01 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.007 0.001 TYR A 507 PHE 0.010 0.001 PHE A 565 TRP 0.002 0.001 TRP A 493 HIS 0.013 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 6593) covalent geometry : angle 0.53718 / 0.28 ( 8925) SS BOND : bond 0.00313 / 0.13 ( 18) SS BOND : angle 0.72696 / 0.40 ( 36) hydrogen bonds : bond 0.04668 / 2.87 ( 160) hydrogen bonds : angle 7.19186 / 4.87 ( 399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 ASP cc_start: 0.8339 (t0) cc_final: 0.7944 (t70) outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.1068 time to fit residues: 10.9648 Evaluate side-chains 65 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 0.0980 chunk 4 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 635 GLN B 34 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.135003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101402 restraints weight = 40442.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104886 restraints weight = 24279.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.107198 restraints weight = 17265.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108873 restraints weight = 13653.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109941 restraints weight = 11574.182| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6611 Z= 0.094 Angle : 0.533 5.873 8961 Z= 0.275 Chirality : 0.042 0.150 969 Planarity : 0.003 0.030 1151 Dihedral : 4.729 26.967 866 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.11 % Favored : 91.76 % Rotamer: Outliers : 1.38 % Allowed : 15.19 % Favored : 83.43 % 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: -1.47 (0.31), residues: 777 helix: -1.07 (0.51), residues: 96 sheet: -1.01 (0.45), residues: 138 loop : -0.97 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.008 0.001 TYR A 507 PHE 0.013 0.001 PHE B 46 TRP 0.002 0.000 TRP A 632 HIS 0.008 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 6593) covalent geometry : angle 0.53186 / 0.27 ( 8925) SS BOND : bond 0.00283 / 0.12 ( 18) SS BOND : angle 0.78184 / 0.44 ( 36) hydrogen bonds : bond 0.04035 / 2.50 ( 160) hydrogen bonds : angle 6.87177 / 4.66 ( 399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.1028 time to fit residues: 10.7113 Evaluate side-chains 65 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain Q residue 7 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.129899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096180 restraints weight = 42485.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099056 restraints weight = 28167.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101052 restraints weight = 21330.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.102479 restraints weight = 17544.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.103419 restraints weight = 15255.120| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6611 Z= 0.262 Angle : 0.602 6.213 8961 Z= 0.314 Chirality : 0.044 0.152 969 Planarity : 0.004 0.033 1151 Dihedral : 5.097 28.535 866 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.45 % Favored : 88.42 % Rotamer: Outliers : 1.24 % Allowed : 16.57 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.31), residues: 777 helix: -1.20 (0.51), residues: 96 sheet: -1.17 (0.42), residues: 147 loop : -1.12 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 656 TYR 0.015 0.002 TYR A 507 PHE 0.015 0.002 PHE B 382 TRP 0.012 0.001 TRP A 489 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.26 ( 6593) covalent geometry : angle 0.60111 / 0.31 ( 8925) SS BOND : bond 0.00329 / 0.14 ( 18) SS BOND : angle 0.75130 / 0.44 ( 36) hydrogen bonds : bond 0.04318 / 2.66 ( 160) hydrogen bonds : angle 6.94014 / 4.72 ( 399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 GLU cc_start: 0.7440 (mp0) cc_final: 0.7235 (mp0) outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.1148 time to fit residues: 10.7850 Evaluate side-chains 62 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain Q residue 7 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 635 GLN B 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.131631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.100939 restraints weight = 41771.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102095 restraints weight = 23901.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102126 restraints weight = 18838.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.102412 restraints weight = 18072.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.102722 restraints weight = 17369.029| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6611 Z= 0.118 Angle : 0.546 5.938 8961 Z= 0.281 Chirality : 0.042 0.148 969 Planarity : 0.003 0.031 1151 Dihedral : 4.883 27.247 866 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.24 % Favored : 91.63 % Rotamer: Outliers : 1.38 % Allowed : 16.85 % Favored : 81.77 % 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: -1.66 (0.31), residues: 777 helix: -1.06 (0.52), residues: 96 sheet: -1.48 (0.43), residues: 138 loop : -1.02 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.008 0.001 TYR A 507 PHE 0.013 0.001 PHE A 565 TRP 0.003 0.001 TRP A 615 HIS 0.007 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6593) covalent geometry : angle 0.54521 / 0.28 ( 8925) SS BOND : bond 0.00267 / 0.11 ( 18) SS BOND : angle 0.69674 / 0.39 ( 36) hydrogen bonds : bond 0.03813 / 2.36 ( 160) hydrogen bonds : angle 6.69665 / 4.56 ( 399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.1172 time to fit residues: 11.5097 Evaluate side-chains 65 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain Q residue 7 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** B 429 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 = 0.4025 r_free = 0.4025 target = 0.131027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096622 restraints weight = 41903.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.099910 restraints weight = 26640.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.102171 restraints weight = 19512.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.103682 restraints weight = 15781.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.104514 restraints weight = 13597.276| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6611 Z= 0.152 Angle : 0.547 5.989 8961 Z= 0.282 Chirality : 0.042 0.144 969 Planarity : 0.003 0.032 1151 Dihedral : 4.869 27.644 866 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.68 % Favored : 89.19 % Rotamer: Outliers : 1.38 % Allowed : 17.13 % Favored : 81.49 % 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: -1.69 (0.31), residues: 777 helix: -1.07 (0.52), residues: 96 sheet: -1.51 (0.43), residues: 133 loop : -1.05 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 656 TYR 0.013 0.001 TYR A 507 PHE 0.013 0.001 PHE A 565 TRP 0.004 0.001 TRP A 489 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 6593) covalent geometry : angle 0.54665 / 0.28 ( 8925) SS BOND : bond 0.00261 / 0.11 ( 18) SS BOND : angle 0.69999 / 0.40 ( 36) hydrogen bonds : bond 0.03761 / 2.34 ( 160) hydrogen bonds : angle 6.64598 / 4.53 ( 399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.1233 time to fit residues: 11.6619 Evaluate side-chains 65 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain Q residue 7 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** B 429 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 = 0.4031 r_free = 0.4031 target = 0.131420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096755 restraints weight = 41507.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100184 restraints weight = 25587.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102534 restraints weight = 18576.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.104022 restraints weight = 14867.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105211 restraints weight = 12752.932| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6611 Z= 0.121 Angle : 0.551 10.689 8961 Z= 0.281 Chirality : 0.042 0.147 969 Planarity : 0.003 0.031 1151 Dihedral : 4.768 26.805 866 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.78 % Favored : 90.09 % Rotamer: Outliers : 1.66 % Allowed : 17.54 % Favored : 80.80 % 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: -1.66 (0.31), residues: 777 helix: -1.02 (0.52), residues: 96 sheet: -1.54 (0.43), residues: 138 loop : -1.01 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 65 TYR 0.011 0.001 TYR A 507 PHE 0.012 0.001 PHE A 565 TRP 0.003 0.001 TRP Q 36 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6593) covalent geometry : angle 0.55026 / 0.28 ( 8925) SS BOND : bond 0.00257 / 0.11 ( 18) SS BOND : angle 0.70540 / 0.40 ( 36) hydrogen bonds : bond 0.03601 / 2.25 ( 160) hydrogen bonds : angle 6.53408 / 4.45 ( 399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.1211 time to fit residues: 11.5951 Evaluate side-chains 63 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain Q residue 7 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** B 429 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 = 0.4019 r_free = 0.4019 target = 0.130625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096248 restraints weight = 42149.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099462 restraints weight = 26691.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.101682 restraints weight = 19687.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103148 restraints weight = 15898.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.103923 restraints weight = 13725.152| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6611 Z= 0.170 Angle : 0.554 7.445 8961 Z= 0.286 Chirality : 0.042 0.142 969 Planarity : 0.003 0.031 1151 Dihedral : 4.828 27.360 866 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.33 % Favored : 88.55 % Rotamer: Outliers : 1.24 % Allowed : 17.40 % Favored : 81.35 % 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: -1.75 (0.31), residues: 777 helix: -1.05 (0.52), residues: 96 sheet: -1.62 (0.43), residues: 133 loop : -1.08 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.012 0.001 TYR A 507 PHE 0.014 0.001 PHE A 565 TRP 0.005 0.001 TRP A 489 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 6593) covalent geometry : angle 0.55323 / 0.29 ( 8925) SS BOND : bond 0.00262 / 0.12 ( 18) SS BOND : angle 0.69195 / 0.40 ( 36) hydrogen bonds : bond 0.03688 / 2.29 ( 160) hydrogen bonds : angle 6.55189 / 4.49 ( 399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 62 average time/residue: 0.1166 time to fit residues: 10.9237 Evaluate side-chains 64 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain Q residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 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 = 0.4020 r_free = 0.4020 target = 0.130712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096300 restraints weight = 42050.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099538 restraints weight = 26560.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.101754 restraints weight = 19531.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103206 restraints weight = 15799.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104306 restraints weight = 13590.885| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 6611 Z= 0.161 Angle : 0.959 59.194 8961 Z= 0.556 Chirality : 0.043 0.294 969 Planarity : 0.004 0.035 1151 Dihedral : 4.835 27.415 866 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.33 % Favored : 88.55 % Rotamer: Outliers : 1.38 % Allowed : 17.27 % Favored : 81.35 % Cbeta Deviations : 0.13 % 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: -1.74 (0.31), residues: 777 helix: -1.05 (0.52), residues: 96 sheet: -1.62 (0.43), residues: 133 loop : -1.08 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.027 0.001 TYR A 507 PHE 0.013 0.001 PHE A 565 TRP 0.004 0.001 TRP A 489 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 6593) covalent geometry : angle 0.96009 / 0.56 ( 8925) SS BOND : bond 0.00246 / 0.11 ( 18) SS BOND : angle 0.68742 / 0.40 ( 36) hydrogen bonds : bond 0.03662 / 2.28 ( 160) hydrogen bonds : angle 6.54934 / 4.49 ( 399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 61 average time/residue: 0.1202 time to fit residues: 10.9931 Evaluate side-chains 62 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain Q residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 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 = 0.4021 r_free = 0.4021 target = 0.130821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.096283 restraints weight = 42055.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.099522 restraints weight = 26619.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.101772 restraints weight = 19560.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102979 restraints weight = 15810.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104141 restraints weight = 13754.436| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 6611 Z= 0.161 Angle : 0.959 59.194 8961 Z= 0.556 Chirality : 0.043 0.294 969 Planarity : 0.004 0.035 1151 Dihedral : 4.835 27.415 866 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.33 % Favored : 88.55 % Rotamer: Outliers : 1.10 % Allowed : 17.40 % Favored : 81.49 % Cbeta Deviations : 0.13 % 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: -1.74 (0.31), residues: 777 helix: -1.05 (0.52), residues: 96 sheet: -1.62 (0.43), residues: 133 loop : -1.08 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.027 0.001 TYR A 507 PHE 0.013 0.001 PHE A 565 TRP 0.004 0.001 TRP A 489 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 6593) covalent geometry : angle 0.96009 / 0.56 ( 8925) SS BOND : bond 0.00246 / 0.11 ( 18) SS BOND : angle 0.68742 / 0.40 ( 36) hydrogen bonds : bond 0.03662 / 2.28 ( 160) hydrogen bonds : angle 6.54934 / 4.49 ( 399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2420.74 seconds wall clock time: 41 minutes 51.90 seconds (2511.90 seconds total)