Starting phenix.real_space_refine on Wed Aug 5 08:35:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyc_38768/08_2026/8xyc_38768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyc_38768/08_2026/8xyc_38768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xyc_38768/08_2026/8xyc_38768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyc_38768/08_2026/8xyc_38768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xyc_38768/08_2026/8xyc_38768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyc_38768/08_2026/8xyc_38768.map" } resolution = 2.51 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= -0.002 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 153 5.49 5 S 15 5.16 5 C 5295 2.51 5 N 1655 2.21 5 O 2126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9244 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 568 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 6031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6031 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 38, 'TRANS': 710} Chain breaks: 3 Chain: "C" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2478 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 44, 'rna3p_pyr': 54} Link IDs: {'rna2p': 19, 'rna3p': 97} Chain breaks: 1 Time building chain proxies: 2.01, per 1000 atoms: 0.22 Number of scatterers: 9244 At special positions: 0 Unit cell: (105.002, 108.25, 114.745, 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 15 16.00 P 153 15.00 O 2126 8.00 N 1655 7.00 C 5295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 260.9 milliseconds 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 51.0% alpha, 15.0% beta 55 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 48 through 78 removed outlier: 4.232A pdb=" N VAL A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 119 through 162 removed outlier: 3.663A pdb=" N GLY A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 187 through 209 removed outlier: 3.547A pdb=" N ILE A 191 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.536A pdb=" N ARG A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 298 through 313 Processing helix chain 'A' and resid 317 through 344 Processing helix chain 'A' and resid 347 through 372 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 374 through 396 removed outlier: 3.648A pdb=" N GLU A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 603 through 623 Processing helix chain 'A' and resid 628 through 656 removed outlier: 4.531A pdb=" N GLU A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ARG A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 835 through 849 removed outlier: 4.000A pdb=" N LEU A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 removed outlier: 4.212A pdb=" N GLU A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 849 through 854' Processing helix chain 'A' and resid 863 through 878 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36 removed outlier: 6.621A pdb=" N ASP A 550 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG A 539 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR A 552 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU A 537 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 554 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY A 535 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR A 556 " --> pdb=" O GLY A 533 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 36 removed outlier: 5.243A pdb=" N PHE A 551 " --> pdb=" O ILE A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 451 through 453 removed outlier: 5.543A pdb=" N TRP A 468 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE A 495 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR A 466 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU A 426 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N SER A 473 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N GLY A 424 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 600 removed outlier: 7.327A pdb=" N LEU A 594 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP A 589 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 596 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 583 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL A 660 " --> pdb=" O ARG A 571 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 573 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ALA A 662 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N ILE A 575 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 825 through 826 340 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 252 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1154 1.29 - 1.42: 3247 1.42 - 1.55: 5028 1.55 - 1.68: 303 1.68 - 1.81: 19 Bond restraints: 9751 Sorted by residual: bond pdb=" C SER A 9 " pdb=" O SER A 9 " ideal model delta sigma weight residual 1.234 1.159 0.075 1.36e-02 5.41e+03 3.04e+01 bond pdb=" N3 DC B 23 " pdb=" C4 DC B 23 " ideal model delta sigma weight residual 1.335 1.368 -0.033 7.00e-03 2.04e+04 2.24e+01 bond pdb=" N3 DC B 26 " pdb=" C4 DC B 26 " ideal model delta sigma weight residual 1.335 1.308 0.027 7.00e-03 2.04e+04 1.54e+01 bond pdb=" C6 G C 4 " pdb=" N1 G C 4 " ideal model delta sigma weight residual 1.391 1.364 0.027 7.00e-03 2.04e+04 1.48e+01 bond pdb=" C ILE A 10 " pdb=" O ILE A 10 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.13e-02 7.83e+03 1.43e+01 ... (remaining 9746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 13192 2.12 - 4.25: 639 4.25 - 6.37: 39 6.37 - 8.50: 7 8.50 - 10.62: 3 Bond angle restraints: 13880 Sorted by residual: angle pdb=" N THR A 626 " pdb=" CA THR A 626 " pdb=" C THR A 626 " ideal model delta sigma weight residual 111.36 121.98 -10.62 1.09e+00 8.42e-01 9.50e+01 angle pdb=" O5' DT D -3 " pdb=" C5' DT D -3 " pdb=" C4' DT D -3 " ideal model delta sigma weight residual 109.40 114.51 -5.11 8.00e-01 1.56e+00 4.09e+01 angle pdb=" N PHE A 183 " pdb=" CA PHE A 183 " pdb=" C PHE A 183 " ideal model delta sigma weight residual 111.75 118.07 -6.32 1.28e+00 6.10e-01 2.44e+01 angle pdb=" C5 G C 4 " pdb=" C6 G C 4 " pdb=" O6 G C 4 " ideal model delta sigma weight residual 128.60 131.50 -2.90 6.00e-01 2.78e+00 2.33e+01 angle pdb=" O5' G C-122 " pdb=" C5' G C-122 " pdb=" C4' G C-122 " ideal model delta sigma weight residual 109.40 113.24 -3.84 8.00e-01 1.56e+00 2.30e+01 ... (remaining 13875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.06: 4915 19.06 - 38.12: 603 38.12 - 57.18: 290 57.18 - 76.24: 171 76.24 - 95.30: 8 Dihedral angle restraints: 5987 sinusoidal: 3810 harmonic: 2177 Sorted by residual: dihedral pdb=" O4' A C -99 " pdb=" C1' A C -99 " pdb=" N9 A C -99 " pdb=" C4 A C -99 " ideal model delta sinusoidal sigma weight residual 68.00 147.39 -79.39 1 1.70e+01 3.46e-03 2.71e+01 dihedral pdb=" O4' A C-103 " pdb=" C1' A C-103 " pdb=" N9 A C-103 " pdb=" C4 A C-103 " ideal model delta sinusoidal sigma weight residual 70.00 2.14 67.86 1 2.00e+01 2.50e-03 1.50e+01 dihedral pdb=" CA ILE A 408 " pdb=" C ILE A 408 " pdb=" N MET A 409 " pdb=" CA MET A 409 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1234 0.057 - 0.115: 234 0.115 - 0.172: 132 0.172 - 0.230: 10 0.230 - 0.287: 1 Chirality restraints: 1611 Sorted by residual: chirality pdb=" C1' U C -10 " pdb=" O4' U C -10 " pdb=" C2' U C -10 " pdb=" N1 U C -10 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA VAL A 215 " pdb=" N VAL A 215 " pdb=" C VAL A 215 " pdb=" CB VAL A 215 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE A 10 " pdb=" N ILE A 10 " pdb=" C ILE A 10 " pdb=" CB ILE A 10 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1608 not shown) Planarity restraints: 1231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 627 " -0.021 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C ARG A 627 " 0.076 2.00e-02 2.50e+03 pdb=" O ARG A 627 " -0.028 2.00e-02 2.50e+03 pdb=" N TRP A 628 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG B 21 " -0.041 2.00e-02 2.50e+03 2.20e-02 1.45e+01 pdb=" N9 DG B 21 " 0.040 2.00e-02 2.50e+03 pdb=" C8 DG B 21 " 0.016 2.00e-02 2.50e+03 pdb=" N7 DG B 21 " -0.017 2.00e-02 2.50e+03 pdb=" C5 DG B 21 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DG B 21 " 0.010 2.00e-02 2.50e+03 pdb=" O6 DG B 21 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG B 21 " 0.014 2.00e-02 2.50e+03 pdb=" C2 DG B 21 " -0.007 2.00e-02 2.50e+03 pdb=" N2 DG B 21 " -0.015 2.00e-02 2.50e+03 pdb=" N3 DG B 21 " 0.024 2.00e-02 2.50e+03 pdb=" C4 DG B 21 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 622 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C GLN A 622 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN A 622 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 623 " 0.017 2.00e-02 2.50e+03 ... (remaining 1228 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 564 2.71 - 3.26: 8493 3.26 - 3.81: 17689 3.81 - 4.35: 21834 4.35 - 4.90: 31694 Nonbonded interactions: 80274 Sorted by model distance: nonbonded pdb=" O2' C C -73 " pdb=" O5' C C -72 " model vdw 2.167 3.040 nonbonded pdb=" O LEU A 20 " pdb=" NZ LYS A 24 " model vdw 2.224 3.120 nonbonded pdb=" N2 DG B 6 " pdb=" O2 C C 20 " model vdw 2.237 3.120 nonbonded pdb=" OP1 DA B 27 " pdb=" NZ LYS A 486 " model vdw 2.281 3.120 nonbonded pdb=" O THR A 264 " pdb=" NZ LYS A 268 " model vdw 2.288 3.120 ... (remaining 80269 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.820 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9751 Z= 0.403 Angle : 0.884 10.622 13880 Z= 0.682 Chirality : 0.057 0.287 1611 Planarity : 0.005 0.044 1231 Dihedral : 21.133 95.296 4575 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.41 % Allowed : 1.12 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.29), residues: 741 helix: 1.42 (0.26), residues: 351 sheet: -0.61 (0.46), residues: 114 loop : -1.16 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 120 TYR 0.020 0.002 TYR A 848 PHE 0.018 0.002 PHE A 471 TRP 0.019 0.002 TRP A 103 HIS 0.006 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.40 ( 9751) covalent geometry : angle 0.88385 / 0.68 (13880) hydrogen bonds : bond 0.14242 / 16.08 ( 473) hydrogen bonds : angle 6.17015 / 7.71 ( 1239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.6976 (t0) cc_final: 0.6734 (t0) REVERT: A 593 LYS cc_start: 0.7140 (pptt) cc_final: 0.6694 (mmtt) REVERT: A 654 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7215 (mt-10) outliers start: 15 outliers final: 4 residues processed: 121 average time/residue: 0.7073 time to fit residues: 90.4426 Evaluate side-chains 71 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 217 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN A 512 GLN A 560 GLN A 835 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.241465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.217105 restraints weight = 8170.292| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 0.68 r_work: 0.4216 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4173 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9751 Z= 0.160 Angle : 0.647 7.594 13880 Z= 0.362 Chirality : 0.042 0.242 1611 Planarity : 0.005 0.041 1231 Dihedral : 22.415 87.283 3064 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.09 % Allowed : 12.68 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.29), residues: 741 helix: 1.85 (0.26), residues: 354 sheet: -0.43 (0.46), residues: 112 loop : -1.03 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 605 TYR 0.015 0.002 TYR A 422 PHE 0.016 0.002 PHE A 152 TRP 0.014 0.002 TRP A 159 HIS 0.006 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 ( 9751) covalent geometry : angle 0.64740 / 0.36 (13880) hydrogen bonds : bond 0.06657 / 7.35 ( 473) hydrogen bonds : angle 4.63990 / 5.94 ( 1239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7669 (mmmm) cc_final: 0.7368 (ptmm) REVERT: A 526 GLU cc_start: 0.7139 (mp0) cc_final: 0.6926 (mp0) REVERT: A 593 LYS cc_start: 0.7038 (pptt) cc_final: 0.6553 (mmtt) outliers start: 13 outliers final: 4 residues processed: 82 average time/residue: 0.7134 time to fit residues: 61.8633 Evaluate side-chains 61 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 180 ASN A 560 GLN A 714 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.240968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.221821 restraints weight = 8137.702| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 0.75 r_work: 0.4202 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4119 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9751 Z= 0.151 Angle : 0.605 7.051 13880 Z= 0.338 Chirality : 0.040 0.230 1611 Planarity : 0.004 0.038 1231 Dihedral : 22.259 85.792 3060 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.89 % Allowed : 14.61 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 741 helix: 2.01 (0.25), residues: 354 sheet: -0.48 (0.47), residues: 112 loop : -0.99 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 605 TYR 0.015 0.002 TYR A 848 PHE 0.014 0.002 PHE A 152 TRP 0.014 0.002 TRP A 628 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 ( 9751) covalent geometry : angle 0.60473 / 0.34 (13880) hydrogen bonds : bond 0.06145 / 6.77 ( 473) hydrogen bonds : angle 4.34861 / 5.63 ( 1239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7221 (mmm-85) cc_final: 0.6831 (tpt170) REVERT: A 189 LYS cc_start: 0.7709 (mmmm) cc_final: 0.7417 (ptmm) REVERT: A 560 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: A 593 LYS cc_start: 0.7114 (pptt) cc_final: 0.6583 (mmtt) outliers start: 18 outliers final: 7 residues processed: 74 average time/residue: 0.6283 time to fit residues: 49.5821 Evaluate side-chains 65 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 732 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN A 714 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.239548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.208134 restraints weight = 8248.239| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 1.11 r_work: 0.4074 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9751 Z= 0.150 Angle : 0.584 7.213 13880 Z= 0.327 Chirality : 0.040 0.228 1611 Planarity : 0.004 0.035 1231 Dihedral : 22.242 85.269 3060 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.37 % Allowed : 15.57 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.29), residues: 741 helix: 2.12 (0.25), residues: 354 sheet: -0.60 (0.47), residues: 108 loop : -0.86 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 151 TYR 0.015 0.002 TYR A 422 PHE 0.015 0.002 PHE A 152 TRP 0.016 0.002 TRP A 628 HIS 0.002 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 ( 9751) covalent geometry : angle 0.58374 / 0.33 (13880) hydrogen bonds : bond 0.05823 / 6.32 ( 473) hydrogen bonds : angle 4.26663 / 5.54 ( 1239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7677 (mmmm) cc_final: 0.7325 (ptmm) REVERT: A 249 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7783 (tptt) REVERT: A 402 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5727 (pp20) REVERT: A 593 LYS cc_start: 0.7427 (pptt) cc_final: 0.6507 (mmtt) REVERT: A 687 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7262 (tp40) outliers start: 21 outliers final: 7 residues processed: 77 average time/residue: 0.6880 time to fit residues: 56.2667 Evaluate side-chains 68 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 732 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 23 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 83 optimal weight: 50.0000 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.241676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.220103 restraints weight = 8329.262| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 0.61 r_work: 0.4229 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9751 Z= 0.118 Angle : 0.520 6.779 13880 Z= 0.298 Chirality : 0.037 0.179 1611 Planarity : 0.004 0.036 1231 Dihedral : 22.203 84.664 3060 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.89 % Allowed : 16.37 % Favored : 80.74 % 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: 1.23 (0.29), residues: 741 helix: 2.42 (0.26), residues: 354 sheet: -0.41 (0.48), residues: 106 loop : -0.78 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 605 TYR 0.012 0.001 TYR A 229 PHE 0.014 0.001 PHE A 152 TRP 0.015 0.001 TRP A 628 HIS 0.001 0.000 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.12 ( 9751) covalent geometry : angle 0.52012 / 0.30 (13880) hydrogen bonds : bond 0.05095 / 5.46 ( 473) hydrogen bonds : angle 4.05356 / 5.27 ( 1239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 151 ARG cc_start: 0.6950 (mtp180) cc_final: 0.6710 (mmm160) REVERT: A 189 LYS cc_start: 0.7457 (mmmm) cc_final: 0.7197 (ptmm) REVERT: A 249 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7813 (tptt) REVERT: A 560 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6314 (tp40) REVERT: A 593 LYS cc_start: 0.7097 (pptt) cc_final: 0.6541 (mmtt) REVERT: A 687 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7015 (tp40) outliers start: 18 outliers final: 9 residues processed: 81 average time/residue: 0.6217 time to fit residues: 53.6432 Evaluate side-chains 76 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 4 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.238282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.216839 restraints weight = 8275.237| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 0.63 r_work: 0.4174 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9751 Z= 0.151 Angle : 0.586 7.124 13880 Z= 0.326 Chirality : 0.040 0.231 1611 Planarity : 0.004 0.034 1231 Dihedral : 22.173 85.325 3060 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.89 % Allowed : 17.34 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.29), residues: 741 helix: 2.26 (0.25), residues: 354 sheet: -0.40 (0.46), residues: 112 loop : -0.88 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 511 TYR 0.015 0.002 TYR A 422 PHE 0.014 0.002 PHE A 152 TRP 0.013 0.002 TRP A 628 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 9751) covalent geometry : angle 0.58640 / 0.33 (13880) hydrogen bonds : bond 0.05731 / 6.26 ( 473) hydrogen bonds : angle 4.16411 / 5.45 ( 1239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7568 (mmmm) cc_final: 0.7275 (ptmm) REVERT: A 560 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.5937 (tp40) REVERT: A 593 LYS cc_start: 0.7186 (pptt) cc_final: 0.6572 (mmtt) REVERT: A 687 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7153 (tp40) outliers start: 18 outliers final: 8 residues processed: 77 average time/residue: 0.6772 time to fit residues: 55.1640 Evaluate side-chains 70 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 18 optimal weight: 0.0670 chunk 4 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 chunk 77 optimal weight: 50.0000 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.242089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.222316 restraints weight = 8409.017| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 0.57 r_work: 0.4243 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9751 Z= 0.118 Angle : 0.527 6.876 13880 Z= 0.297 Chirality : 0.036 0.170 1611 Planarity : 0.004 0.042 1231 Dihedral : 22.155 84.833 3058 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.25 % Allowed : 19.42 % Favored : 78.33 % 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: 1.37 (0.30), residues: 741 helix: 2.52 (0.25), residues: 360 sheet: -0.24 (0.47), residues: 110 loop : -0.83 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 605 TYR 0.010 0.001 TYR A 848 PHE 0.012 0.001 PHE A 152 TRP 0.013 0.001 TRP A 628 HIS 0.001 0.000 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.12 ( 9751) covalent geometry : angle 0.52724 / 0.30 (13880) hydrogen bonds : bond 0.04886 / 5.22 ( 473) hydrogen bonds : angle 3.98679 / 5.19 ( 1239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7393 (mmmm) cc_final: 0.7088 (ptmm) REVERT: A 249 LYS cc_start: 0.7931 (tptt) cc_final: 0.7692 (ttmm) REVERT: A 382 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: A 560 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6075 (tp40) REVERT: A 593 LYS cc_start: 0.7146 (pptt) cc_final: 0.6539 (mmtt) outliers start: 14 outliers final: 6 residues processed: 68 average time/residue: 0.6594 time to fit residues: 47.7334 Evaluate side-chains 66 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 732 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 0.0060 chunk 84 optimal weight: 30.0000 chunk 35 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.238791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.215623 restraints weight = 8251.386| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 0.62 r_work: 0.4181 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4082 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9751 Z= 0.148 Angle : 0.577 7.308 13880 Z= 0.319 Chirality : 0.039 0.224 1611 Planarity : 0.004 0.034 1231 Dihedral : 22.087 85.631 3058 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.53 % Allowed : 18.14 % Favored : 78.33 % 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: 1.23 (0.29), residues: 741 helix: 2.37 (0.25), residues: 360 sheet: -0.33 (0.46), residues: 112 loop : -0.85 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 636 TYR 0.016 0.002 TYR A 422 PHE 0.014 0.002 PHE A 152 TRP 0.013 0.002 TRP A 628 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 ( 9751) covalent geometry : angle 0.57673 / 0.32 (13880) hydrogen bonds : bond 0.05489 / 5.96 ( 473) hydrogen bonds : angle 4.09942 / 5.38 ( 1239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7547 (mmmm) cc_final: 0.7203 (ptmm) REVERT: A 560 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.5974 (tp40) REVERT: A 575 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6325 (mm) REVERT: A 593 LYS cc_start: 0.7151 (pptt) cc_final: 0.6554 (mmtt) REVERT: A 687 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.6977 (tp40) outliers start: 22 outliers final: 6 residues processed: 70 average time/residue: 0.6959 time to fit residues: 51.5789 Evaluate side-chains 65 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 732 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.236087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.215220 restraints weight = 8184.746| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 0.60 r_work: 0.4186 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4102 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9751 Z= 0.179 Angle : 0.646 8.415 13880 Z= 0.351 Chirality : 0.042 0.258 1611 Planarity : 0.005 0.040 1231 Dihedral : 22.008 86.605 3058 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.05 % Allowed : 19.10 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.29), residues: 741 helix: 2.09 (0.25), residues: 360 sheet: -0.53 (0.44), residues: 119 loop : -0.92 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 636 TYR 0.018 0.002 TYR A 422 PHE 0.018 0.002 PHE A 451 TRP 0.016 0.002 TRP A 518 HIS 0.006 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 ( 9751) covalent geometry : angle 0.64609 / 0.35 (13880) hydrogen bonds : bond 0.06223 / 6.88 ( 473) hydrogen bonds : angle 4.30572 / 5.67 ( 1239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7656 (mmmm) cc_final: 0.7354 (ptmm) REVERT: A 402 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5971 (pp20) REVERT: A 480 LYS cc_start: 0.6424 (tptm) cc_final: 0.6131 (mtmt) REVERT: A 560 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.5901 (tp40) REVERT: A 575 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6432 (mm) REVERT: A 593 LYS cc_start: 0.6985 (pptt) cc_final: 0.6561 (mmtt) REVERT: A 687 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6899 (tp40) outliers start: 19 outliers final: 7 residues processed: 69 average time/residue: 0.7274 time to fit residues: 53.1088 Evaluate side-chains 66 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 732 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 76 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 6 optimal weight: 0.0980 chunk 79 optimal weight: 9.9990 chunk 3 optimal weight: 0.0470 chunk 36 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.4280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.241034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.221161 restraints weight = 8237.805| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 0.58 r_work: 0.4216 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4097 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9751 Z= 0.123 Angle : 0.555 8.575 13880 Z= 0.309 Chirality : 0.037 0.197 1611 Planarity : 0.004 0.035 1231 Dihedral : 21.980 85.531 3058 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.93 % Allowed : 20.55 % Favored : 77.53 % 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: 1.25 (0.29), residues: 741 helix: 2.41 (0.25), residues: 360 sheet: -0.11 (0.53), residues: 90 loop : -0.92 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 605 TYR 0.011 0.001 TYR A 848 PHE 0.013 0.001 PHE A 152 TRP 0.012 0.001 TRP A 628 HIS 0.002 0.000 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 ( 9751) covalent geometry : angle 0.55533 / 0.31 (13880) hydrogen bonds : bond 0.05045 / 5.43 ( 473) hydrogen bonds : angle 4.06896 / 5.33 ( 1239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7526 (mmmm) cc_final: 0.7201 (ptmm) REVERT: A 316 TRP cc_start: 0.6485 (OUTLIER) cc_final: 0.5978 (m-10) REVERT: A 480 LYS cc_start: 0.6449 (tptm) cc_final: 0.6195 (mttp) REVERT: A 560 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6775 (tp40) REVERT: A 575 ILE cc_start: 0.6714 (OUTLIER) cc_final: 0.6387 (mm) REVERT: A 593 LYS cc_start: 0.7127 (pptt) cc_final: 0.6540 (mmtt) REVERT: A 687 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6940 (tp40) outliers start: 12 outliers final: 5 residues processed: 64 average time/residue: 0.7134 time to fit residues: 48.4800 Evaluate side-chains 63 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 732 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 9 optimal weight: 0.0970 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.239130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.221572 restraints weight = 8169.731| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 0.51 r_work: 0.4242 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4147 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9751 Z= 0.141 Angle : 0.576 8.643 13880 Z= 0.318 Chirality : 0.038 0.219 1611 Planarity : 0.004 0.034 1231 Dihedral : 21.907 85.845 3058 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.25 % Allowed : 20.39 % Favored : 77.37 % 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: 1.22 (0.30), residues: 741 helix: 2.35 (0.25), residues: 360 sheet: -0.40 (0.45), residues: 112 loop : -0.80 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 605 TYR 0.014 0.002 TYR A 422 PHE 0.013 0.002 PHE A 152 TRP 0.012 0.002 TRP A 628 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 9751) covalent geometry : angle 0.57595 / 0.32 (13880) hydrogen bonds : bond 0.05422 / 5.90 ( 473) hydrogen bonds : angle 4.11458 / 5.41 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3395.05 seconds wall clock time: 58 minutes 36.26 seconds (3516.26 seconds total)