Starting phenix.real_space_refine on Thu Jul 2 15:35:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyc_38768/07_2026/8xyc_38768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyc_38768/07_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_38768/07_2026/8xyc_38768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyc_38768/07_2026/8xyc_38768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xyc_38768/07_2026/8xyc_38768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyc_38768/07_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-dev-6108/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: 1.91, per 1000 atoms: 0.21 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: 0.81 Conformation dependent library (CDL) restraints added in 148.2 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: 1.00 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: 1.69 Time building geometry restraints manager: 1.01 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: 13432 2.12 - 4.25: 399 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=" N LEU A 629 " pdb=" CA LEU A 629 " pdb=" C LEU A 629 " ideal model delta sigma weight residual 112.54 106.71 5.83 1.22e+00 6.72e-01 2.28e+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 - 0.059: 1371 0.059 - 0.119: 201 0.119 - 0.178: 30 0.178 - 0.238: 8 0.238 - 0.297: 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 2.45 2.15 0.30 2.00e-01 2.50e+01 2.21e+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: 1.020 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.340 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- 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= 0.394 Angle : 0.807 10.622 13880 Z= 0.612 Chirality : 0.045 0.297 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 0.00514 / 0.39 ( 9751) covalent geometry : angle 0.80726 / 0.61 (13880) hydrogen bonds : bond 0.14242 / 16.06 ( 473) hydrogen bonds : angle 6.17015 / 7.69 ( 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 : 0.154 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.6976 (t0) cc_final: 0.6735 (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: 0.5296 time to fit residues: 67.8580 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 : 0.184 ------------------------------------------------------------------------------- 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: 0.0060 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4717 r_free = 0.4717 target = 0.242093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.220295 restraints weight = 8208.987| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 0.60 r_work: 0.4235 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4187 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9751 Z= 0.158 Angle : 0.625 7.190 13880 Z= 0.355 Chirality : 0.040 0.218 1611 Planarity : 0.005 0.039 1231 Dihedral : 22.471 91.093 3064 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.25 % Allowed : 11.72 % Favored : 86.04 % 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: 0.74 (0.29), residues: 741 helix: 1.92 (0.26), residues: 354 sheet: -0.34 (0.47), residues: 112 loop : -1.05 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 605 TYR 0.016 0.002 TYR A 422 PHE 0.015 0.002 PHE A 152 TRP 0.014 0.002 TRP A 628 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 ( 9751) covalent geometry : angle 0.62528 / 0.36 (13880) hydrogen bonds : bond 0.06472 / 7.16 ( 473) hydrogen bonds : angle 4.61704 / 5.89 ( 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 84 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7658 (mmmm) cc_final: 0.7365 (ptmm) REVERT: A 593 LYS cc_start: 0.7014 (pptt) cc_final: 0.6551 (mmtt) outliers start: 14 outliers final: 5 residues processed: 81 average time/residue: 0.6999 time to fit residues: 60.0817 Evaluate side-chains 64 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 732 CYS 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: 0.9980 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4714 r_free = 0.4714 target = 0.241577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.222180 restraints weight = 8160.318| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 0.76 r_work: 0.4189 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4064 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1845 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= 0.145 Angle : 0.582 6.926 13880 Z= 0.331 Chirality : 0.039 0.184 1611 Planarity : 0.004 0.039 1231 Dihedral : 22.319 89.276 3060 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.05 % Allowed : 14.13 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.29), residues: 741 helix: 2.08 (0.25), residues: 360 sheet: -0.38 (0.47), residues: 112 loop : -1.00 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 605 TYR 0.014 0.002 TYR A 848 PHE 0.015 0.002 PHE A 152 TRP 0.013 0.002 TRP A 628 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 9751) covalent geometry : angle 0.58172 / 0.33 (13880) hydrogen bonds : bond 0.05957 / 6.51 ( 473) hydrogen bonds : angle 4.30562 / 5.55 ( 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 83 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7295 (mmm-85) cc_final: 0.6907 (tpt170) REVERT: A 189 LYS cc_start: 0.7714 (mmmm) cc_final: 0.7309 (ptmm) REVERT: A 560 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: A 593 LYS cc_start: 0.7382 (pptt) cc_final: 0.6566 (mmtt) outliers start: 19 outliers final: 8 residues processed: 75 average time/residue: 0.6717 time to fit residues: 53.6450 Evaluate side-chains 66 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 130 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 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: 3.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.0270 chunk 82 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.239504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.220074 restraints weight = 8297.904| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 0.58 r_work: 0.4228 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4145 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9751 Z= 0.139 Angle : 0.556 6.670 13880 Z= 0.317 Chirality : 0.038 0.179 1611 Planarity : 0.004 0.038 1231 Dihedral : 22.281 88.730 3060 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.05 % Allowed : 15.73 % Favored : 81.22 % 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: 1.04 (0.29), residues: 741 helix: 2.21 (0.25), residues: 360 sheet: -0.48 (0.48), residues: 108 loop : -0.90 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.013 0.001 TYR A 848 PHE 0.014 0.001 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 0.00265 / 0.14 ( 9751) covalent geometry : angle 0.55626 / 0.32 (13880) hydrogen bonds : bond 0.05556 / 5.98 ( 473) hydrogen bonds : angle 4.19758 / 5.42 ( 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: 19 poor density : 68 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.5954 (OUTLIER) cc_final: 0.5301 (t0) REVERT: A 189 LYS cc_start: 0.7543 (mmmm) cc_final: 0.7295 (ptmm) REVERT: A 402 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5796 (pp20) REVERT: A 593 LYS cc_start: 0.6979 (pptt) cc_final: 0.6540 (mmtt) REVERT: A 687 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7034 (tp40) outliers start: 19 outliers final: 7 residues processed: 78 average time/residue: 0.6690 time to fit residues: 55.5413 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 : 0.263 ------------------------------------------------------------------------------- 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 185 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 446 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 0.0040 chunk 29 optimal weight: 0.0170 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 83 optimal weight: 50.0000 overall best weight: 0.3028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.243853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.217212 restraints weight = 8383.515| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 0.85 r_work: 0.4172 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4111 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9751 Z= 0.118 Angle : 0.518 6.932 13880 Z= 0.298 Chirality : 0.036 0.155 1611 Planarity : 0.004 0.037 1231 Dihedral : 22.235 88.030 3060 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.05 % Allowed : 16.05 % Favored : 80.90 % 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: 1.33 (0.29), residues: 741 helix: 2.47 (0.25), residues: 360 sheet: -0.34 (0.48), residues: 106 loop : -0.79 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.011 0.001 TYR A 229 PHE 0.014 0.001 PHE A 152 TRP 0.014 0.001 TRP A 628 HIS 0.001 0.000 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 ( 9751) covalent geometry : angle 0.51819 / 0.30 (13880) hydrogen bonds : bond 0.04878 / 5.18 ( 473) hydrogen bonds : angle 4.00287 / 5.18 ( 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 92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6969 (mtp180) cc_final: 0.6709 (tpt170) REVERT: A 151 ARG cc_start: 0.6906 (mtp180) cc_final: 0.6678 (mmm160) REVERT: A 189 LYS cc_start: 0.7511 (mmmm) cc_final: 0.7148 (ptmm) REVERT: A 529 GLU cc_start: 0.7884 (mp0) cc_final: 0.7656 (mp0) REVERT: A 560 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6008 (tp-100) REVERT: A 593 LYS cc_start: 0.7132 (pptt) cc_final: 0.6516 (mmtt) REVERT: A 687 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7042 (tp40) outliers start: 19 outliers final: 7 residues processed: 86 average time/residue: 0.6788 time to fit residues: 62.0289 Evaluate side-chains 69 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 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: 0.2980 chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.240550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.214559 restraints weight = 8349.346| |-----------------------------------------------------------------------------| r_work (start): 0.4494 rms_B_bonded: 0.86 r_work: 0.4172 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9751 Z= 0.133 Angle : 0.541 6.774 13880 Z= 0.307 Chirality : 0.038 0.174 1611 Planarity : 0.004 0.036 1231 Dihedral : 22.183 88.432 3058 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.73 % Allowed : 17.82 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.29), residues: 741 helix: 2.44 (0.25), residues: 360 sheet: -0.27 (0.46), residues: 112 loop : -0.82 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.013 0.001 TYR A 848 PHE 0.013 0.001 PHE A 152 TRP 0.013 0.001 TRP A 628 HIS 0.001 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 9751) covalent geometry : angle 0.54054 / 0.31 (13880) hydrogen bonds : bond 0.05186 / 5.58 ( 473) hydrogen bonds : angle 4.02558 / 5.26 ( 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 79 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.5720 (OUTLIER) cc_final: 0.5093 (t0) REVERT: A 189 LYS cc_start: 0.7561 (mmmm) cc_final: 0.7245 (ptmm) REVERT: A 560 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6387 (tp-100) REVERT: A 593 LYS cc_start: 0.6995 (pptt) cc_final: 0.6526 (mmtt) REVERT: A 687 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6990 (tp40) outliers start: 17 outliers final: 7 residues processed: 74 average time/residue: 0.7632 time to fit residues: 59.6641 Evaluate side-chains 71 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 185 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 40.0000 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4700 r_free = 0.4700 target = 0.239823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.219309 restraints weight = 8356.624| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 0.58 r_work: 0.4233 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2333 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= 0.137 Angle : 0.549 6.804 13880 Z= 0.311 Chirality : 0.038 0.156 1611 Planarity : 0.004 0.035 1231 Dihedral : 22.168 88.707 3058 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.37 % Allowed : 17.82 % Favored : 78.81 % 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: 1.28 (0.29), residues: 741 helix: 2.42 (0.25), residues: 360 sheet: -0.28 (0.46), residues: 112 loop : -0.84 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 605 TYR 0.013 0.002 TYR A 422 PHE 0.014 0.002 PHE A 152 TRP 0.013 0.001 TRP A 628 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 ( 9751) covalent geometry : angle 0.54863 / 0.31 (13880) hydrogen bonds : bond 0.05247 / 5.68 ( 473) hydrogen bonds : angle 4.03756 / 5.30 ( 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 81 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.5732 (OUTLIER) cc_final: 0.5051 (t0) REVERT: A 189 LYS cc_start: 0.7545 (mmmm) cc_final: 0.7267 (ptmm) REVERT: A 560 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6528 (tp40) REVERT: A 593 LYS cc_start: 0.6945 (pptt) cc_final: 0.6527 (mmtt) REVERT: A 687 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6992 (tp40) outliers start: 21 outliers final: 8 residues processed: 74 average time/residue: 0.7233 time to fit residues: 56.8319 Evaluate side-chains 68 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 366 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 0.0170 chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.235996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.215492 restraints weight = 8208.768| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 0.57 r_work: 0.4167 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9751 Z= 0.191 Angle : 0.649 7.496 13880 Z= 0.358 Chirality : 0.043 0.222 1611 Planarity : 0.005 0.034 1231 Dihedral : 22.186 89.955 3058 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.37 % Allowed : 18.46 % Favored : 78.17 % 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: 0.93 (0.29), residues: 741 helix: 2.06 (0.25), residues: 360 sheet: -0.43 (0.44), residues: 119 loop : -0.90 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 605 TYR 0.019 0.002 TYR A 422 PHE 0.019 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 0.00385 / 0.19 ( 9751) covalent geometry : angle 0.64880 / 0.36 (13880) hydrogen bonds : bond 0.06405 / 7.08 ( 473) hydrogen bonds : angle 4.30871 / 5.66 ( 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 81 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7659 (mmmm) cc_final: 0.7327 (ptmm) REVERT: A 575 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6398 (mm) REVERT: A 593 LYS cc_start: 0.7269 (pptt) cc_final: 0.6614 (mmtt) REVERT: A 687 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7190 (tp40) outliers start: 21 outliers final: 5 residues processed: 72 average time/residue: 0.7615 time to fit residues: 57.9200 Evaluate side-chains 67 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.238421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.217538 restraints weight = 8210.770| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 0.62 r_work: 0.4182 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9751 Z= 0.146 Angle : 0.587 7.516 13880 Z= 0.329 Chirality : 0.039 0.173 1611 Planarity : 0.004 0.037 1231 Dihedral : 22.194 89.483 3058 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.25 % Allowed : 20.22 % 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: 1.12 (0.29), residues: 741 helix: 2.19 (0.25), residues: 362 sheet: -0.36 (0.46), residues: 112 loop : -0.77 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.013 0.002 TYR A 848 PHE 0.013 0.002 PHE A 152 TRP 0.014 0.002 TRP A 518 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 ( 9751) covalent geometry : angle 0.58686 / 0.33 (13880) hydrogen bonds : bond 0.05494 / 5.96 ( 473) hydrogen bonds : angle 4.13454 / 5.43 ( 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 72 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7667 (mmmm) cc_final: 0.7347 (ptmm) REVERT: A 560 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6424 (tp-100) REVERT: A 575 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6325 (mm) REVERT: A 593 LYS cc_start: 0.7189 (pptt) cc_final: 0.6585 (mmtt) REVERT: A 687 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7193 (tp40) outliers start: 14 outliers final: 6 residues processed: 66 average time/residue: 0.7467 time to fit residues: 52.1608 Evaluate side-chains 66 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 273 ILE 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 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 76 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 3 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 487 GLN ** 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 = 0.4692 r_free = 0.4692 target = 0.238912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.219735 restraints weight = 8217.882| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 0.54 r_work: 0.4215 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9751 Z= 0.139 Angle : 0.574 9.187 13880 Z= 0.322 Chirality : 0.038 0.167 1611 Planarity : 0.004 0.037 1231 Dihedral : 22.165 89.268 3058 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.25 % Allowed : 20.22 % 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: 1.16 (0.29), residues: 741 helix: 2.28 (0.25), residues: 360 sheet: -0.07 (0.52), residues: 90 loop : -0.91 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.013 0.001 TYR A 422 PHE 0.013 0.001 PHE A 152 TRP 0.014 0.002 TRP A 628 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 ( 9751) covalent geometry : angle 0.57361 / 0.32 (13880) hydrogen bonds : bond 0.05400 / 5.86 ( 473) hydrogen bonds : angle 4.10533 / 5.38 ( 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 71 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7444 (mmmm) cc_final: 0.7156 (ptmm) REVERT: A 402 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5849 (pp20) REVERT: A 575 ILE cc_start: 0.6520 (OUTLIER) cc_final: 0.6217 (mm) REVERT: A 593 LYS cc_start: 0.6991 (pptt) cc_final: 0.6568 (mmtt) REVERT: A 687 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7052 (tp40) outliers start: 14 outliers final: 6 residues processed: 66 average time/residue: 0.7448 time to fit residues: 52.0645 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 : 0.267 ------------------------------------------------------------------------------- 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 273 ILE 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 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: 6.9990 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 GLN A 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.238574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.219116 restraints weight = 8174.268| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 0.56 r_work: 0.4204 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4082 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2400 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= 0.148 Angle : 0.583 8.960 13880 Z= 0.326 Chirality : 0.039 0.164 1611 Planarity : 0.004 0.036 1231 Dihedral : 22.136 89.358 3058 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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 : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.29), residues: 741 helix: 2.25 (0.25), residues: 360 sheet: -0.03 (0.52), residues: 90 loop : -0.91 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 490 TYR 0.015 0.002 TYR A 422 PHE 0.013 0.002 PHE A 152 TRP 0.014 0.002 TRP A 518 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 ( 9751) covalent geometry : angle 0.58294 / 0.33 (13880) hydrogen bonds : bond 0.05502 / 5.98 ( 473) hydrogen bonds : angle 4.13309 / 5.41 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3334.48 seconds wall clock time: 57 minutes 40.71 seconds (3460.71 seconds total)