Starting phenix.real_space_refine on Sat Aug 23 02:21:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyc_38768/08_2025/8xyc_38768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyc_38768/08_2025/8xyc_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_2025/8xyc_38768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyc_38768/08_2025/8xyc_38768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xyc_38768/08_2025/8xyc_38768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyc_38768/08_2025/8xyc_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-2.0-5787/lib/python3.9/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: 2.32, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 235.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.15 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: 2.02 Time building geometry restraints manager: 1.10 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=" 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 bond pdb=" N GLY A 624 " pdb=" CA GLY A 624 " ideal model delta sigma weight residual 1.447 1.482 -0.035 1.01e-02 9.80e+03 1.21e+01 bond pdb=" N ARG A 627 " pdb=" CA ARG A 627 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" N LEU A 181 " pdb=" CA LEU A 181 " ideal model delta sigma weight residual 1.456 1.500 -0.045 1.33e-02 5.65e+03 1.12e+01 ... (remaining 9746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 13567 2.42 - 4.84: 277 4.84 - 7.26: 31 7.26 - 9.67: 2 9.67 - 12.09: 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=" O3' DT D -3 " pdb=" C3' DT D -3 " pdb=" C2' DT D -3 " ideal model delta sigma weight residual 111.50 99.41 12.09 1.50e+00 4.44e-01 6.50e+01 angle pdb=" C4' DG B 21 " pdb=" C3' DG B 21 " pdb=" O3' DG B 21 " ideal model delta sigma weight residual 110.00 100.10 9.90 1.50e+00 4.44e-01 4.36e+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=" 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: 1391 0.059 - 0.119: 182 0.119 - 0.178: 29 0.178 - 0.238: 7 0.238 - 0.297: 2 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=" C3' DT D -3 " pdb=" C4' DT D -3 " pdb=" O3' DT D -3 " pdb=" C2' DT D -3 " both_signs ideal model delta sigma weight residual False -2.66 -2.93 0.27 2.00e-01 2.50e+01 1.82e+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 ... (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: 0.980 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 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= 0.299 Angle : 0.792 12.092 13880 Z= 0.483 Chirality : 0.044 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 aren 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 covalent geometry : bond 0.00491 ( 9751) covalent geometry : angle 0.79193 (13880) hydrogen bonds : bond 0.14242 ( 473) hydrogen bonds : angle 6.17015 ( 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 : 0.175 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: 0.7116 time to fit residues: 90.8626 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 : 0.293 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 512 GLN ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.242606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.211486 restraints weight = 8172.917| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 0.90 r_work: 0.4153 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4075 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1735 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= 0.143 Angle : 0.614 7.208 13880 Z= 0.324 Chirality : 0.036 0.158 1611 Planarity : 0.004 0.038 1231 Dihedral : 22.300 92.222 3064 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.41 % Allowed : 11.24 % Favored : 86.36 % 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 aren not related in a simple way. whole: 0.93 (0.29), residues: 741 helix: 2.12 (0.26), residues: 360 sheet: -0.38 (0.47), residues: 112 loop : -1.03 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.013 0.001 TYR A 848 PHE 0.016 0.002 PHE A 152 TRP 0.016 0.002 TRP A 628 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9751) covalent geometry : angle 0.61418 (13880) hydrogen bonds : bond 0.05359 ( 473) hydrogen bonds : angle 4.36540 ( 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 82 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7350 (mmm-85) cc_final: 0.6969 (tpt170) REVERT: A 189 LYS cc_start: 0.7669 (mmmm) cc_final: 0.7307 (ptmm) REVERT: A 434 GLU cc_start: 0.6452 (pm20) cc_final: 0.5797 (pp20) REVERT: A 593 LYS cc_start: 0.7381 (pptt) cc_final: 0.6625 (mmtt) outliers start: 15 outliers final: 7 residues processed: 77 average time/residue: 0.7224 time to fit residues: 58.8838 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 : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 273 ILE 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: 4.9990 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 714 ASN A 835 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.237945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.216821 restraints weight = 8259.101| |-----------------------------------------------------------------------------| r_work (start): 0.4516 rms_B_bonded: 0.58 r_work: 0.4229 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4163 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1938 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= 0.159 Angle : 0.608 7.177 13880 Z= 0.320 Chirality : 0.036 0.159 1611 Planarity : 0.004 0.034 1231 Dihedral : 22.110 92.211 3060 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.37 % Allowed : 13.48 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.29), residues: 741 helix: 2.17 (0.25), residues: 360 sheet: -0.36 (0.47), residues: 112 loop : -0.94 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 490 TYR 0.015 0.002 TYR A 422 PHE 0.016 0.002 PHE A 152 TRP 0.018 0.002 TRP A 628 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9751) covalent geometry : angle 0.60847 (13880) hydrogen bonds : bond 0.05510 ( 473) hydrogen bonds : angle 4.25269 ( 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 88 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7156 (mmm-85) cc_final: 0.6850 (tpt170) REVERT: A 189 LYS cc_start: 0.7607 (mmmm) cc_final: 0.7366 (ptmm) REVERT: A 593 LYS cc_start: 0.6951 (pptt) cc_final: 0.6570 (mmtt) outliers start: 21 outliers final: 4 residues processed: 80 average time/residue: 0.8409 time to fit residues: 70.8230 Evaluate side-chains 67 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 446 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.0270 chunk 82 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.238349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.216854 restraints weight = 8279.912| |-----------------------------------------------------------------------------| r_work (start): 0.4521 rms_B_bonded: 0.63 r_work: 0.4225 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4175 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2177 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= 0.151 Angle : 0.590 6.941 13880 Z= 0.309 Chirality : 0.036 0.154 1611 Planarity : 0.004 0.038 1231 Dihedral : 22.023 92.077 3058 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.37 % Allowed : 14.13 % 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 aren not related in a simple way. whole: 1.08 (0.29), residues: 741 helix: 2.28 (0.25), residues: 360 sheet: -0.46 (0.46), residues: 114 loop : -0.94 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.014 0.002 TYR A 422 PHE 0.014 0.002 PHE A 152 TRP 0.017 0.002 TRP A 628 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9751) covalent geometry : angle 0.58996 (13880) hydrogen bonds : bond 0.05216 ( 473) hydrogen bonds : angle 4.14791 ( 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 96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7150 (mmm-85) cc_final: 0.6904 (tpt170) REVERT: A 189 LYS cc_start: 0.7572 (mmmm) cc_final: 0.7290 (ptmm) REVERT: A 402 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5668 (pp20) REVERT: A 529 GLU cc_start: 0.7918 (mp0) cc_final: 0.7698 (mp0) REVERT: A 593 LYS cc_start: 0.6895 (pptt) cc_final: 0.6525 (mmtt) REVERT: A 687 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6964 (tp40) outliers start: 21 outliers final: 6 residues processed: 87 average time/residue: 0.6958 time to fit residues: 64.1436 Evaluate side-chains 70 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4697 r_free = 0.4697 target = 0.239180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.222367 restraints weight = 8309.918| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 0.48 r_work: 0.4257 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.4062 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9751 Z= 0.139 Angle : 0.583 6.800 13880 Z= 0.305 Chirality : 0.035 0.148 1611 Planarity : 0.004 0.036 1231 Dihedral : 21.978 91.788 3058 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.53 % Allowed : 17.01 % 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 aren not related in a simple way. whole: 1.21 (0.30), residues: 741 helix: 2.38 (0.26), residues: 360 sheet: -0.39 (0.46), residues: 114 loop : -0.88 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.012 0.001 TYR A 848 PHE 0.013 0.001 PHE A 152 TRP 0.015 0.002 TRP A 628 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9751) covalent geometry : angle 0.58296 (13880) hydrogen bonds : bond 0.04937 ( 473) hydrogen bonds : angle 4.07463 ( 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 86 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: A 32 ARG cc_start: 0.7283 (mmm-85) cc_final: 0.6861 (tpt170) REVERT: A 185 ASN cc_start: 0.5493 (OUTLIER) cc_final: 0.4865 (t0) REVERT: A 189 LYS cc_start: 0.7627 (mmmm) cc_final: 0.7185 (ptmm) REVERT: A 249 LYS cc_start: 0.7879 (tptt) cc_final: 0.7665 (ttmm) REVERT: A 382 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6830 (tt0) REVERT: A 396 LEU cc_start: 0.6466 (tp) cc_final: 0.6192 (mt) REVERT: A 402 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5450 (pp20) REVERT: A 529 GLU cc_start: 0.8049 (mp0) cc_final: 0.7791 (mp0) REVERT: A 593 LYS cc_start: 0.7325 (pptt) cc_final: 0.6520 (mmtt) REVERT: A 687 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7158 (tp40) REVERT: A 824 ASN cc_start: 0.7112 (t0) cc_final: 0.6742 (t0) outliers start: 22 outliers final: 7 residues processed: 78 average time/residue: 0.6713 time to fit residues: 55.4912 Evaluate side-chains 67 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU 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 366 LEU Chi-restraints excluded: chain A residue 382 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 4 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 835 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.238080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.216358 restraints weight = 8347.836| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 0.62 r_work: 0.4181 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4076 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2428 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= 0.152 Angle : 0.600 7.011 13880 Z= 0.313 Chirality : 0.036 0.147 1611 Planarity : 0.004 0.036 1231 Dihedral : 21.973 92.148 3058 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.17 % Allowed : 17.34 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.29), residues: 741 helix: 2.33 (0.25), residues: 360 sheet: -0.38 (0.45), residues: 114 loop : -0.85 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.014 0.002 TYR A 422 PHE 0.013 0.002 PHE A 152 TRP 0.015 0.002 TRP A 628 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9751) covalent geometry : angle 0.59976 (13880) hydrogen bonds : bond 0.05142 ( 473) hydrogen bonds : angle 4.11965 ( 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 83 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: A 32 ARG cc_start: 0.7275 (mmm-85) cc_final: 0.6851 (tpt170) REVERT: A 189 LYS cc_start: 0.7581 (mmmm) cc_final: 0.7235 (ptmm) REVERT: A 316 TRP cc_start: 0.6514 (OUTLIER) cc_final: 0.6013 (m-10) REVERT: A 396 LEU cc_start: 0.6617 (tp) cc_final: 0.6266 (mt) REVERT: A 402 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5539 (pp20) REVERT: A 593 LYS cc_start: 0.7199 (pptt) cc_final: 0.6558 (mmtt) REVERT: A 687 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7136 (tp40) REVERT: A 824 ASN cc_start: 0.6962 (t0) cc_final: 0.6626 (t0) outliers start: 26 outliers final: 7 residues processed: 75 average time/residue: 0.7051 time to fit residues: 56.0211 Evaluate side-chains 67 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU 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 366 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 484 SER 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: 3.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.239104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.217356 restraints weight = 8370.938| |-----------------------------------------------------------------------------| r_work (start): 0.4525 rms_B_bonded: 0.62 r_work: 0.4217 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4164 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9751 Z= 0.134 Angle : 0.578 7.268 13880 Z= 0.302 Chirality : 0.035 0.147 1611 Planarity : 0.004 0.035 1231 Dihedral : 21.944 91.908 3058 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.21 % Allowed : 18.46 % 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 aren not related in a simple way. whole: 1.25 (0.29), residues: 741 helix: 2.42 (0.25), residues: 360 sheet: -0.14 (0.52), residues: 92 loop : -0.93 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.012 0.001 TYR A 848 PHE 0.012 0.001 PHE A 152 TRP 0.015 0.001 TRP A 628 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9751) covalent geometry : angle 0.57807 (13880) hydrogen bonds : bond 0.04854 ( 473) hydrogen bonds : angle 4.03781 ( 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 78 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: A 32 ARG cc_start: 0.7088 (mmm-85) cc_final: 0.6792 (tpt170) REVERT: A 189 LYS cc_start: 0.7545 (mmmm) cc_final: 0.7204 (ptmm) REVERT: A 316 TRP cc_start: 0.6422 (OUTLIER) cc_final: 0.5908 (m-10) REVERT: A 396 LEU cc_start: 0.6473 (tp) cc_final: 0.6223 (mt) REVERT: A 402 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.5548 (pp20) REVERT: A 529 GLU cc_start: 0.7898 (mp0) cc_final: 0.7658 (mp0) REVERT: A 593 LYS cc_start: 0.6960 (pptt) cc_final: 0.6535 (mmtt) REVERT: A 687 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6952 (tp40) REVERT: A 824 ASN cc_start: 0.6763 (t0) cc_final: 0.6521 (t0) outliers start: 20 outliers final: 8 residues processed: 71 average time/residue: 0.7265 time to fit residues: 54.4582 Evaluate side-chains 69 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU 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 316 TRP 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 484 SER 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: 4.9990 chunk 59 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.0030 chunk 12 optimal weight: 1.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.238277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.217301 restraints weight = 8296.492| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 0.60 r_work: 0.4210 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2565 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= 0.145 Angle : 0.589 7.614 13880 Z= 0.307 Chirality : 0.035 0.147 1611 Planarity : 0.004 0.034 1231 Dihedral : 21.860 92.231 3058 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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 aren not related in a simple way. whole: 1.24 (0.29), residues: 741 helix: 2.41 (0.25), residues: 360 sheet: -0.39 (0.44), residues: 114 loop : -0.85 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.014 0.002 TYR A 422 PHE 0.012 0.002 PHE A 152 TRP 0.016 0.002 TRP A 628 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9751) covalent geometry : angle 0.58871 (13880) hydrogen bonds : bond 0.04985 ( 473) hydrogen bonds : angle 4.05629 ( 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: 21 poor density : 59 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: A 32 ARG cc_start: 0.7217 (mmm-85) cc_final: 0.6815 (tpt170) REVERT: A 189 LYS cc_start: 0.7645 (mmmm) cc_final: 0.7303 (ptmm) REVERT: A 316 TRP cc_start: 0.6498 (OUTLIER) cc_final: 0.6001 (m-10) REVERT: A 396 LEU cc_start: 0.6598 (tp) cc_final: 0.6244 (mt) REVERT: A 480 LYS cc_start: 0.6432 (tptm) cc_final: 0.6184 (mttp) REVERT: A 529 GLU cc_start: 0.8018 (mp0) cc_final: 0.7761 (mp0) REVERT: A 560 GLN cc_start: 0.6510 (OUTLIER) cc_final: 0.6204 (tp-100) REVERT: A 575 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6376 (mm) REVERT: A 593 LYS cc_start: 0.7043 (pptt) cc_final: 0.6540 (mmtt) REVERT: A 687 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6983 (tp40) REVERT: A 824 ASN cc_start: 0.6841 (t0) cc_final: 0.6571 (t0) outliers start: 21 outliers final: 7 residues processed: 71 average time/residue: 0.7275 time to fit residues: 54.7244 Evaluate side-chains 69 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU 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 366 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 484 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 560 GLN A 608 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.236947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.214850 restraints weight = 8249.424| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 0.63 r_work: 0.4197 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9751 Z= 0.170 Angle : 0.620 7.796 13880 Z= 0.321 Chirality : 0.037 0.156 1611 Planarity : 0.004 0.042 1231 Dihedral : 21.843 92.771 3058 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.41 % Allowed : 19.26 % 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 aren not related in a simple way. whole: 1.13 (0.29), residues: 741 helix: 2.28 (0.25), residues: 360 sheet: -0.39 (0.44), residues: 114 loop : -0.86 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 605 TYR 0.015 0.002 TYR A 422 PHE 0.014 0.002 PHE A 451 TRP 0.014 0.002 TRP A 628 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9751) covalent geometry : angle 0.61998 (13880) hydrogen bonds : bond 0.05326 ( 473) hydrogen bonds : angle 4.14478 ( 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 74 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: A 32 ARG cc_start: 0.7159 (mmm-85) cc_final: 0.6895 (tpt170) REVERT: A 189 LYS cc_start: 0.7583 (mmmm) cc_final: 0.7250 (ptmm) REVERT: A 316 TRP cc_start: 0.6481 (OUTLIER) cc_final: 0.5982 (m-10) REVERT: A 396 LEU cc_start: 0.6632 (tp) cc_final: 0.6324 (mt) REVERT: A 480 LYS cc_start: 0.6487 (tptm) cc_final: 0.6213 (mttp) REVERT: A 529 GLU cc_start: 0.7863 (mp0) cc_final: 0.7614 (mp0) REVERT: A 575 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6379 (mm) REVERT: A 593 LYS cc_start: 0.6972 (pptt) cc_final: 0.6544 (mmtt) REVERT: A 687 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7051 (tp40) REVERT: A 824 ASN cc_start: 0.6834 (t0) cc_final: 0.6559 (t0) outliers start: 15 outliers final: 8 residues processed: 70 average time/residue: 0.7359 time to fit residues: 54.2987 Evaluate side-chains 69 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU 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 366 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 487 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: 3.9990 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 3 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4701 r_free = 0.4701 target = 0.239517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.220536 restraints weight = 8296.878| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 0.55 r_work: 0.4241 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.2684 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= 0.126 Angle : 0.572 8.984 13880 Z= 0.298 Chirality : 0.034 0.149 1611 Planarity : 0.004 0.035 1231 Dihedral : 21.818 92.070 3058 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.25 % Allowed : 20.06 % Favored : 77.69 % 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 aren not related in a simple way. whole: 1.30 (0.29), residues: 741 helix: 2.47 (0.25), residues: 360 sheet: -0.18 (0.50), residues: 96 loop : -0.91 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 605 TYR 0.012 0.001 TYR A 848 PHE 0.010 0.001 PHE A 152 TRP 0.014 0.001 TRP A 628 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9751) covalent geometry : angle 0.57193 (13880) hydrogen bonds : bond 0.04638 ( 473) hydrogen bonds : angle 4.00801 ( 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 72 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: A 402 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5571 (pp20) REVERT: A 529 GLU cc_start: 0.7791 (mp0) cc_final: 0.7577 (mp0) REVERT: A 560 GLN cc_start: 0.6236 (OUTLIER) cc_final: 0.6001 (tp-100) REVERT: A 575 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6220 (mm) REVERT: A 593 LYS cc_start: 0.6938 (pptt) cc_final: 0.6528 (mmtt) REVERT: A 687 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6915 (tp40) REVERT: A 824 ASN cc_start: 0.6773 (t0) cc_final: 0.6514 (t0) outliers start: 14 outliers final: 6 residues processed: 67 average time/residue: 0.7348 time to fit residues: 51.8263 Evaluate side-chains 70 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU 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 484 SER Chi-restraints excluded: chain A residue 487 GLN 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: 8.9990 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.234585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.207155 restraints weight = 8149.360| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 0.82 r_work: 0.4141 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9751 Z= 0.230 Angle : 0.705 9.073 13880 Z= 0.363 Chirality : 0.040 0.165 1611 Planarity : 0.005 0.041 1231 Dihedral : 21.867 93.805 3058 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.21 % Allowed : 19.58 % Favored : 77.21 % 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 aren not related in a simple way. whole: 0.91 (0.29), residues: 741 helix: 1.99 (0.25), residues: 360 sheet: -0.42 (0.45), residues: 113 loop : -0.83 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 605 TYR 0.018 0.002 TYR A 422 PHE 0.020 0.003 PHE A 451 TRP 0.016 0.002 TRP A 518 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 9751) covalent geometry : angle 0.70454 (13880) hydrogen bonds : bond 0.06188 ( 473) hydrogen bonds : angle 4.35220 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3309.18 seconds wall clock time: 57 minutes 3.53 seconds (3423.53 seconds total)