Starting phenix.real_space_refine on Thu Mar 13 18:32:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyc_38768/03_2025/8xyc_38768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyc_38768/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xyc_38768/03_2025/8xyc_38768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyc_38768/03_2025/8xyc_38768.map" model { file = "/net/cci-nas-00/data/ceres_data/8xyc_38768/03_2025/8xyc_38768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyc_38768/03_2025/8xyc_38768.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.32, per 1000 atoms: 0.68 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: 2.41 Conformation dependent library (CDL) restraints added in 741.5 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: 3.85 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: 4.47 Time building geometry restraints manager: 2.85 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: 1.200 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- 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= 0.296 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP A 103 HIS 0.006 0.001 HIS A 11 PHE 0.018 0.002 PHE A 471 TYR 0.020 0.002 TYR A 848 ARG 0.005 0.001 ARG A 120 *********************** 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 : 0.754 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: 1.4491 time to fit residues: 186.0202 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 : 0.796 ------------------------------------------------------------------------------- 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 73 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.0770 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.241124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.210829 restraints weight = 8122.071| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 0.86 r_work: 0.4142 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work: 0.4083 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1676 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= 0.201 Angle : 0.635 6.986 13880 Z= 0.334 Chirality : 0.037 0.156 1611 Planarity : 0.004 0.037 1231 Dihedral : 22.307 92.459 3064 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.25 % Allowed : 11.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.29), residues: 741 helix: 2.02 (0.26), residues: 360 sheet: -0.39 (0.47), residues: 112 loop : -1.06 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 628 HIS 0.003 0.001 HIS A 11 PHE 0.017 0.002 PHE A 152 TYR 0.014 0.002 TYR A 848 ARG 0.006 0.000 ARG A 224 *********************** 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 79 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7345 (mmm-85) cc_final: 0.6885 (tpt170) REVERT: A 189 LYS cc_start: 0.7750 (mmmm) cc_final: 0.7374 (ptmm) REVERT: A 434 GLU cc_start: 0.6391 (pm20) cc_final: 0.5790 (pp20) REVERT: A 593 LYS cc_start: 0.7324 (pptt) cc_final: 0.6660 (mmtt) outliers start: 14 outliers final: 6 residues processed: 74 average time/residue: 1.5450 time to fit residues: 121.4846 Evaluate side-chains 63 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 842 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 0.0020 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.240619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.220524 restraints weight = 8369.563| |-----------------------------------------------------------------------------| r_work (start): 0.4543 rms_B_bonded: 0.61 r_work: 0.4226 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9751 Z= 0.166 Angle : 0.564 6.964 13880 Z= 0.298 Chirality : 0.035 0.159 1611 Planarity : 0.004 0.035 1231 Dihedral : 22.075 91.379 3060 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.05 % Allowed : 13.32 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.30), residues: 741 helix: 2.37 (0.25), residues: 360 sheet: -0.36 (0.46), residues: 112 loop : -0.89 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 628 HIS 0.002 0.001 HIS A 107 PHE 0.015 0.001 PHE A 152 TYR 0.011 0.001 TYR A 848 ARG 0.005 0.000 ARG A 490 *********************** 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 94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 151 ARG cc_start: 0.6950 (mtp180) cc_final: 0.6721 (mmm160) REVERT: A 189 LYS cc_start: 0.7481 (mmmm) cc_final: 0.7229 (ptmm) REVERT: A 208 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7064 (mp) REVERT: A 434 GLU cc_start: 0.6407 (pm20) cc_final: 0.5698 (pp20) REVERT: A 593 LYS cc_start: 0.7123 (pptt) cc_final: 0.6563 (mmtt) outliers start: 19 outliers final: 3 residues processed: 87 average time/residue: 1.8482 time to fit residues: 169.4818 Evaluate side-chains 65 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4709 r_free = 0.4709 target = 0.240729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.213610 restraints weight = 8292.489| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 0.82 r_work: 0.4143 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4064 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9751 Z= 0.166 Angle : 0.564 7.052 13880 Z= 0.296 Chirality : 0.034 0.153 1611 Planarity : 0.004 0.039 1231 Dihedral : 21.973 91.867 3060 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.37 % Allowed : 14.45 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.30), residues: 741 helix: 2.53 (0.25), residues: 360 sheet: -0.36 (0.46), residues: 112 loop : -0.82 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 628 HIS 0.002 0.001 HIS A 107 PHE 0.013 0.001 PHE A 152 TYR 0.012 0.001 TYR A 848 ARG 0.005 0.000 ARG A 490 *********************** 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 95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.5564 (OUTLIER) cc_final: 0.4895 (t0) REVERT: A 189 LYS cc_start: 0.7558 (mmmm) cc_final: 0.7231 (ptmm) REVERT: A 529 GLU cc_start: 0.7954 (mp0) cc_final: 0.7741 (mp0) REVERT: A 593 LYS cc_start: 0.7239 (pptt) cc_final: 0.6540 (mmtt) outliers start: 21 outliers final: 8 residues processed: 86 average time/residue: 1.3937 time to fit residues: 127.6431 Evaluate side-chains 73 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 366 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 = 0.4647 r_free = 0.4647 target = 0.233491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.211637 restraints weight = 8151.053| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 0.77 r_work: 0.4131 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4069 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9751 Z= 0.387 Angle : 0.795 9.026 13880 Z= 0.409 Chirality : 0.045 0.182 1611 Planarity : 0.006 0.038 1231 Dihedral : 22.165 94.591 3058 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.17 % Allowed : 16.05 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 741 helix: 1.70 (0.25), residues: 360 sheet: -0.44 (0.44), residues: 115 loop : -0.98 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 518 HIS 0.006 0.002 HIS A 107 PHE 0.026 0.003 PHE A 411 TYR 0.021 0.003 TYR A 422 ARG 0.008 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7903 (mmmm) cc_final: 0.7571 (ptmm) REVERT: A 402 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5841 (pp20) REVERT: A 480 LYS cc_start: 0.6498 (tptm) cc_final: 0.6079 (mttp) REVERT: A 529 GLU cc_start: 0.7953 (mp0) cc_final: 0.7688 (mp0) REVERT: A 560 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6177 (tp-100) REVERT: A 593 LYS cc_start: 0.7141 (pptt) cc_final: 0.6644 (mmtt) REVERT: A 687 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7241 (tp40) outliers start: 26 outliers final: 9 residues processed: 79 average time/residue: 2.5854 time to fit residues: 216.8496 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 : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 732 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4665 r_free = 0.4665 target = 0.235758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.217293 restraints weight = 8142.104| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 0.52 r_work: 0.4187 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4066 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9751 Z= 0.265 Angle : 0.675 7.883 13880 Z= 0.351 Chirality : 0.039 0.156 1611 Planarity : 0.005 0.036 1231 Dihedral : 22.092 93.158 3058 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 741 helix: 1.83 (0.25), residues: 360 sheet: -0.39 (0.45), residues: 115 loop : -1.02 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 518 HIS 0.004 0.001 HIS A 11 PHE 0.016 0.002 PHE A 451 TYR 0.017 0.002 TYR A 422 ARG 0.007 0.001 ARG A 559 *********************** 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: 21 poor density : 58 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7791 (mmmm) cc_final: 0.7494 (ptmm) REVERT: A 316 TRP cc_start: 0.6517 (OUTLIER) cc_final: 0.5886 (m-10) REVERT: A 402 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5941 (pp20) REVERT: A 480 LYS cc_start: 0.6511 (tptm) cc_final: 0.6200 (mttp) REVERT: A 593 LYS cc_start: 0.7157 (pptt) cc_final: 0.6588 (mmtt) REVERT: A 687 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7116 (tp40) outliers start: 21 outliers final: 9 residues processed: 73 average time/residue: 1.4419 time to fit residues: 111.9674 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 : 0.767 ------------------------------------------------------------------------------- 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 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 631 SER 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 9 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 84 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 835 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.239211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.218184 restraints weight = 8293.961| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 0.60 r_work: 0.4239 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4191 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2455 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= 0.163 Angle : 0.576 7.158 13880 Z= 0.303 Chirality : 0.035 0.146 1611 Planarity : 0.004 0.037 1231 Dihedral : 21.958 91.330 3058 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.73 % Allowed : 18.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.29), residues: 741 helix: 2.29 (0.25), residues: 360 sheet: -0.04 (0.53), residues: 90 loop : -0.96 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 628 HIS 0.003 0.001 HIS A 11 PHE 0.013 0.001 PHE A 152 TYR 0.012 0.001 TYR A 848 ARG 0.004 0.000 ARG A 605 *********************** 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: 17 poor density : 61 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7600 (mmmm) cc_final: 0.7314 (ptmm) REVERT: A 316 TRP cc_start: 0.6389 (OUTLIER) cc_final: 0.5820 (m-10) REVERT: A 593 LYS cc_start: 0.6873 (pptt) cc_final: 0.6534 (mmtt) REVERT: A 687 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6944 (tp40) outliers start: 17 outliers final: 8 residues processed: 70 average time/residue: 1.5410 time to fit residues: 115.1965 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 : 0.695 ------------------------------------------------------------------------------- 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 316 TRP Chi-restraints excluded: chain A residue 366 LEU 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 37 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4666 r_free = 0.4666 target = 0.235713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.216019 restraints weight = 8290.868| |-----------------------------------------------------------------------------| r_work (start): 0.4505 rms_B_bonded: 0.57 r_work: 0.4189 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9751 Z= 0.269 Angle : 0.677 7.736 13880 Z= 0.351 Chirality : 0.039 0.157 1611 Planarity : 0.005 0.035 1231 Dihedral : 21.957 92.779 3058 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.37 % Allowed : 19.26 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 741 helix: 2.03 (0.25), residues: 360 sheet: -0.46 (0.44), residues: 119 loop : -0.97 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 518 HIS 0.004 0.001 HIS A 11 PHE 0.016 0.002 PHE A 451 TYR 0.018 0.002 TYR A 422 ARG 0.005 0.001 ARG A 559 *********************** 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 83 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7708 (mmmm) cc_final: 0.7444 (ptmm) REVERT: A 316 TRP cc_start: 0.6452 (OUTLIER) cc_final: 0.5821 (m-10) REVERT: A 402 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5913 (pp20) REVERT: A 560 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6092 (tp-100) REVERT: A 593 LYS cc_start: 0.6967 (pptt) cc_final: 0.6569 (mmtt) REVERT: A 687 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7035 (tp40) outliers start: 21 outliers final: 11 residues processed: 77 average time/residue: 1.3935 time to fit residues: 114.0524 Evaluate side-chains 73 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 273 ILE 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 608 GLN Chi-restraints excluded: chain A residue 631 SER 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 84 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.0030 chunk 43 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 overall best weight: 0.3628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 835 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.240981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.214412 restraints weight = 8321.778| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 0.84 r_work: 0.4149 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4078 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9751 Z= 0.158 Angle : 0.569 7.365 13880 Z= 0.298 Chirality : 0.034 0.148 1611 Planarity : 0.004 0.037 1231 Dihedral : 21.874 91.052 3058 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.89 % Allowed : 19.90 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.30), residues: 741 helix: 2.47 (0.25), residues: 360 sheet: 0.10 (0.54), residues: 90 loop : -0.97 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 628 HIS 0.001 0.000 HIS A 11 PHE 0.010 0.001 PHE A 152 TYR 0.011 0.001 TYR A 848 ARG 0.005 0.000 ARG A 605 *********************** 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 85 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.5387 (t0) cc_final: 0.4645 (t0) REVERT: A 189 LYS cc_start: 0.7603 (mmmm) cc_final: 0.7172 (ptmm) REVERT: A 249 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7807 (tptt) REVERT: A 560 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6477 (tp40) REVERT: A 593 LYS cc_start: 0.7217 (pptt) cc_final: 0.6508 (mmtt) outliers start: 18 outliers final: 7 residues processed: 77 average time/residue: 1.3112 time to fit residues: 107.9919 Evaluate side-chains 62 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 366 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 81 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 0.0050 chunk 82 optimal weight: 8.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- 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 = 0.4681 r_free = 0.4681 target = 0.236765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.216405 restraints weight = 8308.484| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 0.58 r_work: 0.4191 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4100 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9751 Z= 0.218 Angle : 0.634 9.026 13880 Z= 0.329 Chirality : 0.037 0.161 1611 Planarity : 0.004 0.035 1231 Dihedral : 21.833 92.353 3058 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.09 % Allowed : 20.71 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.30), residues: 741 helix: 2.23 (0.25), residues: 360 sheet: -0.26 (0.46), residues: 112 loop : -0.87 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 628 HIS 0.003 0.001 HIS A 11 PHE 0.013 0.002 PHE A 60 TYR 0.016 0.002 TYR A 422 ARG 0.006 0.000 ARG A 605 ********************** 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 70 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7599 (mmmm) cc_final: 0.7296 (ptmm) REVERT: A 560 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6389 (tp-100) REVERT: A 593 LYS cc_start: 0.7035 (pptt) cc_final: 0.6527 (mmtt) REVERT: A 687 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6865 (tp40) outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 1.3581 time to fit residues: 92.7832 Evaluate side-chains 64 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 560 GLN 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 86 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 714 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.236487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.216168 restraints weight = 8233.191| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 0.58 r_work: 0.4193 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4108 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9751 Z= 0.240 Angle : 0.657 9.236 13880 Z= 0.342 Chirality : 0.038 0.159 1611 Planarity : 0.005 0.035 1231 Dihedral : 21.837 92.824 3058 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.41 % Allowed : 20.39 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 741 helix: 2.10 (0.25), residues: 360 sheet: -0.32 (0.46), residues: 112 loop : -0.88 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 628 HIS 0.003 0.001 HIS A 11 PHE 0.014 0.002 PHE A 451 TYR 0.017 0.002 TYR A 422 ARG 0.008 0.001 ARG A 605 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7130.83 seconds wall clock time: 124 minutes 46.49 seconds (7486.49 seconds total)