Starting phenix.real_space_refine on Thu Jan 16 05:40:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyc_38768/01_2025/8xyc_38768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyc_38768/01_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_38768/01_2025/8xyc_38768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyc_38768/01_2025/8xyc_38768.map" model { file = "/net/cci-nas-00/data/ceres_data/8xyc_38768/01_2025/8xyc_38768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyc_38768/01_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-5571/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: 5.98, per 1000 atoms: 0.65 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: 2.24 Conformation dependent library (CDL) restraints added in 696.3 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: 3.83 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: 4.43 Time building geometry restraints manager: 2.61 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: 0.700 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.220 Find NCS groups from input model: 0.080 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:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.000 ------------------------------------------------------------------------------- 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 : 0.833 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: 1.5195 time to fit residues: 194.5850 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 : 0.764 ------------------------------------------------------------------------------- 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 = 0.210835 restraints weight = 8122.082| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 0.86 r_work: 0.4177 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 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 : 0.787 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7309 (mmm-85) cc_final: 0.6867 (tpt170) REVERT: A 189 LYS cc_start: 0.7676 (mmmm) cc_final: 0.7361 (ptmm) REVERT: A 434 GLU cc_start: 0.6370 (pm20) cc_final: 0.5835 (pp20) REVERT: A 593 LYS cc_start: 0.7144 (pptt) cc_final: 0.6652 (mmtt) outliers start: 14 outliers final: 6 residues processed: 74 average time/residue: 1.5361 time to fit residues: 120.7448 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 : 0.862 ------------------------------------------------------------------------------- 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: 0.0970 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4705 r_free = 0.4705 target = 0.240353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.220250 restraints weight = 8357.161| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 0.61 r_work: 0.4227 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4132 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2112 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= 0.169 Angle : 0.568 7.015 13880 Z= 0.300 Chirality : 0.035 0.158 1611 Planarity : 0.004 0.036 1231 Dihedral : 22.076 91.457 3060 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.05 % Allowed : 13.16 % Favored : 83.79 % 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: 1.17 (0.30), residues: 741 helix: 2.35 (0.25), residues: 360 sheet: -0.36 (0.47), residues: 112 loop : -0.90 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 628 HIS 0.002 0.001 HIS A 107 PHE 0.016 0.001 PHE A 152 TYR 0.012 0.001 TYR A 422 ARG 0.004 0.000 ARG A 32 *********************** 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 93 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7491 (mmmm) cc_final: 0.7242 (ptmm) REVERT: A 208 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7044 (mp) REVERT: A 434 GLU cc_start: 0.6412 (pm20) cc_final: 0.5710 (pp20) REVERT: A 529 GLU cc_start: 0.8036 (mp0) cc_final: 0.7779 (mp0) REVERT: A 593 LYS cc_start: 0.7082 (pptt) cc_final: 0.6562 (mmtt) outliers start: 19 outliers final: 3 residues processed: 86 average time/residue: 1.3969 time to fit residues: 127.6579 Evaluate side-chains 66 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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: 0.7980 chunk 29 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 81 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4719 r_free = 0.4719 target = 0.242377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.222903 restraints weight = 8311.354| |-----------------------------------------------------------------------------| r_work (start): 0.4557 rms_B_bonded: 0.57 r_work: 0.4247 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9751 Z= 0.159 Angle : 0.555 6.843 13880 Z= 0.291 Chirality : 0.034 0.152 1611 Planarity : 0.004 0.039 1231 Dihedral : 21.953 91.751 3060 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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 (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: 1.38 (0.30), residues: 741 helix: 2.56 (0.25), residues: 360 sheet: -0.35 (0.46), residues: 112 loop : -0.83 (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 11 PHE 0.012 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 93 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7455 (mmmm) cc_final: 0.7183 (ptmm) REVERT: A 221 CYS cc_start: 0.6882 (m) cc_final: 0.6681 (m) REVERT: A 560 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6698 (tp-100) REVERT: A 593 LYS cc_start: 0.7089 (pptt) cc_final: 0.6543 (mmtt) outliers start: 21 outliers final: 8 residues processed: 86 average time/residue: 1.4651 time to fit residues: 133.6985 Evaluate side-chains 70 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 366 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 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: 0.9980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 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 835 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.232873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.211939 restraints weight = 8146.773| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 0.62 r_work: 0.4166 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4107 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2135 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= 0.391 Angle : 0.798 9.058 13880 Z= 0.410 Chirality : 0.045 0.177 1611 Planarity : 0.006 0.043 1231 Dihedral : 22.117 94.575 3058 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.85 % Allowed : 16.69 % 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 (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: 0.64 (0.29), residues: 741 helix: 1.72 (0.25), residues: 360 sheet: -0.40 (0.45), residues: 115 loop : -0.97 (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 0.023 0.003 PHE A 411 TYR 0.022 0.003 TYR A 422 ARG 0.009 0.001 ARG A 511 *********************** 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 84 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7843 (mmmm) cc_final: 0.7550 (ptmm) REVERT: A 480 LYS cc_start: 0.6503 (tptm) cc_final: 0.6124 (mttp) REVERT: A 593 LYS cc_start: 0.7079 (pptt) cc_final: 0.6636 (mmtt) REVERT: A 687 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7185 (tp40) outliers start: 24 outliers final: 11 residues processed: 76 average time/residue: 1.5557 time to fit residues: 125.3077 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 : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 437 ASP 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 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: 0.8980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4664 r_free = 0.4664 target = 0.235152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.213189 restraints weight = 8152.421| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 0.59 r_work: 0.4183 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4108 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9751 Z= 0.248 Angle : 0.659 7.764 13880 Z= 0.344 Chirality : 0.038 0.153 1611 Planarity : 0.005 0.039 1231 Dihedral : 22.059 93.038 3058 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.85 % Allowed : 17.82 % 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: 0.84 (0.29), residues: 741 helix: 1.93 (0.25), residues: 360 sheet: -0.26 (0.46), residues: 108 loop : -0.96 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 518 HIS 0.004 0.001 HIS A 11 PHE 0.015 0.002 PHE A 411 TYR 0.016 0.002 TYR A 422 ARG 0.005 0.001 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7765 (mmmm) cc_final: 0.7457 (ptmm) REVERT: A 316 TRP cc_start: 0.6482 (OUTLIER) cc_final: 0.5843 (m-10) REVERT: A 402 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5836 (pp20) REVERT: A 480 LYS cc_start: 0.6461 (tptm) cc_final: 0.6131 (mttp) REVERT: A 593 LYS cc_start: 0.7033 (pptt) cc_final: 0.6570 (mmtt) REVERT: A 687 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7071 (tp40) outliers start: 24 outliers final: 9 residues processed: 75 average time/residue: 1.4852 time to fit residues: 119.1896 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 : 0.803 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 84 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 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 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 = 0.4694 r_free = 0.4694 target = 0.238983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.218464 restraints weight = 8282.401| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 0.60 r_work: 0.4201 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4082 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9751 Z= 0.170 Angle : 0.583 6.638 13880 Z= 0.306 Chirality : 0.035 0.147 1611 Planarity : 0.004 0.037 1231 Dihedral : 21.935 91.552 3058 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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 (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: 1.14 (0.29), residues: 741 helix: 2.28 (0.25), residues: 360 sheet: -0.06 (0.53), residues: 90 loop : -0.97 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 628 HIS 0.002 0.001 HIS A 11 PHE 0.012 0.001 PHE A 152 TYR 0.013 0.001 TYR A 848 ARG 0.005 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 87 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6669 (mm-30) REVERT: A 189 LYS cc_start: 0.7653 (mmmm) cc_final: 0.7334 (ptmm) REVERT: A 316 TRP cc_start: 0.6454 (OUTLIER) cc_final: 0.5891 (m-10) REVERT: A 402 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5919 (pp20) REVERT: A 480 LYS cc_start: 0.6503 (tptm) cc_final: 0.6213 (mttp) REVERT: A 560 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6294 (tp-100) REVERT: A 593 LYS cc_start: 0.7158 (pptt) cc_final: 0.6564 (mmtt) REVERT: A 687 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7087 (tp40) outliers start: 21 outliers final: 8 residues processed: 78 average time/residue: 1.3756 time to fit residues: 114.4093 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 : 0.755 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 25 optimal weight: 0.0570 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: 1.9990 chunk 40 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 81 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.4695 r_free = 0.4695 target = 0.238949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.218239 restraints weight = 8356.346| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 0.61 r_work: 0.4193 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9751 Z= 0.181 Angle : 0.589 7.541 13880 Z= 0.308 Chirality : 0.035 0.148 1611 Planarity : 0.004 0.040 1231 Dihedral : 21.868 91.691 3058 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.05 % Allowed : 19.42 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.29), residues: 741 helix: 2.36 (0.25), residues: 360 sheet: 0.02 (0.53), residues: 90 loop : -0.96 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 628 HIS 0.002 0.001 HIS A 11 PHE 0.011 0.001 PHE A 152 TYR 0.013 0.001 TYR A 422 ARG 0.005 0.000 ARG A 605 *********************** 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 78 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6628 (mm-30) REVERT: A 189 LYS cc_start: 0.7571 (mmmm) cc_final: 0.7264 (ptmm) REVERT: A 316 TRP cc_start: 0.6486 (OUTLIER) cc_final: 0.5936 (m-10) REVERT: A 402 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5863 (pp20) REVERT: A 480 LYS cc_start: 0.6528 (tptm) cc_final: 0.6278 (mttp) REVERT: A 560 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6544 (tp40) REVERT: A 593 LYS cc_start: 0.7123 (pptt) cc_final: 0.6567 (mmtt) REVERT: A 687 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7050 (tp40) outliers start: 19 outliers final: 8 residues processed: 72 average time/residue: 1.4525 time to fit residues: 111.3872 Evaluate side-chains 69 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 10 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- 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 = 0.4685 r_free = 0.4685 target = 0.237841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.218792 restraints weight = 8252.439| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 0.53 r_work: 0.4218 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4141 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9751 Z= 0.215 Angle : 0.633 7.750 13880 Z= 0.329 Chirality : 0.036 0.151 1611 Planarity : 0.004 0.035 1231 Dihedral : 21.838 92.475 3058 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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 : 0.00 % 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: 1.13 (0.30), residues: 741 helix: 2.24 (0.25), residues: 360 sheet: -0.32 (0.46), residues: 112 loop : -0.85 (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 0.012 0.002 PHE A 60 TYR 0.016 0.002 TYR A 422 ARG 0.006 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 80 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6559 (mm-30) REVERT: A 189 LYS cc_start: 0.7599 (mmmm) cc_final: 0.7303 (ptmm) REVERT: A 316 TRP cc_start: 0.6426 (OUTLIER) cc_final: 0.5868 (m-10) REVERT: A 402 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5847 (pp20) REVERT: A 515 GLU cc_start: 0.7037 (tp30) cc_final: 0.6827 (tp30) REVERT: A 560 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6170 (tp-100) REVERT: A 593 LYS cc_start: 0.6946 (pptt) cc_final: 0.6542 (mmtt) REVERT: A 687 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7030 (tp40) outliers start: 20 outliers final: 9 residues processed: 74 average time/residue: 1.4849 time to fit residues: 116.8306 Evaluate side-chains 73 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 631 SER 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 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: 2.9990 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.0030 chunk 82 optimal weight: 8.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.234907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.213742 restraints weight = 8327.803| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 0.62 r_work: 0.4180 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9751 Z= 0.280 Angle : 0.690 8.727 13880 Z= 0.358 Chirality : 0.039 0.163 1611 Planarity : 0.005 0.057 1231 Dihedral : 21.883 93.344 3058 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.73 % Allowed : 20.39 % Favored : 76.89 % 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: 0.92 (0.30), residues: 741 helix: 1.99 (0.25), residues: 360 sheet: -0.36 (0.46), residues: 113 loop : -0.85 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 518 HIS 0.004 0.001 HIS A 11 PHE 0.017 0.002 PHE A 451 TYR 0.018 0.002 TYR A 422 ARG 0.011 0.001 ARG A 559 ********************** 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 74 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6630 (mm-30) REVERT: A 189 LYS cc_start: 0.7769 (mmmm) cc_final: 0.7469 (ptmm) REVERT: A 316 TRP cc_start: 0.6405 (OUTLIER) cc_final: 0.5781 (m-10) REVERT: A 402 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5822 (pp20) REVERT: A 515 GLU cc_start: 0.7261 (tp30) cc_final: 0.7052 (tp30) REVERT: A 560 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6469 (tp40) REVERT: A 593 LYS cc_start: 0.7002 (pptt) cc_final: 0.6558 (mmtt) REVERT: A 687 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7051 (tp40) outliers start: 17 outliers final: 10 residues processed: 69 average time/residue: 1.4281 time to fit residues: 105.1679 Evaluate side-chains 69 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- 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: 4.9990 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 714 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.237889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.216275 restraints weight = 8256.486| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 0.61 r_work: 0.4227 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4171 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2613 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= 0.199 Angle : 0.620 9.100 13880 Z= 0.323 Chirality : 0.036 0.154 1611 Planarity : 0.004 0.037 1231 Dihedral : 21.839 92.007 3058 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.73 % Allowed : 20.39 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.13 (0.30), residues: 741 helix: 2.21 (0.25), residues: 360 sheet: -0.12 (0.49), residues: 104 loop : -0.87 (0.35), residues: 277 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 0.011 0.002 PHE A 60 TYR 0.015 0.002 TYR A 422 ARG 0.008 0.000 ARG A 605 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6610.79 seconds wall clock time: 117 minutes 45.77 seconds (7065.77 seconds total)