Starting phenix.real_space_refine on Fri Nov 15 15:27:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyc_38768/11_2024/8xyc_38768.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyc_38768/11_2024/8xyc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyc_38768/11_2024/8xyc_38768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyc_38768/11_2024/8xyc_38768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyc_38768/11_2024/8xyc_38768.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyc_38768/11_2024/8xyc_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-5513/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: 6.08, per 1000 atoms: 0.66 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: 2.61 Conformation dependent library (CDL) restraints added in 723.3 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: 4.04 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: 4.75 Time building geometry restraints manager: 2.91 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: 0.730 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.960 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: 0.000 Load rotamer database and sin/cos tables:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.780 ------------------------------------------------------------------------------- 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 : 0.868 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: 1.5847 time to fit residues: 202.8983 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 : 0.759 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 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 : 0.659 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7301 (mmm-85) cc_final: 0.6795 (tpt170) REVERT: A 65 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.7143 (mmm-85) REVERT: A 146 GLU cc_start: 0.6760 (mp0) cc_final: 0.6546 (mp0) REVERT: A 189 LYS cc_start: 0.7570 (mmmm) cc_final: 0.7243 (ptmm) REVERT: A 434 GLU cc_start: 0.6398 (pm20) cc_final: 0.5553 (pp20) REVERT: A 593 LYS cc_start: 0.6961 (pptt) cc_final: 0.6637 (mmtt) outliers start: 14 outliers final: 6 residues processed: 74 average time/residue: 1.5474 time to fit residues: 121.3820 Evaluate side-chains 64 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 43 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9751 Z= 0.233 Angle : 0.643 7.751 13880 Z= 0.336 Chirality : 0.038 0.163 1611 Planarity : 0.005 0.033 1231 Dihedral : 22.148 92.517 3060 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.05 % Allowed : 13.80 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.25), residues: 360 sheet: -0.44 (0.47), residues: 112 loop : -0.95 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 628 HIS 0.004 0.001 HIS A 11 PHE 0.016 0.002 PHE A 152 TYR 0.016 0.002 TYR A 422 ARG 0.006 0.001 ARG A 605 *********************** 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 92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7566 (mmmm) cc_final: 0.7250 (ptmm) REVERT: A 593 LYS cc_start: 0.7000 (pptt) cc_final: 0.6597 (mmtt) outliers start: 19 outliers final: 5 residues processed: 85 average time/residue: 1.6629 time to fit residues: 149.2688 Evaluate side-chains 72 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 732 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 9751 Z= 0.400 Angle : 0.814 9.290 13880 Z= 0.420 Chirality : 0.045 0.177 1611 Planarity : 0.006 0.053 1231 Dihedral : 22.269 94.115 3060 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.17 % Allowed : 15.25 % Favored : 80.58 % 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: 0.33 (0.29), residues: 741 helix: 1.46 (0.25), residues: 360 sheet: -0.54 (0.45), residues: 115 loop : -1.11 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 518 HIS 0.006 0.002 HIS A 11 PHE 0.023 0.003 PHE A 411 TYR 0.023 0.003 TYR A 422 ARG 0.010 0.001 ARG A 511 *********************** 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 89 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7699 (mmmm) cc_final: 0.7388 (ptmm) REVERT: A 221 CYS cc_start: 0.7189 (m) cc_final: 0.6870 (m) REVERT: A 480 LYS cc_start: 0.6982 (tptm) cc_final: 0.6226 (mtmt) REVERT: A 529 GLU cc_start: 0.8169 (mp0) cc_final: 0.7944 (mp0) REVERT: A 593 LYS cc_start: 0.7056 (pptt) cc_final: 0.6623 (mmtt) REVERT: A 687 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7274 (tp40) outliers start: 26 outliers final: 11 residues processed: 80 average time/residue: 1.5834 time to fit residues: 134.3065 Evaluate side-chains 71 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 44 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2178 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= 0.197 Angle : 0.613 7.237 13880 Z= 0.322 Chirality : 0.036 0.156 1611 Planarity : 0.004 0.038 1231 Dihedral : 22.115 91.451 3058 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.53 % Allowed : 17.34 % Favored : 79.13 % 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: 0.86 (0.30), residues: 741 helix: 2.00 (0.25), residues: 360 sheet: -0.45 (0.47), residues: 110 loop : -0.93 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 628 HIS 0.003 0.001 HIS A 11 PHE 0.016 0.002 PHE A 152 TYR 0.014 0.002 TYR A 422 ARG 0.004 0.000 ARG A 32 *********************** 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 87 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7344 (mmm-85) cc_final: 0.6907 (tpt170) REVERT: A 189 LYS cc_start: 0.7556 (mmmm) cc_final: 0.7226 (ptmm) REVERT: A 221 CYS cc_start: 0.7016 (m) cc_final: 0.6813 (m) REVERT: A 316 TRP cc_start: 0.6454 (OUTLIER) cc_final: 0.5776 (m-10) REVERT: A 402 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5759 (pp20) REVERT: A 480 LYS cc_start: 0.6886 (tptm) cc_final: 0.6179 (mttp) REVERT: A 529 GLU cc_start: 0.8056 (mp0) cc_final: 0.7806 (mp0) REVERT: A 593 LYS cc_start: 0.6954 (pptt) cc_final: 0.6555 (mmtt) REVERT: A 687 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7133 (tp40) outliers start: 22 outliers final: 7 residues processed: 79 average time/residue: 1.5383 time to fit residues: 128.7843 Evaluate side-chains 72 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 575 ILE Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 732 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2405 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= 0.177 Angle : 0.585 6.919 13880 Z= 0.308 Chirality : 0.035 0.150 1611 Planarity : 0.004 0.037 1231 Dihedral : 22.001 91.010 3058 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.85 % Allowed : 17.66 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.30), residues: 741 helix: 2.25 (0.25), residues: 360 sheet: -0.41 (0.46), residues: 112 loop : -0.97 (0.35), residues: 269 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 0.013 0.001 PHE A 152 TYR 0.013 0.001 TYR A 422 ARG 0.004 0.000 ARG A 32 *********************** 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 93 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7193 (mmm-85) cc_final: 0.6807 (tpt170) REVERT: A 189 LYS cc_start: 0.7411 (mmmm) cc_final: 0.7083 (ptmm) REVERT: A 221 CYS cc_start: 0.6931 (m) cc_final: 0.6688 (m) REVERT: A 316 TRP cc_start: 0.6501 (OUTLIER) cc_final: 0.5890 (m-10) REVERT: A 402 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5762 (pp20) REVERT: A 480 LYS cc_start: 0.6834 (tptm) cc_final: 0.6225 (mttp) REVERT: A 529 GLU cc_start: 0.8112 (mp0) cc_final: 0.7865 (mp0) REVERT: A 593 LYS cc_start: 0.6930 (pptt) cc_final: 0.6537 (mmtt) REVERT: A 687 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7129 (tp40) outliers start: 24 outliers final: 8 residues processed: 84 average time/residue: 1.6710 time to fit residues: 148.9866 Evaluate side-chains 73 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2493 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= 0.183 Angle : 0.592 7.150 13880 Z= 0.310 Chirality : 0.035 0.149 1611 Planarity : 0.004 0.036 1231 Dihedral : 21.933 91.531 3058 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.05 % Allowed : 18.62 % 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: 1.12 (0.29), residues: 741 helix: 2.32 (0.25), residues: 360 sheet: -0.41 (0.45), residues: 112 loop : -0.94 (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 0.014 0.002 PHE A 152 TYR 0.014 0.002 TYR A 422 ARG 0.006 0.000 ARG A 490 *********************** 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 83 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7219 (mmm-85) cc_final: 0.6786 (tpt170) REVERT: A 189 LYS cc_start: 0.7431 (mmmm) cc_final: 0.7100 (ptmm) REVERT: A 221 CYS cc_start: 0.6946 (m) cc_final: 0.6692 (m) REVERT: A 316 TRP cc_start: 0.6443 (OUTLIER) cc_final: 0.5822 (m-10) REVERT: A 480 LYS cc_start: 0.6940 (tptm) cc_final: 0.6308 (mttp) REVERT: A 560 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.6112 (tp-100) REVERT: A 593 LYS cc_start: 0.6909 (pptt) cc_final: 0.6519 (mmtt) REVERT: A 687 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7128 (tp40) outliers start: 19 outliers final: 9 residues processed: 76 average time/residue: 1.5386 time to fit residues: 123.9541 Evaluate side-chains 70 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 560 GLN A 608 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9751 Z= 0.286 Angle : 0.691 8.271 13880 Z= 0.358 Chirality : 0.040 0.160 1611 Planarity : 0.005 0.066 1231 Dihedral : 21.973 92.736 3058 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.01 % Allowed : 18.62 % 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: 0.81 (0.29), residues: 741 helix: 1.95 (0.25), residues: 360 sheet: -0.39 (0.44), residues: 115 loop : -1.00 (0.36), residues: 266 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 0.019 0.002 TYR A 422 ARG 0.007 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 86 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7299 (mmm-85) cc_final: 0.6940 (tpt170) REVERT: A 189 LYS cc_start: 0.7622 (mmmm) cc_final: 0.7297 (ptmm) REVERT: A 221 CYS cc_start: 0.7014 (m) cc_final: 0.6788 (p) REVERT: A 316 TRP cc_start: 0.6492 (OUTLIER) cc_final: 0.5826 (m-10) REVERT: A 339 HIS cc_start: 0.4901 (OUTLIER) cc_final: 0.4265 (t70) REVERT: A 480 LYS cc_start: 0.7034 (tptm) cc_final: 0.6302 (mtmt) REVERT: A 593 LYS cc_start: 0.6971 (pptt) cc_final: 0.6565 (mmtt) REVERT: A 687 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7225 (tp40) outliers start: 25 outliers final: 9 residues processed: 78 average time/residue: 1.6045 time to fit residues: 133.0592 Evaluate side-chains 73 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 339 HIS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 70 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2454 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= 0.233 Angle : 0.648 7.941 13880 Z= 0.337 Chirality : 0.038 0.154 1611 Planarity : 0.005 0.036 1231 Dihedral : 21.928 92.150 3058 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.73 % Allowed : 20.22 % Favored : 77.05 % 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: 0.89 (0.29), residues: 741 helix: 1.98 (0.25), residues: 362 sheet: -0.47 (0.45), residues: 112 loop : -0.86 (0.36), residues: 267 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 0.016 0.002 TYR A 422 ARG 0.006 0.001 ARG A 490 *********************** 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 78 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7285 (mmm-85) cc_final: 0.6906 (tpt170) REVERT: A 189 LYS cc_start: 0.7549 (mmmm) cc_final: 0.7221 (ptmm) REVERT: A 316 TRP cc_start: 0.6445 (OUTLIER) cc_final: 0.5785 (m-10) REVERT: A 480 LYS cc_start: 0.7015 (tptm) cc_final: 0.6344 (mtmt) REVERT: A 560 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.6191 (tp-100) REVERT: A 593 LYS cc_start: 0.6958 (pptt) cc_final: 0.6541 (mmtt) REVERT: A 687 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7206 (tp40) outliers start: 17 outliers final: 10 residues processed: 73 average time/residue: 1.6003 time to fit residues: 123.8545 Evaluate side-chains 72 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 487 GLN 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 86 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 560 GLN A 608 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2490 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= 0.232 Angle : 0.656 9.105 13880 Z= 0.339 Chirality : 0.037 0.157 1611 Planarity : 0.005 0.036 1231 Dihedral : 21.886 92.001 3058 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.89 % Allowed : 20.06 % Favored : 77.05 % 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: 1.99 (0.25), residues: 362 sheet: -0.46 (0.45), residues: 114 loop : -0.92 (0.36), residues: 265 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 152 TYR 0.016 0.002 TYR A 422 ARG 0.007 0.001 ARG A 490 ********************** 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 75 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7361 (mmm-85) cc_final: 0.6854 (tpt170) REVERT: A 189 LYS cc_start: 0.7541 (mmmm) cc_final: 0.7212 (ptmm) REVERT: A 316 TRP cc_start: 0.6422 (OUTLIER) cc_final: 0.5757 (m-10) REVERT: A 480 LYS cc_start: 0.6962 (tptm) cc_final: 0.6383 (mtmt) REVERT: A 560 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.6218 (tp-100) REVERT: A 593 LYS cc_start: 0.6955 (pptt) cc_final: 0.6540 (mmtt) REVERT: A 687 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7203 (tp40) outliers start: 18 outliers final: 10 residues processed: 69 average time/residue: 1.5441 time to fit residues: 113.0699 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 : 0.743 ------------------------------------------------------------------------------- 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 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 487 GLN 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 19 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.0040 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 560 GLN A 608 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.238279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.217650 restraints weight = 8235.981| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 0.59 r_work: 0.4279 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.4231 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9751 Z= 0.175 Angle : 0.599 9.079 13880 Z= 0.311 Chirality : 0.035 0.158 1611 Planarity : 0.004 0.038 1231 Dihedral : 21.801 91.286 3058 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.05 % Allowed : 19.90 % Favored : 77.05 % 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: 1.10 (0.30), residues: 741 helix: 2.25 (0.25), residues: 362 sheet: -0.34 (0.46), residues: 112 loop : -0.93 (0.35), residues: 267 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 0.012 0.001 PHE A 152 TYR 0.012 0.001 TYR A 848 ARG 0.007 0.000 ARG A 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.82 seconds wall clock time: 55 minutes 53.31 seconds (3353.31 seconds total)