Starting phenix.real_space_refine on Fri Aug 22 19:11:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfy_33801/08_2025/7yfy_33801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfy_33801/08_2025/7yfy_33801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yfy_33801/08_2025/7yfy_33801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfy_33801/08_2025/7yfy_33801.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfy_33801/08_2025/7yfy_33801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfy_33801/08_2025/7yfy_33801.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.124 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: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 4172 2.51 5 N 1172 2.21 5 O 1339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6770 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5898 Classifications: {'peptide': 734} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 697} Chain breaks: 3 Chain: "C" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 320 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 550 Classifications: {'RNA': 26} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 10, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.98, per 1000 atoms: 0.29 Number of scatterers: 6770 At special positions: 0 Unit cell: (73.916, 85.873, 114.135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 41 15.00 Mg 2 11.99 O 1339 8.00 N 1172 7.00 C 4172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 378.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 38.0% alpha, 19.3% beta 12 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.558A pdb=" N HIS A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.893A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.538A pdb=" N TYR A 321 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 removed outlier: 3.578A pdb=" N VAL A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.806A pdb=" N LYS A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 removed outlier: 3.590A pdb=" N GLN A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 540 removed outlier: 3.541A pdb=" N ASN A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 586 through 593 removed outlier: 3.544A pdb=" N VAL A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 591 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.505A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 removed outlier: 3.785A pdb=" N ILE A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 662 removed outlier: 3.632A pdb=" N TYR A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.500A pdb=" N TYR A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.889A pdb=" N GLN A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'A' and resid 778 through 802 removed outlier: 4.292A pdb=" N VAL A 783 " --> pdb=" O HIS A 779 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP A 784 " --> pdb=" O GLN A 780 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 4.427A pdb=" N LYS A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR A 822 " --> pdb=" O GLY A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 834 through 838 Processing helix chain 'A' and resid 914 through 926 Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 962 through 967 removed outlier: 4.073A pdb=" N GLY A 966 " --> pdb=" O GLN A 963 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 769 through 774 removed outlier: 3.549A pdb=" N VAL A 774 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 756 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 743 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL A 739 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL A 744 " --> pdb=" O ASP A 813 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 808 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A 848 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 810 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL A 850 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG A 812 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N MET A 845 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN A 909 " --> pdb=" O MET A 845 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL A 847 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS A 903 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER A 223 " --> pdb=" O ALA A 861 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 231 removed outlier: 4.554A pdb=" N LEU A 372 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 341 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 removed outlier: 7.131A pdb=" N GLN A 240 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 426 Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.676A pdb=" N ASP A 429 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 577 through 579 Processing sheet with id=AA8, first strand: chain 'A' and resid 638 through 642 removed outlier: 6.817A pdb=" N TRP A 604 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL A 640 " --> pdb=" O TRP A 604 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 606 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A 642 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR A 608 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL A 667 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE A 697 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS A 669 " --> pdb=" O ILE A 697 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1256 1.33 - 1.45: 1857 1.45 - 1.57: 3738 1.57 - 1.69: 80 1.69 - 1.81: 69 Bond restraints: 7000 Sorted by residual: bond pdb=" N ARG A 510 " pdb=" CA ARG A 510 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.17e-02 7.31e+03 7.07e+00 bond pdb=" N ARG A 707 " pdb=" CA ARG A 707 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.06e-02 8.90e+03 6.31e+00 bond pdb=" N ASN A 422 " pdb=" CA ASN A 422 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.16e+00 bond pdb=" N LYS A 943 " pdb=" CA LYS A 943 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.88e+00 bond pdb=" N ASP A 645 " pdb=" CA ASP A 645 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.35e-02 5.49e+03 5.87e+00 ... (remaining 6995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 9142 1.71 - 3.42: 429 3.42 - 5.13: 85 5.13 - 6.84: 16 6.84 - 8.55: 3 Bond angle restraints: 9675 Sorted by residual: angle pdb=" N ASN A 422 " pdb=" CA ASN A 422 " pdb=" C ASN A 422 " ideal model delta sigma weight residual 113.23 105.49 7.74 1.24e+00 6.50e-01 3.90e+01 angle pdb=" C LYS A 506 " pdb=" CA LYS A 506 " pdb=" CB LYS A 506 " ideal model delta sigma weight residual 110.88 102.33 8.55 1.57e+00 4.06e-01 2.97e+01 angle pdb=" C3' OMC B 26 " pdb=" C2' OMC B 26 " pdb=" C1' OMC B 26 " ideal model delta sigma weight residual 101.50 106.27 -4.77 1.00e+00 1.00e+00 2.27e+01 angle pdb=" C CYS A 317 " pdb=" N ILE A 318 " pdb=" CA ILE A 318 " ideal model delta sigma weight residual 120.33 124.00 -3.67 8.00e-01 1.56e+00 2.11e+01 angle pdb=" N TYR A 420 " pdb=" CA TYR A 420 " pdb=" C TYR A 420 " ideal model delta sigma weight residual 112.34 106.92 5.42 1.30e+00 5.92e-01 1.74e+01 ... (remaining 9670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 4023 35.22 - 70.44: 211 70.44 - 105.66: 25 105.66 - 140.87: 0 140.87 - 176.09: 2 Dihedral angle restraints: 4261 sinusoidal: 2112 harmonic: 2149 Sorted by residual: dihedral pdb=" O4' U B 20 " pdb=" C1' U B 20 " pdb=" N1 U B 20 " pdb=" C2 U B 20 " ideal model delta sinusoidal sigma weight residual 232.00 55.91 176.09 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B 19 " pdb=" C1' C B 19 " pdb=" N1 C B 19 " pdb=" C2 C B 19 " ideal model delta sinusoidal sigma weight residual 232.00 60.07 171.93 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' U B 21 " pdb=" C1' U B 21 " pdb=" N1 U B 21 " pdb=" C2 U B 21 " ideal model delta sinusoidal sigma weight residual -128.00 -57.44 -70.56 1 1.70e+01 3.46e-03 2.22e+01 ... (remaining 4258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 909 0.056 - 0.112: 180 0.112 - 0.168: 40 0.168 - 0.224: 2 0.224 - 0.280: 1 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CA LYS A 506 " pdb=" N LYS A 506 " pdb=" C LYS A 506 " pdb=" CB LYS A 506 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE A 383 " pdb=" N ILE A 383 " pdb=" C ILE A 383 " pdb=" CB ILE A 383 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA ARG A 895 " pdb=" N ARG A 895 " pdb=" C ARG A 895 " pdb=" CB ARG A 895 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 1129 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 704 " -0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 705 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 705 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 705 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 241 " 0.010 2.00e-02 2.50e+03 1.65e-02 5.42e+00 pdb=" CG TYR A 241 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 241 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 241 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 241 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 241 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 241 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 241 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 333 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C ASP A 333 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP A 333 " 0.015 2.00e-02 2.50e+03 pdb=" N MET A 334 " 0.013 2.00e-02 2.50e+03 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 28 2.51 - 3.11: 4778 3.11 - 3.71: 10379 3.71 - 4.30: 14501 4.30 - 4.90: 23477 Nonbonded interactions: 53163 Sorted by model distance: nonbonded pdb=" OD2 ASP A 743 " pdb="MG MG A1002 " model vdw 1.918 2.170 nonbonded pdb=" OP1 A B 3 " pdb="MG MG A1001 " model vdw 1.977 2.170 nonbonded pdb=" OXT LEU A 971 " pdb="MG MG A1001 " model vdw 2.055 2.170 nonbonded pdb=" O2' G B 22 " pdb=" N2 G B 23 " model vdw 2.142 3.120 nonbonded pdb=" OE1 GLN A 718 " pdb="MG MG A1001 " model vdw 2.196 2.170 ... (remaining 53158 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 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 0.043 7000 Z= 0.240 Angle : 0.862 8.549 9675 Z= 0.483 Chirality : 0.049 0.280 1132 Planarity : 0.006 0.084 1071 Dihedral : 19.540 176.092 2869 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 1.35 % Allowed : 15.32 % Favored : 83.33 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.30), residues: 726 helix: 0.82 (0.34), residues: 224 sheet: -1.22 (0.38), residues: 168 loop : -1.91 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 339 TYR 0.039 0.002 TYR A 241 PHE 0.015 0.002 PHE A 325 TRP 0.009 0.001 TRP A 358 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 7000) covalent geometry : angle 0.86163 ( 9675) hydrogen bonds : bond 0.17105 ( 283) hydrogen bonds : angle 7.10056 ( 759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.7284 (mmt) cc_final: 0.6856 (mmm) REVERT: A 496 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.7561 (p) REVERT: A 706 THR cc_start: 0.7834 (p) cc_final: 0.7631 (p) REVERT: A 737 LEU cc_start: 0.7669 (pt) cc_final: 0.7446 (pt) REVERT: A 752 MET cc_start: 0.5399 (tpt) cc_final: 0.4996 (tmm) REVERT: A 753 ARG cc_start: 0.6931 (mmm-85) cc_final: 0.5804 (mtm110) outliers start: 9 outliers final: 2 residues processed: 91 average time/residue: 0.1037 time to fit residues: 12.3280 Evaluate side-chains 76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 509 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.225516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.174158 restraints weight = 8111.021| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 3.29 r_work: 0.3940 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7000 Z= 0.149 Angle : 0.647 5.966 9675 Z= 0.335 Chirality : 0.045 0.174 1132 Planarity : 0.005 0.052 1071 Dihedral : 19.932 175.562 1407 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.70 % Allowed : 15.62 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.31), residues: 726 helix: 1.43 (0.34), residues: 237 sheet: -1.03 (0.39), residues: 168 loop : -1.87 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 510 TYR 0.013 0.002 TYR A 454 PHE 0.011 0.002 PHE A 325 TRP 0.007 0.001 TRP A 358 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7000) covalent geometry : angle 0.64719 ( 9675) hydrogen bonds : bond 0.04353 ( 283) hydrogen bonds : angle 5.36179 ( 759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.252 Fit side-chains REVERT: A 242 HIS cc_start: 0.7713 (m-70) cc_final: 0.7440 (m-70) REVERT: A 258 MET cc_start: 0.7590 (mmt) cc_final: 0.7340 (mmm) REVERT: A 335 LYS cc_start: 0.7105 (mmtt) cc_final: 0.6720 (mmmt) REVERT: A 361 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.6932 (p90) REVERT: A 396 TYR cc_start: 0.6244 (OUTLIER) cc_final: 0.5978 (t80) REVERT: A 450 PHE cc_start: 0.5978 (OUTLIER) cc_final: 0.5550 (t80) REVERT: A 514 ASP cc_start: 0.8557 (m-30) cc_final: 0.8178 (p0) REVERT: A 752 MET cc_start: 0.5399 (tpt) cc_final: 0.4642 (tmm) REVERT: A 753 ARG cc_start: 0.6908 (mmm-85) cc_final: 0.6533 (mmt180) outliers start: 18 outliers final: 9 residues processed: 99 average time/residue: 0.0806 time to fit residues: 11.0444 Evaluate side-chains 88 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.197751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.133777 restraints weight = 8224.113| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.97 r_work: 0.3569 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7000 Z= 0.249 Angle : 0.721 7.196 9675 Z= 0.369 Chirality : 0.047 0.164 1132 Planarity : 0.005 0.050 1071 Dihedral : 19.903 177.918 1400 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.60 % Allowed : 18.32 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.31), residues: 726 helix: 1.32 (0.34), residues: 224 sheet: -1.23 (0.37), residues: 185 loop : -1.63 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 652 TYR 0.019 0.002 TYR A 425 PHE 0.015 0.002 PHE A 325 TRP 0.012 0.002 TRP A 358 HIS 0.012 0.002 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 7000) covalent geometry : angle 0.72053 ( 9675) hydrogen bonds : bond 0.04982 ( 283) hydrogen bonds : angle 5.28093 ( 759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.243 Fit side-chains REVERT: A 242 HIS cc_start: 0.8093 (m-70) cc_final: 0.7566 (m-70) REVERT: A 269 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6792 (p) REVERT: A 335 LYS cc_start: 0.7217 (mmtt) cc_final: 0.6994 (mmmt) REVERT: A 361 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.6690 (p90) REVERT: A 450 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.5458 (t80) REVERT: A 505 MET cc_start: 0.8331 (tpp) cc_final: 0.7900 (tpp) REVERT: A 514 ASP cc_start: 0.8438 (m-30) cc_final: 0.8135 (p0) REVERT: A 752 MET cc_start: 0.4973 (tpt) cc_final: 0.4530 (tmm) REVERT: A 753 ARG cc_start: 0.6909 (mmm-85) cc_final: 0.6474 (mmt180) outliers start: 24 outliers final: 16 residues processed: 92 average time/residue: 0.0695 time to fit residues: 9.3456 Evaluate side-chains 88 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 420 TYR Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 70 optimal weight: 0.2980 chunk 46 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 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 = 0.4494 r_free = 0.4494 target = 0.201077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.151833 restraints weight = 8211.354| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.73 r_work: 0.3564 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7000 Z= 0.133 Angle : 0.601 6.227 9675 Z= 0.307 Chirality : 0.044 0.178 1132 Planarity : 0.004 0.043 1071 Dihedral : 19.789 178.787 1400 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.90 % Allowed : 18.17 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.31), residues: 726 helix: 1.67 (0.35), residues: 224 sheet: -1.11 (0.38), residues: 173 loop : -1.64 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 652 TYR 0.011 0.001 TYR A 454 PHE 0.012 0.001 PHE A 325 TRP 0.008 0.001 TRP A 586 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7000) covalent geometry : angle 0.60055 ( 9675) hydrogen bonds : bond 0.03928 ( 283) hydrogen bonds : angle 4.95629 ( 759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.167 Fit side-chains REVERT: A 239 TYR cc_start: 0.6619 (m-10) cc_final: 0.6024 (m-10) REVERT: A 242 HIS cc_start: 0.8151 (m-70) cc_final: 0.7651 (m-70) REVERT: A 329 MET cc_start: 0.7036 (mmm) cc_final: 0.6746 (mpp) REVERT: A 361 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.6677 (p90) REVERT: A 450 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.5275 (t80) REVERT: A 505 MET cc_start: 0.8244 (tpp) cc_final: 0.7830 (tpp) REVERT: A 512 MET cc_start: 0.5690 (ttt) cc_final: 0.5241 (ttp) REVERT: A 568 MET cc_start: 0.7448 (mtp) cc_final: 0.7190 (mtm) REVERT: A 752 MET cc_start: 0.4902 (tpt) cc_final: 0.4545 (tmm) REVERT: A 753 ARG cc_start: 0.6756 (mmm-85) cc_final: 0.5779 (mtm110) REVERT: A 964 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7673 (mt) outliers start: 26 outliers final: 17 residues processed: 91 average time/residue: 0.0594 time to fit residues: 7.9381 Evaluate side-chains 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.199145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136040 restraints weight = 8307.321| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.03 r_work: 0.3592 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7000 Z= 0.186 Angle : 0.638 6.366 9675 Z= 0.326 Chirality : 0.045 0.157 1132 Planarity : 0.004 0.042 1071 Dihedral : 19.745 179.783 1400 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.35 % Allowed : 18.47 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.31), residues: 726 helix: 1.55 (0.35), residues: 225 sheet: -1.19 (0.37), residues: 185 loop : -1.67 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.015 0.002 TYR A 770 PHE 0.014 0.002 PHE A 325 TRP 0.010 0.002 TRP A 930 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 7000) covalent geometry : angle 0.63785 ( 9675) hydrogen bonds : bond 0.04204 ( 283) hydrogen bonds : angle 4.94880 ( 759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.193 Fit side-chains REVERT: A 239 TYR cc_start: 0.6660 (m-10) cc_final: 0.5992 (m-10) REVERT: A 242 HIS cc_start: 0.8218 (m-70) cc_final: 0.7818 (m-70) REVERT: A 300 ILE cc_start: 0.6363 (OUTLIER) cc_final: 0.5486 (mp) REVERT: A 361 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.6592 (p90) REVERT: A 427 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6721 (tp) REVERT: A 441 VAL cc_start: 0.3265 (OUTLIER) cc_final: 0.3000 (p) REVERT: A 450 PHE cc_start: 0.5888 (OUTLIER) cc_final: 0.5334 (t80) REVERT: A 512 MET cc_start: 0.5756 (ttt) cc_final: 0.5397 (ttp) REVERT: A 752 MET cc_start: 0.4891 (tpt) cc_final: 0.4441 (tmm) REVERT: A 753 ARG cc_start: 0.6274 (mmm-85) cc_final: 0.6036 (mpt180) REVERT: A 964 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7643 (mt) outliers start: 29 outliers final: 19 residues processed: 95 average time/residue: 0.0702 time to fit residues: 9.3904 Evaluate side-chains 93 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 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 421 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 = 0.4628 r_free = 0.4628 target = 0.211081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.160248 restraints weight = 8102.535| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 3.34 r_work: 0.3742 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7000 Z= 0.117 Angle : 0.578 7.864 9675 Z= 0.293 Chirality : 0.043 0.167 1132 Planarity : 0.004 0.038 1071 Dihedral : 19.596 179.035 1400 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.60 % Allowed : 20.12 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.31), residues: 726 helix: 1.81 (0.35), residues: 224 sheet: -1.08 (0.38), residues: 173 loop : -1.72 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 707 TYR 0.009 0.001 TYR A 454 PHE 0.018 0.001 PHE A 256 TRP 0.008 0.001 TRP A 586 HIS 0.002 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7000) covalent geometry : angle 0.57803 ( 9675) hydrogen bonds : bond 0.03532 ( 283) hydrogen bonds : angle 4.78059 ( 759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.257 Fit side-chains REVERT: A 239 TYR cc_start: 0.6749 (m-10) cc_final: 0.6126 (m-10) REVERT: A 242 HIS cc_start: 0.8170 (m-70) cc_final: 0.7786 (m-70) REVERT: A 300 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.5538 (mp) REVERT: A 329 MET cc_start: 0.7171 (mmm) cc_final: 0.6856 (mpp) REVERT: A 361 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.6630 (p90) REVERT: A 427 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6840 (tp) REVERT: A 441 VAL cc_start: 0.3265 (OUTLIER) cc_final: 0.2995 (p) REVERT: A 450 PHE cc_start: 0.6170 (OUTLIER) cc_final: 0.5502 (t80) REVERT: A 451 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6885 (mm) REVERT: A 505 MET cc_start: 0.8286 (tpp) cc_final: 0.7754 (tpp) REVERT: A 512 MET cc_start: 0.5819 (ttt) cc_final: 0.5264 (ttp) REVERT: A 752 MET cc_start: 0.4930 (tpt) cc_final: 0.4611 (tmm) outliers start: 24 outliers final: 11 residues processed: 88 average time/residue: 0.0806 time to fit residues: 10.0037 Evaluate side-chains 82 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 30 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 4 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 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 = 0.4601 r_free = 0.4601 target = 0.207638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.157543 restraints weight = 8089.056| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.37 r_work: 0.3679 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7000 Z= 0.204 Angle : 0.648 6.388 9675 Z= 0.329 Chirality : 0.045 0.156 1132 Planarity : 0.005 0.042 1071 Dihedral : 19.616 177.089 1400 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.35 % Allowed : 19.82 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.31), residues: 726 helix: 1.58 (0.35), residues: 224 sheet: -1.11 (0.38), residues: 178 loop : -1.79 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.015 0.002 TYR A 770 PHE 0.014 0.002 PHE A 325 TRP 0.010 0.002 TRP A 930 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 7000) covalent geometry : angle 0.64763 ( 9675) hydrogen bonds : bond 0.04204 ( 283) hydrogen bonds : angle 4.93775 ( 759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.247 Fit side-chains REVERT: A 239 TYR cc_start: 0.6777 (m-10) cc_final: 0.6128 (m-10) REVERT: A 242 HIS cc_start: 0.8086 (m-70) cc_final: 0.7664 (m-70) REVERT: A 300 ILE cc_start: 0.6441 (OUTLIER) cc_final: 0.5591 (mt) REVERT: A 361 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.6700 (p90) REVERT: A 427 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6956 (tp) REVERT: A 450 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5513 (t80) REVERT: A 451 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6932 (mm) REVERT: A 512 MET cc_start: 0.5877 (ttt) cc_final: 0.5535 (ttp) REVERT: A 752 MET cc_start: 0.4641 (tpt) cc_final: 0.4416 (tmm) REVERT: A 964 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7881 (mt) outliers start: 29 outliers final: 16 residues processed: 96 average time/residue: 0.0610 time to fit residues: 8.6573 Evaluate side-chains 90 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.2980 chunk 67 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 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 = 0.4627 r_free = 0.4627 target = 0.210991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.160705 restraints weight = 8101.499| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 3.36 r_work: 0.3743 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7000 Z= 0.116 Angle : 0.582 7.170 9675 Z= 0.294 Chirality : 0.042 0.160 1132 Planarity : 0.004 0.036 1071 Dihedral : 19.515 177.329 1400 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.05 % Allowed : 20.12 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.31), residues: 726 helix: 1.77 (0.35), residues: 225 sheet: -1.10 (0.39), residues: 174 loop : -1.78 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.009 0.001 TYR A 454 PHE 0.012 0.001 PHE A 325 TRP 0.007 0.001 TRP A 586 HIS 0.003 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7000) covalent geometry : angle 0.58220 ( 9675) hydrogen bonds : bond 0.03519 ( 283) hydrogen bonds : angle 4.74611 ( 759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.248 Fit side-chains REVERT: A 239 TYR cc_start: 0.6606 (m-10) cc_final: 0.5975 (m-10) REVERT: A 242 HIS cc_start: 0.8131 (m-70) cc_final: 0.7703 (m-70) REVERT: A 300 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5292 (mt) REVERT: A 361 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6523 (p90) REVERT: A 427 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.7012 (tp) REVERT: A 450 PHE cc_start: 0.6204 (OUTLIER) cc_final: 0.5544 (t80) REVERT: A 451 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7042 (mm) REVERT: A 505 MET cc_start: 0.8281 (tpp) cc_final: 0.7499 (tpp) REVERT: A 512 MET cc_start: 0.5769 (ttt) cc_final: 0.5235 (ttp) REVERT: A 568 MET cc_start: 0.7619 (mtp) cc_final: 0.7402 (mtm) REVERT: A 752 MET cc_start: 0.4876 (tpt) cc_final: 0.4423 (tmm) REVERT: A 964 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7865 (mt) outliers start: 27 outliers final: 15 residues processed: 91 average time/residue: 0.0710 time to fit residues: 9.4030 Evaluate side-chains 89 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 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 = 0.4606 r_free = 0.4606 target = 0.208498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.157919 restraints weight = 8138.277| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 3.31 r_work: 0.3697 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7000 Z= 0.181 Angle : 0.634 6.731 9675 Z= 0.321 Chirality : 0.044 0.151 1132 Planarity : 0.004 0.041 1071 Dihedral : 19.526 175.527 1400 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.20 % Allowed : 19.82 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.31), residues: 726 helix: 1.59 (0.35), residues: 225 sheet: -1.11 (0.38), residues: 179 loop : -1.77 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 327 TYR 0.018 0.002 TYR A 770 PHE 0.013 0.002 PHE A 325 TRP 0.009 0.001 TRP A 586 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 7000) covalent geometry : angle 0.63351 ( 9675) hydrogen bonds : bond 0.04045 ( 283) hydrogen bonds : angle 4.87371 ( 759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.245 Fit side-chains REVERT: A 239 TYR cc_start: 0.6806 (m-10) cc_final: 0.6149 (m-10) REVERT: A 242 HIS cc_start: 0.8005 (m-70) cc_final: 0.7596 (m-70) REVERT: A 256 PHE cc_start: 0.7195 (m-10) cc_final: 0.6950 (m-80) REVERT: A 300 ILE cc_start: 0.6194 (OUTLIER) cc_final: 0.5323 (mt) REVERT: A 361 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.6813 (p90) REVERT: A 427 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7102 (tp) REVERT: A 450 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5483 (t80) REVERT: A 451 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7029 (mm) REVERT: A 505 MET cc_start: 0.8315 (tpp) cc_final: 0.7535 (tpp) REVERT: A 512 MET cc_start: 0.6053 (ttt) cc_final: 0.5671 (ttp) REVERT: A 726 GLU cc_start: 0.7401 (mp0) cc_final: 0.6752 (mp0) REVERT: A 752 MET cc_start: 0.4990 (tpt) cc_final: 0.4583 (tmm) REVERT: A 964 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7965 (mt) outliers start: 28 outliers final: 19 residues processed: 92 average time/residue: 0.0591 time to fit residues: 8.2320 Evaluate side-chains 92 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 0.5980 chunk 28 optimal weight: 0.0470 chunk 73 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 63 optimal weight: 0.0070 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 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 = 0.4641 r_free = 0.4641 target = 0.212632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.161099 restraints weight = 8049.488| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 3.29 r_work: 0.3762 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7000 Z= 0.107 Angle : 0.572 7.598 9675 Z= 0.288 Chirality : 0.042 0.152 1132 Planarity : 0.004 0.036 1071 Dihedral : 19.395 176.491 1400 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.45 % Allowed : 20.57 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.32), residues: 726 helix: 1.82 (0.35), residues: 229 sheet: -0.97 (0.39), residues: 173 loop : -1.77 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.009 0.001 TYR A 888 PHE 0.012 0.001 PHE A 325 TRP 0.006 0.001 TRP A 586 HIS 0.005 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7000) covalent geometry : angle 0.57224 ( 9675) hydrogen bonds : bond 0.03345 ( 283) hydrogen bonds : angle 4.66939 ( 759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.211 Fit side-chains REVERT: A 239 TYR cc_start: 0.6672 (m-10) cc_final: 0.6234 (m-80) REVERT: A 242 HIS cc_start: 0.7972 (m-70) cc_final: 0.7625 (m-70) REVERT: A 300 ILE cc_start: 0.5875 (OUTLIER) cc_final: 0.5023 (mt) REVERT: A 361 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.6514 (p90) REVERT: A 450 PHE cc_start: 0.6062 (OUTLIER) cc_final: 0.5423 (t80) REVERT: A 451 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7062 (mm) REVERT: A 505 MET cc_start: 0.8307 (tpp) cc_final: 0.7498 (tpp) REVERT: A 512 MET cc_start: 0.5908 (ttt) cc_final: 0.5347 (ttp) REVERT: A 726 GLU cc_start: 0.7511 (mp0) cc_final: 0.6931 (mp0) REVERT: A 767 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7764 (t) REVERT: A 794 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5853 (mm) REVERT: A 964 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7930 (mt) outliers start: 23 outliers final: 13 residues processed: 89 average time/residue: 0.0627 time to fit residues: 8.2000 Evaluate side-chains 90 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 63 optimal weight: 0.0010 chunk 65 optimal weight: 0.8980 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 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 = 0.4613 r_free = 0.4613 target = 0.209631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.159935 restraints weight = 8100.106| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 3.55 r_work: 0.3700 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7000 Z= 0.171 Angle : 0.641 13.376 9675 Z= 0.320 Chirality : 0.044 0.151 1132 Planarity : 0.004 0.037 1071 Dihedral : 19.392 177.788 1400 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.60 % Allowed : 20.72 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.32), residues: 726 helix: 1.70 (0.35), residues: 229 sheet: -1.02 (0.37), residues: 185 loop : -1.76 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 753 TYR 0.012 0.002 TYR A 650 PHE 0.051 0.002 PHE A 256 TRP 0.024 0.002 TRP A 586 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7000) covalent geometry : angle 0.64125 ( 9675) hydrogen bonds : bond 0.03874 ( 283) hydrogen bonds : angle 4.77724 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.50 seconds wall clock time: 30 minutes 23.51 seconds (1823.51 seconds total)