Starting phenix.real_space_refine on Wed Mar 12 02:55:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfy_33801/03_2025/7yfy_33801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfy_33801/03_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_33801/03_2025/7yfy_33801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfy_33801/03_2025/7yfy_33801.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfy_33801/03_2025/7yfy_33801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfy_33801/03_2025/7yfy_33801.cif" } resolution = 3.4 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= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.37, per 1000 atoms: 0.65 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: 1.83 Conformation dependent library (CDL) restraints added in 650.5 milliseconds 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: 2.19 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: 2.75 Time building geometry restraints manager: 2.13 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.920 Find NCS groups from input model: 0.070 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.550 ------------------------------------------------------------------------------- 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= 0.297 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 (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: -1.34 (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 TRP 0.009 0.001 TRP A 358 HIS 0.007 0.001 HIS A 526 PHE 0.015 0.002 PHE A 325 TYR 0.039 0.002 TYR A 241 ARG 0.005 0.001 ARG A 339 *********************** 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 : 0.669 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: 0.7562 (p) REVERT: A 706 THR cc_start: 0.7834 (p) cc_final: 0.7632 (p) REVERT: A 737 LEU cc_start: 0.7669 (pt) cc_final: 0.7445 (pt) REVERT: A 752 MET cc_start: 0.5399 (tpt) cc_final: 0.4975 (tmm) REVERT: A 753 ARG cc_start: 0.6931 (mmm-85) cc_final: 0.6708 (mmt180) outliers start: 9 outliers final: 2 residues processed: 91 average time/residue: 0.2212 time to fit residues: 26.4725 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 : 0.774 ------------------------------------------------------------------------------- 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 64 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 = 0.4647 r_free = 0.4647 target = 0.211418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.160587 restraints weight = 8087.444| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 3.08 r_work: 0.3747 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7000 Z= 0.387 Angle : 0.745 6.957 9675 Z= 0.384 Chirality : 0.048 0.161 1132 Planarity : 0.005 0.055 1071 Dihedral : 20.049 175.732 1407 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.23 % Favored : 94.63 % Rotamer: Outliers : 3.30 % Allowed : 17.42 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.11 (0.31), residues: 726 helix: 1.10 (0.34), residues: 231 sheet: -1.27 (0.37), residues: 185 loop : -1.79 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 358 HIS 0.010 0.002 HIS A 526 PHE 0.014 0.002 PHE A 325 TYR 0.017 0.002 TYR A 454 ARG 0.007 0.001 ARG A 367 *********************** 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 105 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.742 Fit side-chains REVERT: A 242 HIS cc_start: 0.7962 (m-70) cc_final: 0.7603 (m-70) REVERT: A 335 LYS cc_start: 0.7226 (mmtt) cc_final: 0.6933 (mmmt) REVERT: A 361 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.6899 (p90) REVERT: A 396 TYR cc_start: 0.6238 (OUTLIER) cc_final: 0.5982 (t80) REVERT: A 450 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5495 (t80) REVERT: A 514 ASP cc_start: 0.8628 (m-30) cc_final: 0.8194 (p0) REVERT: A 752 MET cc_start: 0.5223 (tpt) cc_final: 0.4529 (tmm) REVERT: A 753 ARG cc_start: 0.7056 (mmm-85) cc_final: 0.6625 (mmt180) outliers start: 22 outliers final: 12 residues processed: 100 average time/residue: 0.1657 time to fit residues: 23.0706 Evaluate side-chains 85 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE 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 411 LEU 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 575 ASN 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 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 28 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 64 optimal weight: 0.0000 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.197893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.147965 restraints weight = 8252.234| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.80 r_work: 0.3513 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7000 Z= 0.334 Angle : 0.683 6.477 9675 Z= 0.350 Chirality : 0.046 0.161 1132 Planarity : 0.005 0.047 1071 Dihedral : 19.925 177.598 1402 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.45 % Allowed : 19.37 % 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 (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: -0.97 (0.31), residues: 726 helix: 1.36 (0.34), residues: 223 sheet: -1.34 (0.37), residues: 185 loop : -1.65 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 586 HIS 0.007 0.001 HIS A 526 PHE 0.014 0.002 PHE A 325 TYR 0.018 0.002 TYR A 425 ARG 0.004 0.000 ARG A 652 *********************** 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 93 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.686 Fit side-chains REVERT: A 242 HIS cc_start: 0.8121 (m-70) cc_final: 0.7561 (m-70) REVERT: A 269 VAL cc_start: 0.7281 (OUTLIER) cc_final: 0.6857 (p) REVERT: A 361 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.6747 (p90) REVERT: A 450 PHE cc_start: 0.5888 (OUTLIER) cc_final: 0.5361 (t80) REVERT: A 505 MET cc_start: 0.8189 (tpp) cc_final: 0.7876 (tpp) REVERT: A 530 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7412 (mt) REVERT: A 613 MET cc_start: 0.7078 (mmm) cc_final: 0.6797 (mmm) REVERT: A 752 MET cc_start: 0.4865 (tpt) cc_final: 0.4395 (tmm) REVERT: A 753 ARG cc_start: 0.6854 (mmm-85) cc_final: 0.6468 (mpt180) outliers start: 23 outliers final: 15 residues processed: 86 average time/residue: 0.1568 time to fit residues: 19.3445 Evaluate side-chains 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE 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 450 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 666 MET 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 913 LEU Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.0050 chunk 47 optimal weight: 2.9990 overall best weight: 0.4772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 927 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.203192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.151609 restraints weight = 8166.676| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.35 r_work: 0.3627 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7000 Z= 0.153 Angle : 0.574 5.968 9675 Z= 0.293 Chirality : 0.043 0.180 1132 Planarity : 0.004 0.042 1071 Dihedral : 19.716 178.771 1400 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.90 % Allowed : 18.62 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.31), residues: 726 helix: 1.75 (0.35), residues: 225 sheet: -1.08 (0.39), residues: 168 loop : -1.62 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 586 HIS 0.002 0.000 HIS A 927 PHE 0.009 0.001 PHE A 325 TYR 0.009 0.001 TYR A 826 ARG 0.002 0.000 ARG A 327 *********************** 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 103 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.643 Fit side-chains REVERT: A 239 TYR cc_start: 0.6479 (m-10) cc_final: 0.5889 (m-10) REVERT: A 242 HIS cc_start: 0.8132 (m-70) cc_final: 0.7715 (m-70) REVERT: A 300 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5453 (mp) REVERT: A 304 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.6711 (pt) REVERT: A 329 MET cc_start: 0.6769 (mmm) cc_final: 0.6524 (mpp) REVERT: A 361 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.6492 (p90) REVERT: A 450 PHE cc_start: 0.5793 (OUTLIER) cc_final: 0.5235 (t80) REVERT: A 505 MET cc_start: 0.8191 (tpp) cc_final: 0.7858 (tpp) REVERT: A 512 MET cc_start: 0.5580 (ttt) cc_final: 0.5079 (ttp) REVERT: A 514 ASP cc_start: 0.8521 (m-30) cc_final: 0.8127 (p0) REVERT: A 613 MET cc_start: 0.7028 (mmm) cc_final: 0.6769 (mmm) REVERT: A 752 MET cc_start: 0.4851 (tpt) cc_final: 0.4608 (tmm) REVERT: A 753 ARG cc_start: 0.6513 (mmm-85) cc_final: 0.5691 (mtm110) REVERT: A 964 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7682 (mt) outliers start: 26 outliers final: 11 residues processed: 99 average time/residue: 0.1734 time to fit residues: 23.6755 Evaluate side-chains 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 304 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 540 ASN 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 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 48 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.198864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136397 restraints weight = 8140.655| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.12 r_work: 0.3563 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7000 Z= 0.304 Angle : 0.650 6.310 9675 Z= 0.332 Chirality : 0.045 0.154 1132 Planarity : 0.005 0.042 1071 Dihedral : 19.706 179.328 1400 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.50 % Allowed : 17.72 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.31), residues: 726 helix: 1.54 (0.35), residues: 226 sheet: -1.22 (0.37), residues: 178 loop : -1.67 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 930 HIS 0.007 0.001 HIS A 526 PHE 0.018 0.002 PHE A 325 TYR 0.015 0.002 TYR A 770 ARG 0.002 0.000 ARG A 354 *********************** 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: 30 poor density : 71 time to evaluate : 0.651 Fit side-chains REVERT: A 239 TYR cc_start: 0.6600 (m-10) cc_final: 0.5946 (m-10) REVERT: A 242 HIS cc_start: 0.8194 (m-70) cc_final: 0.7842 (m-70) REVERT: A 300 ILE cc_start: 0.6274 (OUTLIER) cc_final: 0.5373 (mp) REVERT: A 361 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.6579 (p90) REVERT: A 441 VAL cc_start: 0.2899 (OUTLIER) cc_final: 0.2615 (p) REVERT: A 450 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.5358 (t80) REVERT: A 451 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6926 (mm) REVERT: A 512 MET cc_start: 0.5716 (ttt) cc_final: 0.5349 (ttp) REVERT: A 514 ASP cc_start: 0.8222 (m-30) cc_final: 0.7931 (p0) REVERT: A 752 MET cc_start: 0.4951 (tpt) cc_final: 0.4565 (tmm) REVERT: A 753 ARG cc_start: 0.6294 (mmm-85) cc_final: 0.6042 (mpt180) REVERT: A 964 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7679 (mt) outliers start: 30 outliers final: 15 residues processed: 97 average time/residue: 0.1448 time to fit residues: 20.4735 Evaluate side-chains 91 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE 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 430 VAL Chi-restraints excluded: chain A residue 441 VAL 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 530 LEU Chi-restraints excluded: chain A residue 537 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.205661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.155190 restraints weight = 8153.258| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 3.11 r_work: 0.3683 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7000 Z= 0.329 Angle : 0.662 7.252 9675 Z= 0.337 Chirality : 0.046 0.160 1132 Planarity : 0.005 0.045 1071 Dihedral : 19.702 177.447 1400 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.80 % Allowed : 19.82 % Favored : 75.38 % 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: -1.02 (0.31), residues: 726 helix: 1.40 (0.35), residues: 226 sheet: -1.39 (0.36), residues: 185 loop : -1.75 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 586 HIS 0.007 0.001 HIS A 353 PHE 0.018 0.002 PHE A 325 TYR 0.014 0.002 TYR A 454 ARG 0.001 0.000 ARG A 750 *********************** 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 107 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.772 Fit side-chains REVERT: A 239 TYR cc_start: 0.6804 (m-10) cc_final: 0.6123 (m-10) REVERT: A 242 HIS cc_start: 0.8101 (m-70) cc_final: 0.7676 (m-70) REVERT: A 300 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.5583 (mt) REVERT: A 361 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.6831 (p90) REVERT: A 450 PHE cc_start: 0.5986 (OUTLIER) cc_final: 0.5378 (t80) REVERT: A 451 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6906 (mm) REVERT: A 505 MET cc_start: 0.8181 (tpp) cc_final: 0.7866 (tpp) REVERT: A 512 MET cc_start: 0.5933 (ttt) cc_final: 0.5530 (ttp) REVERT: A 568 MET cc_start: 0.7725 (mtp) cc_final: 0.7523 (mtm) REVERT: A 752 MET cc_start: 0.4918 (tpt) cc_final: 0.4589 (tmm) REVERT: A 845 MET cc_start: 0.6398 (mpp) cc_final: 0.5761 (mtt) REVERT: A 964 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7891 (mt) outliers start: 32 outliers final: 22 residues processed: 103 average time/residue: 0.1456 time to fit residues: 21.5527 Evaluate side-chains 96 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE 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 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 441 VAL 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 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 634 ILE 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 859 TYR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.207565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.156736 restraints weight = 8039.866| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 3.25 r_work: 0.3686 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7000 Z= 0.281 Angle : 0.641 7.692 9675 Z= 0.325 Chirality : 0.045 0.166 1132 Planarity : 0.004 0.041 1071 Dihedral : 19.659 176.356 1400 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.80 % Allowed : 20.72 % Favored : 74.47 % 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: -1.05 (0.31), residues: 726 helix: 1.44 (0.35), residues: 225 sheet: -1.31 (0.37), residues: 177 loop : -1.89 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 586 HIS 0.006 0.001 HIS A 892 PHE 0.016 0.002 PHE A 325 TYR 0.018 0.002 TYR A 770 ARG 0.002 0.000 ARG A 937 *********************** 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 104 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.687 Fit side-chains REVERT: A 239 TYR cc_start: 0.6655 (m-10) cc_final: 0.6033 (m-10) REVERT: A 242 HIS cc_start: 0.8071 (m-70) cc_final: 0.7434 (m90) REVERT: A 300 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.5433 (mt) REVERT: A 361 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.6456 (p90) REVERT: A 450 PHE cc_start: 0.6025 (OUTLIER) cc_final: 0.5441 (t80) REVERT: A 451 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7073 (mm) REVERT: A 505 MET cc_start: 0.8212 (tpp) cc_final: 0.7863 (tpp) REVERT: A 512 MET cc_start: 0.5898 (ttt) cc_final: 0.5518 (ttp) REVERT: A 666 MET cc_start: 0.8177 (ttt) cc_final: 0.7850 (mtp) REVERT: A 845 MET cc_start: 0.6352 (mpp) cc_final: 0.5713 (mtt) REVERT: A 964 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7823 (mt) outliers start: 32 outliers final: 19 residues processed: 100 average time/residue: 0.1351 time to fit residues: 20.1532 Evaluate side-chains 93 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE 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 365 ILE Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL 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 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 658 LEU 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 859 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.206594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.156439 restraints weight = 8103.314| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 3.31 r_work: 0.3674 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7000 Z= 0.308 Angle : 0.669 13.037 9675 Z= 0.338 Chirality : 0.045 0.160 1132 Planarity : 0.005 0.044 1071 Dihedral : 19.659 174.969 1400 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.20 % Allowed : 21.77 % Favored : 74.02 % 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 (0.31), residues: 726 helix: 1.40 (0.35), residues: 225 sheet: -1.45 (0.37), residues: 185 loop : -1.88 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 930 HIS 0.006 0.001 HIS A 892 PHE 0.016 0.002 PHE A 325 TYR 0.013 0.002 TYR A 454 ARG 0.002 0.000 ARG A 937 *********************** 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 98 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.698 Fit side-chains REVERT: A 239 TYR cc_start: 0.6640 (m-10) cc_final: 0.6019 (m-10) REVERT: A 242 HIS cc_start: 0.8095 (m-70) cc_final: 0.7457 (m90) REVERT: A 300 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.5381 (mt) REVERT: A 361 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.6524 (p90) REVERT: A 450 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5577 (t80) REVERT: A 451 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7099 (mm) REVERT: A 505 MET cc_start: 0.8188 (tpp) cc_final: 0.7869 (tpp) REVERT: A 512 MET cc_start: 0.5846 (ttt) cc_final: 0.5479 (ttp) REVERT: A 752 MET cc_start: 0.5089 (tmm) cc_final: 0.4309 (tpt) REVERT: A 845 MET cc_start: 0.6318 (mpp) cc_final: 0.5675 (mtt) REVERT: A 964 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7860 (mt) outliers start: 28 outliers final: 21 residues processed: 95 average time/residue: 0.1367 time to fit residues: 19.7405 Evaluate side-chains 95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE 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 375 LEU Chi-restraints excluded: chain A residue 411 LEU 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 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 859 TYR 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 31 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.0470 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.207461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.157389 restraints weight = 8079.369| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 3.35 r_work: 0.3689 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7000 Z= 0.222 Angle : 0.629 13.585 9675 Z= 0.316 Chirality : 0.043 0.149 1132 Planarity : 0.004 0.039 1071 Dihedral : 19.560 174.925 1400 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.35 % Allowed : 21.32 % Favored : 74.32 % 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: -1.02 (0.31), residues: 726 helix: 1.54 (0.35), residues: 226 sheet: -1.35 (0.38), residues: 178 loop : -1.91 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 586 HIS 0.004 0.001 HIS A 892 PHE 0.015 0.001 PHE A 325 TYR 0.019 0.001 TYR A 770 ARG 0.002 0.000 ARG A 753 *********************** 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 101 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 239 TYR cc_start: 0.6755 (m-10) cc_final: 0.6119 (m-10) REVERT: A 242 HIS cc_start: 0.7971 (m-70) cc_final: 0.7510 (m90) REVERT: A 300 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5181 (mt) REVERT: A 361 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.6527 (p90) REVERT: A 450 PHE cc_start: 0.6090 (OUTLIER) cc_final: 0.5459 (t80) REVERT: A 505 MET cc_start: 0.8194 (tpp) cc_final: 0.7875 (tpp) REVERT: A 512 MET cc_start: 0.6036 (ttt) cc_final: 0.5629 (ttp) REVERT: A 752 MET cc_start: 0.5501 (tmm) cc_final: 0.4486 (tpt) REVERT: A 845 MET cc_start: 0.6298 (mpp) cc_final: 0.5706 (mtt) REVERT: A 964 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7912 (mt) outliers start: 29 outliers final: 22 residues processed: 98 average time/residue: 0.1360 time to fit residues: 19.9933 Evaluate side-chains 93 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE 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 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 515 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 859 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.207183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.157516 restraints weight = 8213.872| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.74 r_work: 0.3650 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7000 Z= 0.269 Angle : 0.655 12.586 9675 Z= 0.330 Chirality : 0.045 0.318 1132 Planarity : 0.004 0.040 1071 Dihedral : 19.495 174.434 1400 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.05 % Allowed : 21.47 % Favored : 74.47 % 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: -1.07 (0.31), residues: 726 helix: 1.43 (0.35), residues: 225 sheet: -1.36 (0.37), residues: 185 loop : -1.89 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 586 HIS 0.005 0.001 HIS A 892 PHE 0.015 0.002 PHE A 325 TYR 0.011 0.001 TYR A 650 ARG 0.002 0.000 ARG A 675 ********************** 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 97 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.761 Fit side-chains REVERT: A 239 TYR cc_start: 0.6729 (m-10) cc_final: 0.6061 (m-10) REVERT: A 242 HIS cc_start: 0.8155 (m-70) cc_final: 0.7760 (m-70) REVERT: A 300 ILE cc_start: 0.5887 (OUTLIER) cc_final: 0.5023 (mt) REVERT: A 361 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.6527 (p90) REVERT: A 450 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5491 (t80) REVERT: A 505 MET cc_start: 0.8215 (tpp) cc_final: 0.7887 (tpp) REVERT: A 512 MET cc_start: 0.5738 (ttt) cc_final: 0.5291 (ttp) REVERT: A 775 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: A 845 MET cc_start: 0.6322 (mpp) cc_final: 0.5699 (mtt) REVERT: A 964 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7795 (mt) outliers start: 27 outliers final: 21 residues processed: 94 average time/residue: 0.1308 time to fit residues: 18.6168 Evaluate side-chains 96 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE 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 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 515 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 859 TYR 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 13 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.209316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.159716 restraints weight = 8108.006| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 3.44 r_work: 0.3715 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7000 Z= 0.189 Angle : 0.609 10.957 9675 Z= 0.307 Chirality : 0.043 0.289 1132 Planarity : 0.004 0.038 1071 Dihedral : 19.326 175.191 1400 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.60 % Allowed : 21.77 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.31), residues: 726 helix: 1.68 (0.35), residues: 225 sheet: -1.32 (0.37), residues: 185 loop : -1.87 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 586 HIS 0.003 0.001 HIS A 892 PHE 0.014 0.001 PHE A 325 TYR 0.014 0.001 TYR A 770 ARG 0.002 0.000 ARG A 753 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3354.35 seconds wall clock time: 58 minutes 27.82 seconds (3507.82 seconds total)