Starting phenix.real_space_refine on Sat Dec 28 00:27:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfy_33801/12_2024/7yfy_33801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfy_33801/12_2024/7yfy_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_33801/12_2024/7yfy_33801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfy_33801/12_2024/7yfy_33801.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfy_33801/12_2024/7yfy_33801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfy_33801/12_2024/7yfy_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-5532/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: 4.62, per 1000 atoms: 0.68 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: 2.04 Conformation dependent library (CDL) restraints added in 767.3 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: 2.26 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: 2.97 Time building geometry restraints manager: 2.30 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: 0.560 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.140 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- 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 : 0.797 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: 0.2209 time to fit residues: 26.3755 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 : 0.673 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 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 : 0.762 Fit side-chains REVERT: A 242 HIS cc_start: 0.7590 (m-70) cc_final: 0.7339 (m-70) REVERT: A 258 MET cc_start: 0.7434 (mmt) cc_final: 0.7209 (mmm) REVERT: A 335 LYS cc_start: 0.7247 (mmtt) cc_final: 0.6928 (mmmt) REVERT: A 361 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6653 (p90) REVERT: A 396 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.6022 (t80) REVERT: A 450 PHE cc_start: 0.4987 (OUTLIER) cc_final: 0.4690 (t80) REVERT: A 752 MET cc_start: 0.5133 (tpt) cc_final: 0.4710 (tmm) outliers start: 22 outliers final: 12 residues processed: 100 average time/residue: 0.1778 time to fit residues: 24.5880 Evaluate side-chains 83 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 38 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7000 Z= 0.192 Angle : 0.600 6.023 9675 Z= 0.308 Chirality : 0.044 0.180 1132 Planarity : 0.004 0.044 1071 Dihedral : 19.841 177.574 1402 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.70 % Allowed : 19.67 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.31), residues: 726 helix: 1.66 (0.35), residues: 223 sheet: -1.04 (0.39), residues: 168 loop : -1.61 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 586 HIS 0.004 0.001 HIS A 526 PHE 0.011 0.001 PHE A 325 TYR 0.017 0.001 TYR A 425 ARG 0.005 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 90 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.743 Fit side-chains REVERT: A 239 TYR cc_start: 0.7006 (m-10) cc_final: 0.6500 (m-10) REVERT: A 242 HIS cc_start: 0.7605 (m-70) cc_final: 0.7313 (m-70) REVERT: A 258 MET cc_start: 0.7479 (mmt) cc_final: 0.7241 (mmm) REVERT: A 335 LYS cc_start: 0.7191 (mmtt) cc_final: 0.6605 (mmmt) REVERT: A 361 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6510 (p90) REVERT: A 450 PHE cc_start: 0.4989 (OUTLIER) cc_final: 0.4564 (t80) REVERT: A 568 MET cc_start: 0.7012 (mtp) cc_final: 0.6768 (mtm) REVERT: A 752 MET cc_start: 0.4961 (tpt) cc_final: 0.4220 (tmm) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 0.1642 time to fit residues: 20.2366 Evaluate side-chains 78 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 777 MET 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 68 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.0470 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN A 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7000 Z= 0.155 Angle : 0.572 5.859 9675 Z= 0.291 Chirality : 0.042 0.173 1132 Planarity : 0.004 0.042 1071 Dihedral : 19.654 179.167 1402 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.00 % Allowed : 18.62 % Favored : 78.38 % 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: -0.67 (0.31), residues: 726 helix: 1.59 (0.35), residues: 232 sheet: -1.01 (0.38), residues: 168 loop : -1.65 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 604 HIS 0.003 0.000 HIS A 526 PHE 0.010 0.001 PHE A 325 TYR 0.009 0.001 TYR A 826 ARG 0.002 0.000 ARG A 750 *********************** 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 95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.660 Fit side-chains REVERT: A 239 TYR cc_start: 0.6960 (m-10) cc_final: 0.6484 (m-10) REVERT: A 242 HIS cc_start: 0.7632 (m-70) cc_final: 0.7297 (m-70) REVERT: A 258 MET cc_start: 0.7276 (mmt) cc_final: 0.7052 (mmm) REVERT: A 329 MET cc_start: 0.7233 (mmm) cc_final: 0.6950 (mpp) REVERT: A 361 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6392 (p90) REVERT: A 450 PHE cc_start: 0.5144 (OUTLIER) cc_final: 0.4544 (t80) REVERT: A 505 MET cc_start: 0.7818 (tpp) cc_final: 0.7380 (tpp) REVERT: A 568 MET cc_start: 0.7031 (mtp) cc_final: 0.6801 (mtm) outliers start: 20 outliers final: 13 residues processed: 90 average time/residue: 0.1642 time to fit residues: 20.8879 Evaluate side-chains 82 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 385 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 756 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7000 Z= 0.410 Angle : 0.722 10.949 9675 Z= 0.369 Chirality : 0.046 0.165 1132 Planarity : 0.005 0.051 1071 Dihedral : 19.727 178.308 1400 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.50 % Allowed : 18.17 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.30), residues: 726 helix: 1.02 (0.34), residues: 232 sheet: -1.29 (0.36), residues: 185 loop : -1.83 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 586 HIS 0.011 0.002 HIS A 526 PHE 0.020 0.002 PHE A 325 TYR 0.017 0.002 TYR A 650 ARG 0.006 0.001 ARG A 327 *********************** 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 100 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.865 Fit side-chains REVERT: A 242 HIS cc_start: 0.7781 (m-70) cc_final: 0.7555 (m-70) REVERT: A 258 MET cc_start: 0.7260 (mmt) cc_final: 0.7048 (mmm) REVERT: A 361 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6605 (p90) REVERT: A 427 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7120 (tp) REVERT: A 441 VAL cc_start: 0.4034 (OUTLIER) cc_final: 0.3694 (p) REVERT: A 450 PHE cc_start: 0.5126 (OUTLIER) cc_final: 0.4565 (t80) REVERT: A 707 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.4090 (mpt180) REVERT: A 964 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7765 (mt) outliers start: 30 outliers final: 18 residues processed: 95 average time/residue: 0.1689 time to fit residues: 22.7763 Evaluate side-chains 90 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU 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 427 ILE 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 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 634 ILE Chi-restraints excluded: chain A residue 707 ARG 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 913 LEU 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 24 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7000 Z= 0.334 Angle : 0.683 12.775 9675 Z= 0.344 Chirality : 0.045 0.160 1132 Planarity : 0.005 0.045 1071 Dihedral : 19.693 177.129 1400 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.71 % Allowed : 18.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.30), residues: 726 helix: 1.11 (0.34), residues: 231 sheet: -1.28 (0.37), residues: 178 loop : -1.98 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 586 HIS 0.006 0.001 HIS A 892 PHE 0.017 0.002 PHE A 325 TYR 0.014 0.002 TYR A 454 ARG 0.002 0.000 ARG A 700 *********************** 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 109 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.751 Fit side-chains REVERT: A 239 TYR cc_start: 0.7037 (m-10) cc_final: 0.6450 (m-10) REVERT: A 242 HIS cc_start: 0.7654 (m-70) cc_final: 0.7441 (m-70) REVERT: A 258 MET cc_start: 0.7315 (mmt) cc_final: 0.7070 (mmm) REVERT: A 300 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.6061 (mp) REVERT: A 361 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.6578 (p90) REVERT: A 427 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7321 (tp) REVERT: A 450 PHE cc_start: 0.5166 (OUTLIER) cc_final: 0.4564 (t80) REVERT: A 451 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6333 (mm) REVERT: A 613 MET cc_start: 0.6407 (mmm) cc_final: 0.6199 (mmm) REVERT: A 964 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7777 (mt) outliers start: 38 outliers final: 21 residues processed: 103 average time/residue: 0.1694 time to fit residues: 25.1177 Evaluate side-chains 93 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 666 MET Chi-restraints excluded: chain A residue 742 MET 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 8 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3178 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= 0.233 Angle : 0.628 12.836 9675 Z= 0.316 Chirality : 0.044 0.155 1132 Planarity : 0.004 0.038 1071 Dihedral : 19.612 176.680 1400 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.35 % Allowed : 20.12 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.31), residues: 726 helix: 1.46 (0.35), residues: 224 sheet: -1.24 (0.38), residues: 177 loop : -1.85 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 586 HIS 0.005 0.001 HIS A 892 PHE 0.014 0.001 PHE A 325 TYR 0.011 0.001 TYR A 454 ARG 0.005 0.000 ARG A 327 *********************** 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 98 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.707 Fit side-chains REVERT: A 239 TYR cc_start: 0.6948 (m-10) cc_final: 0.6354 (m-10) REVERT: A 242 HIS cc_start: 0.7599 (m-70) cc_final: 0.7390 (m-70) REVERT: A 258 MET cc_start: 0.7245 (mmt) cc_final: 0.7028 (mmm) REVERT: A 300 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6188 (mp) REVERT: A 361 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6389 (p90) REVERT: A 427 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7344 (tp) REVERT: A 450 PHE cc_start: 0.5144 (OUTLIER) cc_final: 0.4567 (t80) REVERT: A 451 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6411 (mm) REVERT: A 666 MET cc_start: 0.8047 (ttt) cc_final: 0.7734 (mtp) REVERT: A 964 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7818 (mt) outliers start: 29 outliers final: 16 residues processed: 95 average time/residue: 0.1578 time to fit residues: 21.7192 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 : 0.904 ------------------------------------------------------------------------------- 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 375 LEU 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 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 599 ILE Chi-restraints excluded: chain A residue 658 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 964 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7000 Z= 0.193 Angle : 0.601 13.690 9675 Z= 0.300 Chirality : 0.043 0.161 1132 Planarity : 0.004 0.038 1071 Dihedral : 19.529 176.234 1400 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.05 % Allowed : 20.27 % 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 (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: -0.85 (0.31), residues: 726 helix: 1.67 (0.35), residues: 224 sheet: -1.16 (0.38), residues: 172 loop : -1.84 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 586 HIS 0.003 0.001 HIS A 353 PHE 0.014 0.001 PHE A 325 TYR 0.019 0.001 TYR A 770 ARG 0.001 0.000 ARG A 812 *********************** 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: 27 poor density : 71 time to evaluate : 0.787 Fit side-chains REVERT: A 239 TYR cc_start: 0.6944 (m-10) cc_final: 0.6376 (m-10) REVERT: A 258 MET cc_start: 0.7189 (mmt) cc_final: 0.6980 (mmm) REVERT: A 300 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6277 (mp) REVERT: A 361 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.6356 (p90) REVERT: A 427 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7385 (tp) REVERT: A 450 PHE cc_start: 0.5336 (OUTLIER) cc_final: 0.4725 (t80) REVERT: A 451 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6430 (mm) REVERT: A 666 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7729 (mtp) REVERT: A 845 MET cc_start: 0.5555 (mpp) cc_final: 0.5209 (mtt) REVERT: A 964 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7774 (mt) outliers start: 27 outliers final: 18 residues processed: 93 average time/residue: 0.1516 time to fit residues: 20.4449 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 : 0.756 ------------------------------------------------------------------------------- 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 515 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 666 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 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 29 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 HIS ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 7000 Z= 0.431 Angle : 0.740 13.472 9675 Z= 0.375 Chirality : 0.048 0.297 1132 Planarity : 0.005 0.048 1071 Dihedral : 19.637 174.661 1400 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.35 % Allowed : 20.27 % 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: -1.31 (0.31), residues: 726 helix: 0.96 (0.34), residues: 232 sheet: -1.33 (0.37), residues: 184 loop : -1.99 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 586 HIS 0.009 0.002 HIS A 892 PHE 0.017 0.002 PHE A 325 TYR 0.023 0.002 TYR A 458 ARG 0.003 0.000 ARG A 707 *********************** 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 99 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.748 Fit side-chains REVERT: A 239 TYR cc_start: 0.7039 (m-10) cc_final: 0.6382 (m-10) REVERT: A 258 MET cc_start: 0.7258 (mmt) cc_final: 0.6965 (mmm) REVERT: A 300 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6149 (mp) REVERT: A 361 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6490 (p90) REVERT: A 427 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7126 (tp) REVERT: A 450 PHE cc_start: 0.5508 (OUTLIER) cc_final: 0.4843 (t80) REVERT: A 451 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6451 (mm) REVERT: A 845 MET cc_start: 0.5828 (mpp) cc_final: 0.5410 (mtt) REVERT: A 964 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7792 (mt) outliers start: 29 outliers final: 21 residues processed: 93 average time/residue: 0.1533 time to fit residues: 20.9092 Evaluate side-chains 94 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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 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 964 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 6 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7000 Z= 0.170 Angle : 0.633 14.341 9675 Z= 0.314 Chirality : 0.044 0.284 1132 Planarity : 0.004 0.038 1071 Dihedral : 19.484 175.131 1400 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.30 % Allowed : 21.77 % Favored : 74.92 % 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: -0.91 (0.31), residues: 726 helix: 1.62 (0.35), residues: 224 sheet: -1.25 (0.38), residues: 172 loop : -1.85 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 586 HIS 0.012 0.001 HIS A 242 PHE 0.014 0.001 PHE A 325 TYR 0.022 0.001 TYR A 770 ARG 0.002 0.000 ARG A 920 ********************** 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 92 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.687 Fit side-chains REVERT: A 239 TYR cc_start: 0.6874 (m-10) cc_final: 0.6353 (m-10) REVERT: A 258 MET cc_start: 0.7195 (mmt) cc_final: 0.6989 (mmm) REVERT: A 300 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6270 (mp) REVERT: A 329 MET cc_start: 0.7118 (mmm) cc_final: 0.6918 (tpp) REVERT: A 361 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6297 (p90) REVERT: A 427 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7429 (tp) REVERT: A 450 PHE cc_start: 0.5327 (OUTLIER) cc_final: 0.4706 (t80) REVERT: A 451 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6466 (mm) REVERT: A 666 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7740 (mtp) REVERT: A 845 MET cc_start: 0.5529 (mpp) cc_final: 0.5217 (mtt) REVERT: A 964 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7848 (mt) outliers start: 22 outliers final: 15 residues processed: 88 average time/residue: 0.1359 time to fit residues: 17.8898 Evaluate side-chains 91 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 427 ILE 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 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 666 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 964 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4610 r_free = 0.4610 target = 0.208930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.158739 restraints weight = 8071.956| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.23 r_work: 0.3720 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7000 Z= 0.217 Angle : 0.641 14.070 9675 Z= 0.318 Chirality : 0.044 0.254 1132 Planarity : 0.004 0.037 1071 Dihedral : 19.401 174.929 1400 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.60 % Allowed : 21.62 % Favored : 74.77 % 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: -0.88 (0.31), residues: 726 helix: 1.59 (0.35), residues: 228 sheet: -1.22 (0.37), residues: 177 loop : -1.82 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 586 HIS 0.005 0.001 HIS A 526 PHE 0.014 0.001 PHE A 325 TYR 0.017 0.002 TYR A 241 ARG 0.002 0.000 ARG A 707 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1497.52 seconds wall clock time: 28 minutes 33.47 seconds (1713.47 seconds total)