Starting phenix.real_space_refine on Fri Dec 27 18:35:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ygn_33817/12_2024/7ygn_33817.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ygn_33817/12_2024/7ygn_33817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ygn_33817/12_2024/7ygn_33817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ygn_33817/12_2024/7ygn_33817.map" model { file = "/net/cci-nas-00/data/ceres_data/7ygn_33817/12_2024/7ygn_33817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ygn_33817/12_2024/7ygn_33817.cif" } resolution = 3.0 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= -0.001 sd= 0.200 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 9 5.49 5 Mg 2 5.21 5 S 43 5.16 5 C 3896 2.51 5 N 1057 2.21 5 O 1126 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: 6133 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 5945 Classifications: {'peptide': 739} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 701} Chain breaks: 2 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'RNA': 9} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 5} Chain breaks: 1 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: 4.22, per 1000 atoms: 0.69 Number of scatterers: 6133 At special positions: 0 Unit cell: (76.09, 84.786, 113.048, 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 43 16.00 P 9 15.00 Mg 2 11.99 O 1126 8.00 N 1057 7.00 C 3896 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: 1.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 39.2% alpha, 24.6% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.678A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 344 through 347 removed outlier: 3.518A pdb=" N ALA A 347 " --> pdb=" O PRO A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 347' Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 402 through 414 removed outlier: 4.603A pdb=" N GLY A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.727A pdb=" N LYS A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 508' Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 522 through 540 Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 586 through 593 removed outlier: 3.579A pdb=" N VAL A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 591 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 631 removed outlier: 4.401A pdb=" N GLY A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 646 through 661 Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.894A pdb=" N GLN A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 724 Processing helix chain 'A' and resid 781 through 802 removed outlier: 4.294A pdb=" N SER A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 788 " --> pdb=" O ASP A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 818 No H-bonds generated for 'chain 'A' and resid 816 through 818' Processing helix chain 'A' and resid 819 through 826 Processing helix chain 'A' and resid 826 through 833 removed outlier: 3.512A pdb=" N LYS A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) 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 961 through 967 removed outlier: 4.081A 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 775 removed outlier: 3.908A pdb=" N ASP A 743 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL A 739 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL A 744 " --> pdb=" O ASP A 813 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 808 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE A 848 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 810 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL A 850 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG A 812 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 908 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL A 849 " --> pdb=" O CYS A 906 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N CYS A 906 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN A 851 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR A 904 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 885 " --> pdb=" O CYS A 906 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER A 223 " --> pdb=" O ALA A 861 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.614A pdb=" N ASN A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.614A pdb=" N ASN A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU A 372 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272 removed outlier: 5.825A pdb=" N HIS A 242 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 306 " --> pdb=" O HIS A 242 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR A 244 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 304 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER A 246 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE A 302 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 423 through 425 removed outlier: 3.514A pdb=" N ARG A 423 " --> pdb=" O THR A 418 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 572 Processing sheet with id=AA9, first strand: chain 'A' and resid 638 through 641 289 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 963 1.30 - 1.43: 1632 1.43 - 1.56: 3607 1.56 - 1.69: 16 1.69 - 1.82: 67 Bond restraints: 6285 Sorted by residual: bond pdb=" C2 OMC B 26 " pdb=" N3 OMC B 26 " ideal model delta sigma weight residual 1.350 1.491 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C4 OMC B 26 " pdb=" N4 OMC B 26 " ideal model delta sigma weight residual 1.332 1.471 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" N3 OMC B 26 " pdb=" C4 OMC B 26 " ideal model delta sigma weight residual 1.317 1.454 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C5 OMC B 26 " pdb=" C6 OMC B 26 " ideal model delta sigma weight residual 1.346 1.481 -0.135 2.00e-02 2.50e+03 4.59e+01 bond pdb=" O3' U B 2 " pdb=" P A B 3 " ideal model delta sigma weight residual 1.607 1.528 0.079 1.50e-02 4.44e+03 2.78e+01 ... (remaining 6280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 8507 4.32 - 8.64: 41 8.64 - 12.96: 1 12.96 - 17.28: 2 17.28 - 21.60: 2 Bond angle restraints: 8553 Sorted by residual: angle pdb=" O3' U B 25 " pdb=" P OMC B 26 " pdb=" OP1 OMC B 26 " ideal model delta sigma weight residual 108.00 86.40 21.60 3.00e+00 1.11e-01 5.18e+01 angle pdb=" O3' U B 25 " pdb=" P OMC B 26 " pdb=" OP2 OMC B 26 " ideal model delta sigma weight residual 108.00 90.04 17.96 3.00e+00 1.11e-01 3.58e+01 angle pdb=" N GLN A 263 " pdb=" CA GLN A 263 " pdb=" C GLN A 263 " ideal model delta sigma weight residual 111.28 105.23 6.05 1.09e+00 8.42e-01 3.09e+01 angle pdb=" OP2 OMC B 26 " pdb=" P OMC B 26 " pdb=" O5' OMC B 26 " ideal model delta sigma weight residual 100.81 116.44 -15.63 3.00e+00 1.11e-01 2.71e+01 angle pdb=" OP1 OMC B 26 " pdb=" P OMC B 26 " pdb=" OP2 OMC B 26 " ideal model delta sigma weight residual 115.29 128.88 -13.59 3.00e+00 1.11e-01 2.05e+01 ... (remaining 8548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3353 17.79 - 35.59: 355 35.59 - 53.38: 67 53.38 - 71.17: 20 71.17 - 88.97: 7 Dihedral angle restraints: 3802 sinusoidal: 1637 harmonic: 2165 Sorted by residual: dihedral pdb=" C4' U B 2 " pdb=" C3' U B 2 " pdb=" C2' U B 2 " pdb=" C1' U B 2 " ideal model delta sinusoidal sigma weight residual 36.00 5.39 30.61 1 8.00e+00 1.56e-02 2.09e+01 dihedral pdb=" O4' U B 2 " pdb=" C2' U B 2 " pdb=" C1' U B 2 " pdb=" C3' U B 2 " ideal model delta sinusoidal sigma weight residual 25.00 -2.36 27.36 1 8.00e+00 1.56e-02 1.68e+01 dihedral pdb=" C5' U B 2 " pdb=" C4' U B 2 " pdb=" C3' U B 2 " pdb=" O3' U B 2 " ideal model delta sinusoidal sigma weight residual 82.00 109.29 -27.29 1 8.00e+00 1.56e-02 1.67e+01 ... (remaining 3799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 837 0.068 - 0.135: 125 0.135 - 0.203: 13 0.203 - 0.271: 1 0.271 - 0.339: 1 Chirality restraints: 977 Sorted by residual: chirality pdb=" P U B 2 " pdb=" OP1 U B 2 " pdb=" OP2 U B 2 " pdb=" O5' U B 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.07 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C3' U B 2 " pdb=" C4' U B 2 " pdb=" O3' U B 2 " pdb=" C2' U B 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE A 905 " pdb=" N ILE A 905 " pdb=" C ILE A 905 " pdb=" CB ILE A 905 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 974 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 2 " -0.044 2.00e-02 2.50e+03 2.47e-02 1.38e+01 pdb=" N1 U B 2 " 0.056 2.00e-02 2.50e+03 pdb=" C2 U B 2 " 0.014 2.00e-02 2.50e+03 pdb=" O2 U B 2 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U B 2 " -0.009 2.00e-02 2.50e+03 pdb=" C4 U B 2 " -0.013 2.00e-02 2.50e+03 pdb=" O4 U B 2 " -0.005 2.00e-02 2.50e+03 pdb=" C5 U B 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U B 2 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 220 " -0.038 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO A 221 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 246 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO A 247 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.028 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 29 2.49 - 3.10: 4032 3.10 - 3.70: 8648 3.70 - 4.30: 12746 4.30 - 4.90: 21940 Nonbonded interactions: 47395 Sorted by model distance: nonbonded pdb=" OP1 U B 1 " pdb="MG MG A1001 " model vdw 1.892 2.170 nonbonded pdb=" O LEU A 971 " pdb="MG MG A1001 " model vdw 1.900 2.170 nonbonded pdb=" OD2 ASP A 743 " pdb="MG MG A1002 " model vdw 2.039 2.170 nonbonded pdb=" OP1 A B 3 " pdb="MG MG A1001 " model vdw 2.114 2.170 nonbonded pdb=" OG SER A 439 " pdb=" OE2 GLU A 447 " model vdw 2.209 3.040 ... (remaining 47390 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.670 Find NCS groups from input model: 0.060 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.006 0.141 6285 Z= 0.422 Angle : 0.854 21.598 8553 Z= 0.441 Chirality : 0.049 0.339 977 Planarity : 0.006 0.058 1051 Dihedral : 15.418 88.968 2400 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.11 (0.31), residues: 733 helix: 1.28 (0.36), residues: 234 sheet: 0.54 (0.36), residues: 198 loop : -1.22 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 728 HIS 0.010 0.001 HIS A 353 PHE 0.017 0.002 PHE A 578 TYR 0.013 0.002 TYR A 239 ARG 0.008 0.001 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.630 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 1.2090 time to fit residues: 98.1667 Evaluate side-chains 63 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 240 GLN A 535 GLN A 746 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6285 Z= 0.223 Angle : 0.553 4.870 8553 Z= 0.287 Chirality : 0.045 0.152 977 Planarity : 0.005 0.057 1051 Dihedral : 9.424 81.209 918 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.94 % Allowed : 12.22 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.49 (0.31), residues: 733 helix: 1.67 (0.35), residues: 238 sheet: 0.68 (0.36), residues: 196 loop : -1.04 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 884 HIS 0.005 0.001 HIS A 927 PHE 0.022 0.002 PHE A 320 TYR 0.015 0.001 TYR A 239 ARG 0.006 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.750 Fit side-chains REVERT: A 258 MET cc_start: 0.6948 (mmp) cc_final: 0.6725 (mtm) REVERT: A 505 MET cc_start: 0.6678 (mmt) cc_final: 0.6271 (mmt) REVERT: A 845 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7365 (ttt) REVERT: A 886 ASP cc_start: 0.8155 (p0) cc_final: 0.7921 (p0) REVERT: A 895 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.5752 (ptp90) outliers start: 13 outliers final: 1 residues processed: 83 average time/residue: 1.4048 time to fit residues: 122.1533 Evaluate side-chains 61 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 895 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN A 539 GLN A 763 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6285 Z= 0.305 Angle : 0.572 5.052 8553 Z= 0.298 Chirality : 0.046 0.167 977 Planarity : 0.005 0.056 1051 Dihedral : 9.126 81.499 918 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.98 % Allowed : 13.11 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.25 (0.31), residues: 733 helix: 1.46 (0.34), residues: 246 sheet: 0.58 (0.36), residues: 196 loop : -1.27 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 604 HIS 0.006 0.001 HIS A 927 PHE 0.021 0.002 PHE A 320 TYR 0.014 0.002 TYR A 239 ARG 0.003 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.694 Fit side-chains REVERT: A 258 MET cc_start: 0.7080 (mmp) cc_final: 0.6657 (mmp) REVERT: A 334 MET cc_start: 0.8342 (mmm) cc_final: 0.8106 (mtt) REVERT: A 520 ASN cc_start: 0.7237 (m110) cc_final: 0.6942 (m-40) REVERT: A 666 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8504 (ttp) REVERT: A 845 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7435 (ttt) REVERT: A 895 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.5707 (ptp90) outliers start: 20 outliers final: 5 residues processed: 87 average time/residue: 1.3228 time to fit residues: 120.6375 Evaluate side-chains 71 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 895 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN A 763 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6285 Z= 0.241 Angle : 0.522 5.984 8553 Z= 0.271 Chirality : 0.044 0.155 977 Planarity : 0.005 0.054 1051 Dihedral : 8.998 80.437 918 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.98 % Allowed : 15.35 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.50 (0.31), residues: 733 helix: 1.81 (0.35), residues: 241 sheet: 0.54 (0.36), residues: 196 loop : -1.06 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 604 HIS 0.004 0.001 HIS A 927 PHE 0.020 0.002 PHE A 320 TYR 0.013 0.001 TYR A 239 ARG 0.002 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 309 ILE cc_start: 0.7345 (mt) cc_final: 0.7052 (mt) REVERT: A 334 MET cc_start: 0.8385 (mmm) cc_final: 0.8146 (mtt) REVERT: A 652 ARG cc_start: 0.7513 (mtm110) cc_final: 0.7310 (ttm110) REVERT: A 663 LYS cc_start: 0.7423 (mtmm) cc_final: 0.7142 (mmmt) REVERT: A 666 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8457 (ttp) REVERT: A 895 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.5788 (ptp90) outliers start: 20 outliers final: 5 residues processed: 80 average time/residue: 1.4541 time to fit residues: 121.5885 Evaluate side-chains 67 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 895 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.0020 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 63 optimal weight: 0.0770 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN A 520 ASN A 535 GLN A 539 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6285 Z= 0.145 Angle : 0.480 6.692 8553 Z= 0.248 Chirality : 0.042 0.139 977 Planarity : 0.004 0.053 1051 Dihedral : 8.921 79.659 918 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.24 % Allowed : 17.88 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 733 helix: 2.25 (0.35), residues: 236 sheet: 0.74 (0.36), residues: 191 loop : -0.80 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 604 HIS 0.004 0.001 HIS A 779 PHE 0.024 0.001 PHE A 272 TYR 0.010 0.001 TYR A 239 ARG 0.005 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 309 ILE cc_start: 0.7404 (mt) cc_final: 0.7096 (mt) REVERT: A 334 MET cc_start: 0.8336 (mmm) cc_final: 0.7937 (mtt) REVERT: A 652 ARG cc_start: 0.7482 (mtm110) cc_final: 0.7262 (ttm110) REVERT: A 663 LYS cc_start: 0.7351 (mtmm) cc_final: 0.7082 (mmmt) REVERT: A 672 MET cc_start: 0.8035 (tpt) cc_final: 0.7749 (mmt) outliers start: 15 outliers final: 6 residues processed: 71 average time/residue: 1.3961 time to fit residues: 103.9691 Evaluate side-chains 61 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 868 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6285 Z= 0.408 Angle : 0.608 7.091 8553 Z= 0.313 Chirality : 0.048 0.177 977 Planarity : 0.005 0.053 1051 Dihedral : 8.960 79.901 918 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.53 % Allowed : 18.33 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.43 (0.31), residues: 733 helix: 1.82 (0.34), residues: 239 sheet: 0.46 (0.35), residues: 196 loop : -1.13 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 604 HIS 0.007 0.001 HIS A 927 PHE 0.022 0.002 PHE A 320 TYR 0.014 0.002 TYR A 239 ARG 0.008 0.001 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 309 ILE cc_start: 0.7579 (mt) cc_final: 0.7265 (mt) REVERT: A 334 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8060 (mtt) REVERT: A 505 MET cc_start: 0.6553 (mmt) cc_final: 0.5766 (mmt) REVERT: A 791 VAL cc_start: 0.7929 (t) cc_final: 0.7561 (t) REVERT: A 895 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.5584 (ptp90) outliers start: 17 outliers final: 7 residues processed: 78 average time/residue: 1.3202 time to fit residues: 108.1499 Evaluate side-chains 72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 895 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6285 Z= 0.208 Angle : 0.515 7.411 8553 Z= 0.264 Chirality : 0.043 0.149 977 Planarity : 0.005 0.053 1051 Dihedral : 8.884 78.643 918 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.24 % Allowed : 18.93 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.66 (0.31), residues: 733 helix: 2.02 (0.35), residues: 241 sheet: 0.71 (0.36), residues: 189 loop : -1.06 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 604 HIS 0.005 0.001 HIS A 779 PHE 0.023 0.001 PHE A 272 TYR 0.011 0.001 TYR A 239 ARG 0.007 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.683 Fit side-chains REVERT: A 309 ILE cc_start: 0.7473 (mt) cc_final: 0.7142 (mt) REVERT: A 334 MET cc_start: 0.8481 (mmm) cc_final: 0.7908 (mtt) REVERT: A 505 MET cc_start: 0.6582 (mmt) cc_final: 0.5854 (mmt) REVERT: A 663 LYS cc_start: 0.7451 (mtmm) cc_final: 0.7134 (mmmt) REVERT: A 895 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.5631 (ptp90) outliers start: 15 outliers final: 7 residues processed: 74 average time/residue: 1.4754 time to fit residues: 114.7103 Evaluate side-chains 65 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 895 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.0980 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6285 Z= 0.204 Angle : 0.533 7.595 8553 Z= 0.271 Chirality : 0.043 0.150 977 Planarity : 0.005 0.053 1051 Dihedral : 8.853 78.113 918 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.24 % Allowed : 19.37 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.72 (0.31), residues: 733 helix: 2.04 (0.35), residues: 242 sheet: 0.70 (0.36), residues: 189 loop : -0.98 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 604 HIS 0.005 0.001 HIS A 779 PHE 0.019 0.001 PHE A 320 TYR 0.011 0.001 TYR A 239 ARG 0.008 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.695 Fit side-chains REVERT: A 309 ILE cc_start: 0.7458 (mt) cc_final: 0.7132 (mt) REVERT: A 334 MET cc_start: 0.8453 (mmm) cc_final: 0.8061 (mtt) REVERT: A 505 MET cc_start: 0.6509 (mmt) cc_final: 0.5766 (mmt) REVERT: A 663 LYS cc_start: 0.7475 (mtmm) cc_final: 0.7149 (mmmt) REVERT: A 895 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.5639 (ptp90) outliers start: 15 outliers final: 7 residues processed: 71 average time/residue: 1.3132 time to fit residues: 98.1725 Evaluate side-chains 65 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 895 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 520 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6285 Z= 0.202 Angle : 0.520 7.707 8553 Z= 0.266 Chirality : 0.043 0.149 977 Planarity : 0.005 0.053 1051 Dihedral : 8.823 77.360 918 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.79 % Allowed : 20.12 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.77 (0.31), residues: 733 helix: 2.13 (0.35), residues: 242 sheet: 0.65 (0.36), residues: 189 loop : -0.95 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 604 HIS 0.005 0.001 HIS A 779 PHE 0.024 0.002 PHE A 272 TYR 0.011 0.001 TYR A 239 ARG 0.009 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 309 ILE cc_start: 0.7420 (mt) cc_final: 0.7094 (mt) REVERT: A 334 MET cc_start: 0.8474 (mmm) cc_final: 0.7964 (mtt) REVERT: A 505 MET cc_start: 0.6511 (mmt) cc_final: 0.5769 (mmt) REVERT: A 663 LYS cc_start: 0.7466 (mtmm) cc_final: 0.7166 (mmmt) REVERT: A 895 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.5635 (ptp90) outliers start: 12 outliers final: 11 residues processed: 73 average time/residue: 1.4180 time to fit residues: 109.1923 Evaluate side-chains 70 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 895 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6285 Z= 0.183 Angle : 0.526 7.809 8553 Z= 0.267 Chirality : 0.043 0.147 977 Planarity : 0.005 0.053 1051 Dihedral : 8.789 76.481 918 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.94 % Allowed : 19.97 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.93 (0.31), residues: 733 helix: 2.39 (0.35), residues: 235 sheet: 0.68 (0.36), residues: 189 loop : -0.84 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 604 HIS 0.005 0.001 HIS A 779 PHE 0.018 0.001 PHE A 320 TYR 0.011 0.001 TYR A 239 ARG 0.007 0.000 ARG A 423 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.716 Fit side-chains REVERT: A 309 ILE cc_start: 0.7363 (mt) cc_final: 0.7037 (mt) REVERT: A 334 MET cc_start: 0.8411 (mmm) cc_final: 0.8041 (mtt) REVERT: A 505 MET cc_start: 0.6529 (mmt) cc_final: 0.6139 (mmt) REVERT: A 663 LYS cc_start: 0.7421 (mtmm) cc_final: 0.7157 (mmmt) REVERT: A 895 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.5628 (ptp90) outliers start: 13 outliers final: 9 residues processed: 68 average time/residue: 1.4168 time to fit residues: 101.2422 Evaluate side-chains 65 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 895 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.2980 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.173581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118304 restraints weight = 6779.246| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.34 r_work: 0.3210 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6285 Z= 0.183 Angle : 0.509 8.001 8553 Z= 0.258 Chirality : 0.043 0.147 977 Planarity : 0.005 0.053 1051 Dihedral : 8.756 75.617 918 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.64 % Allowed : 20.42 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 733 helix: 2.49 (0.35), residues: 235 sheet: 0.69 (0.36), residues: 189 loop : -0.83 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 604 HIS 0.005 0.001 HIS A 779 PHE 0.021 0.001 PHE A 950 TYR 0.011 0.001 TYR A 239 ARG 0.009 0.000 ARG A 423 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2346.83 seconds wall clock time: 42 minutes 51.54 seconds (2571.54 seconds total)