Starting phenix.real_space_refine on Tue Mar 11 21:17:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yam_33717/03_2025/7yam_33717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yam_33717/03_2025/7yam_33717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yam_33717/03_2025/7yam_33717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yam_33717/03_2025/7yam_33717.map" model { file = "/net/cci-nas-00/data/ceres_data/7yam_33717/03_2025/7yam_33717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yam_33717/03_2025/7yam_33717.cif" } resolution = 3.3 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= 0.006 sd= 0.109 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 52 5.16 5 Be 1 3.05 5 C 4254 2.51 5 N 1116 2.21 5 O 1245 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6672 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6667 Classifications: {'peptide': 871} Link IDs: {'PTRANS': 34, 'TRANS': 836} Chain breaks: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.58, per 1000 atoms: 0.69 Number of scatterers: 6672 At special positions: 0 Unit cell: (80.5359, 86.3718, 130.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 52 16.00 Mg 1 11.99 F 3 9.00 O 1245 8.00 N 1116 7.00 C 4254 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 894.1 milliseconds 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 56.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 72 through 78 removed outlier: 3.800A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 256 through 288 Processing helix chain 'A' and resid 290 through 306 removed outlier: 3.991A pdb=" N SER A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.329A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.618A pdb=" N THR A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 341' Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.840A pdb=" N CYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 439 through 443 removed outlier: 4.024A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.602A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 682 through 723 removed outlier: 3.648A pdb=" N MET A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 740 Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.537A pdb=" N ALA A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 760 removed outlier: 3.623A pdb=" N ILE A 759 " --> pdb=" O ASP A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 798 Processing helix chain 'A' and resid 804 through 826 Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 841 through 861 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 904 removed outlier: 4.134A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 142 removed outlier: 4.489A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS A 227 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA A 178 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS A 229 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 197 removed outlier: 4.850A pdb=" N LEU A 181 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 332 removed outlier: 5.942A pdb=" N GLY A 658 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 677 " --> pdb=" O GLY A 658 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA A 660 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 639 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL A 659 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N MET A 641 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N MET A 661 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY A 643 " --> pdb=" O MET A 661 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 347 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE A 569 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER A 349 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N PHE A 617 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET A 568 " --> pdb=" O PHE A 617 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.376A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 462 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.376A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 13.762A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 417 413 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2147 1.34 - 1.46: 779 1.46 - 1.58: 3765 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 6775 Sorted by residual: bond pdb=" F2 BEF A1001 " pdb="BE BEF A1001 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" F3 BEF A1001 " pdb="BE BEF A1001 " ideal model delta sigma weight residual 1.476 1.544 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" N GLN A 747 " pdb=" CA GLN A 747 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.31e-02 5.83e+03 9.51e+00 bond pdb=" F1 BEF A1001 " pdb="BE BEF A1001 " ideal model delta sigma weight residual 1.476 1.538 -0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" CB PRO A 531 " pdb=" CG PRO A 531 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.52e+00 ... (remaining 6770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 9117 2.75 - 5.51: 44 5.51 - 8.26: 5 8.26 - 11.02: 1 11.02 - 13.77: 1 Bond angle restraints: 9168 Sorted by residual: angle pdb=" F2 BEF A1001 " pdb="BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 119.96 106.19 13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" F1 BEF A1001 " pdb="BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 120.12 109.70 10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C ASN A 738 " pdb=" N ILE A 739 " pdb=" CA ILE A 739 " ideal model delta sigma weight residual 122.97 119.83 3.14 9.80e-01 1.04e+00 1.03e+01 angle pdb=" C ASN A 701 " pdb=" N PHE A 702 " pdb=" CA PHE A 702 " ideal model delta sigma weight residual 121.14 116.52 4.62 1.75e+00 3.27e-01 6.96e+00 angle pdb=" N GLN A 747 " pdb=" CA GLN A 747 " pdb=" CB GLN A 747 " ideal model delta sigma weight residual 110.41 114.70 -4.29 1.68e+00 3.54e-01 6.53e+00 ... (remaining 9163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 3661 16.82 - 33.65: 374 33.65 - 50.47: 77 50.47 - 67.29: 11 67.29 - 84.11: 11 Dihedral angle restraints: 4134 sinusoidal: 1629 harmonic: 2505 Sorted by residual: dihedral pdb=" CA CYS A 225 " pdb=" C CYS A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual -180.00 -155.27 -24.73 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLY A 226 " pdb=" C GLY A 226 " pdb=" N LYS A 227 " pdb=" CA LYS A 227 " ideal model delta harmonic sigma weight residual 180.00 -163.23 -16.77 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB MET A 661 " pdb=" CG MET A 661 " pdb=" SD MET A 661 " pdb=" CE MET A 661 " ideal model delta sinusoidal sigma weight residual 180.00 121.25 58.75 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 735 0.033 - 0.066: 264 0.066 - 0.099: 69 0.099 - 0.132: 33 0.132 - 0.165: 2 Chirality restraints: 1103 Sorted by residual: chirality pdb=" CA PHE A 702 " pdb=" N PHE A 702 " pdb=" C PHE A 702 " pdb=" CB PHE A 702 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE A 657 " pdb=" N ILE A 657 " pdb=" C ILE A 657 " pdb=" CB ILE A 657 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA PRO A 531 " pdb=" N PRO A 531 " pdb=" C PRO A 531 " pdb=" CB PRO A 531 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1100 not shown) Planarity restraints: 1155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 747 " 0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C GLN A 747 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN A 747 " 0.022 2.00e-02 2.50e+03 pdb=" N SER A 748 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 136 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO A 137 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 743 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO A 744 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 744 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 744 " -0.021 5.00e-02 4.00e+02 ... (remaining 1152 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 10 2.39 - 3.01: 3717 3.01 - 3.64: 10147 3.64 - 4.27: 14803 4.27 - 4.90: 25787 Nonbonded interactions: 54464 Sorted by model distance: nonbonded pdb=" F1 BEF A1001 " pdb="MG MG A1002 " model vdw 1.756 2.120 nonbonded pdb=" OD2 ASP A 350 " pdb="MG MG A1002 " model vdw 1.997 2.170 nonbonded pdb=" O ASP A 350 " pdb=" OG1 THR A 354 " model vdw 2.106 3.040 nonbonded pdb=" O THR A 352 " pdb="MG MG A1002 " model vdw 2.132 2.170 nonbonded pdb=" OD1 ASP A 644 " pdb="MG MG A1002 " model vdw 2.200 2.170 ... (remaining 54459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.290 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.930 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.003 0.085 6775 Z= 0.233 Angle : 0.535 13.773 9168 Z= 0.272 Chirality : 0.040 0.165 1103 Planarity : 0.004 0.039 1155 Dihedral : 14.474 84.113 2512 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.29), residues: 863 helix: 2.36 (0.24), residues: 478 sheet: -0.15 (0.55), residues: 87 loop : 0.05 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.005 0.001 HIS A 149 PHE 0.024 0.002 PHE A 702 TYR 0.006 0.001 TYR A 380 ARG 0.002 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.736 Fit side-chains REVERT: A 25 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7007 (mttm) REVERT: A 28 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6677 (mp0) REVERT: A 54 ARG cc_start: 0.7331 (mtt90) cc_final: 0.7106 (mtt90) REVERT: A 464 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7536 (mtmm) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.1899 time to fit residues: 32.3067 Evaluate side-chains 104 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.208867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.181397 restraints weight = 6797.933| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.31 r_work: 0.3601 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6775 Z= 0.207 Angle : 0.499 6.482 9168 Z= 0.265 Chirality : 0.040 0.159 1103 Planarity : 0.004 0.042 1155 Dihedral : 4.387 56.627 919 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.94 % Allowed : 8.16 % Favored : 90.91 % 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: 2.06 (0.29), residues: 863 helix: 2.42 (0.24), residues: 479 sheet: -0.02 (0.52), residues: 97 loop : 0.12 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.000 HIS A 149 PHE 0.023 0.001 PHE A 702 TYR 0.021 0.001 TYR A 75 ARG 0.003 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.695 Fit side-chains REVERT: A 17 MET cc_start: 0.7718 (tpp) cc_final: 0.7440 (tpt) REVERT: A 25 LYS cc_start: 0.7590 (mmmt) cc_final: 0.6535 (mttm) REVERT: A 28 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6946 (mp0) REVERT: A 54 ARG cc_start: 0.7276 (mtt90) cc_final: 0.6903 (mtt90) REVERT: A 121 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7132 (tm-30) REVERT: A 464 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8104 (mtmm) REVERT: A 756 LYS cc_start: 0.7908 (mmmm) cc_final: 0.7271 (ptpp) REVERT: A 760 ARG cc_start: 0.8326 (mtm110) cc_final: 0.7861 (mmt-90) REVERT: A 828 SER cc_start: 0.8798 (t) cc_final: 0.8466 (m) outliers start: 7 outliers final: 7 residues processed: 108 average time/residue: 0.2069 time to fit residues: 29.5565 Evaluate side-chains 104 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.0270 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 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 = 0.3740 r_free = 0.3740 target = 0.163166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.129395 restraints weight = 7031.539| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.40 r_work: 0.3361 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6775 Z= 0.198 Angle : 0.477 6.430 9168 Z= 0.251 Chirality : 0.040 0.157 1103 Planarity : 0.004 0.043 1155 Dihedral : 3.803 20.304 916 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.74 % Allowed : 9.63 % Favored : 88.64 % 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: 2.16 (0.29), residues: 863 helix: 2.46 (0.24), residues: 479 sheet: 0.23 (0.58), residues: 82 loop : 0.16 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.001 0.000 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.016 0.001 TYR A 75 ARG 0.003 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.757 Fit side-chains REVERT: A 25 LYS cc_start: 0.7729 (mmmt) cc_final: 0.6695 (mttm) REVERT: A 28 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6908 (mp0) REVERT: A 449 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8150 (mmtm) REVERT: A 464 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8072 (mtmm) REVERT: A 657 ILE cc_start: 0.7435 (mp) cc_final: 0.7150 (mp) REVERT: A 756 LYS cc_start: 0.7874 (mmmm) cc_final: 0.7270 (ptpp) REVERT: A 760 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7889 (mmt-90) REVERT: A 828 SER cc_start: 0.8757 (t) cc_final: 0.8426 (m) outliers start: 13 outliers final: 10 residues processed: 112 average time/residue: 0.2179 time to fit residues: 32.3426 Evaluate side-chains 105 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 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 = 0.3737 r_free = 0.3737 target = 0.162961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.130360 restraints weight = 7060.003| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.42 r_work: 0.3207 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6775 Z= 0.204 Angle : 0.485 6.389 9168 Z= 0.254 Chirality : 0.040 0.157 1103 Planarity : 0.004 0.043 1155 Dihedral : 3.799 20.009 916 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.01 % Allowed : 10.83 % Favored : 87.17 % 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: 2.05 (0.29), residues: 863 helix: 2.43 (0.24), residues: 479 sheet: -0.21 (0.52), residues: 97 loop : 0.14 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.000 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.016 0.001 TYR A 75 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.781 Fit side-chains REVERT: A 17 MET cc_start: 0.7277 (tpp) cc_final: 0.7043 (tpt) REVERT: A 25 LYS cc_start: 0.7579 (mmmt) cc_final: 0.6607 (mttm) REVERT: A 28 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6821 (mp0) REVERT: A 449 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8355 (mmtm) REVERT: A 464 LYS cc_start: 0.8393 (mtmm) cc_final: 0.7894 (mttm) REVERT: A 756 LYS cc_start: 0.7693 (mmmm) cc_final: 0.6961 (ptpp) REVERT: A 828 SER cc_start: 0.8758 (t) cc_final: 0.8420 (m) REVERT: A 853 MET cc_start: 0.8241 (mmm) cc_final: 0.8021 (mmm) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.2031 time to fit residues: 30.0188 Evaluate side-chains 107 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 74 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.163239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.129934 restraints weight = 6953.352| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.46 r_work: 0.3307 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6775 Z= 0.202 Angle : 0.480 6.429 9168 Z= 0.252 Chirality : 0.039 0.156 1103 Planarity : 0.004 0.044 1155 Dihedral : 3.798 20.100 916 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.27 % Allowed : 11.76 % Favored : 85.96 % 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: 2.03 (0.29), residues: 863 helix: 2.42 (0.24), residues: 480 sheet: -0.32 (0.51), residues: 97 loop : 0.16 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.000 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.014 0.001 TYR A 75 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.783 Fit side-chains REVERT: A 17 MET cc_start: 0.7383 (tpp) cc_final: 0.7117 (tpt) REVERT: A 25 LYS cc_start: 0.7696 (mmmt) cc_final: 0.6667 (mttm) REVERT: A 28 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6915 (mp0) REVERT: A 449 LYS cc_start: 0.8998 (mmtp) cc_final: 0.8391 (mmtm) REVERT: A 464 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8112 (mttm) REVERT: A 756 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7097 (ptpp) REVERT: A 760 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7823 (mmt180) REVERT: A 800 ASP cc_start: 0.6704 (t0) cc_final: 0.6125 (t0) REVERT: A 828 SER cc_start: 0.8765 (t) cc_final: 0.8444 (m) REVERT: A 853 MET cc_start: 0.8322 (mmm) cc_final: 0.8106 (mmm) outliers start: 17 outliers final: 13 residues processed: 106 average time/residue: 0.2077 time to fit residues: 29.7738 Evaluate side-chains 108 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 36 optimal weight: 0.0050 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 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 = 0.3744 r_free = 0.3744 target = 0.163862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.130153 restraints weight = 6956.745| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.41 r_work: 0.3215 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6775 Z= 0.180 Angle : 0.466 6.606 9168 Z= 0.245 Chirality : 0.039 0.154 1103 Planarity : 0.004 0.044 1155 Dihedral : 3.730 19.760 916 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.01 % Allowed : 12.57 % Favored : 85.43 % 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: 2.12 (0.29), residues: 863 helix: 2.49 (0.24), residues: 479 sheet: -0.35 (0.51), residues: 97 loop : 0.23 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.000 HIS A 140 PHE 0.023 0.001 PHE A 702 TYR 0.014 0.001 TYR A 75 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.718 Fit side-chains REVERT: A 17 MET cc_start: 0.7259 (tpp) cc_final: 0.6950 (tpt) REVERT: A 25 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7208 (mttm) REVERT: A 449 LYS cc_start: 0.8996 (mmtp) cc_final: 0.8361 (mmtm) REVERT: A 606 GLN cc_start: 0.7586 (tp40) cc_final: 0.7340 (mm-40) REVERT: A 756 LYS cc_start: 0.7662 (mmmm) cc_final: 0.6813 (ptpp) REVERT: A 760 ARG cc_start: 0.8321 (mtm110) cc_final: 0.7710 (mmt180) REVERT: A 800 ASP cc_start: 0.6843 (t0) cc_final: 0.6341 (t0) REVERT: A 801 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7581 (t0) REVERT: A 828 SER cc_start: 0.8719 (t) cc_final: 0.8422 (m) REVERT: A 853 MET cc_start: 0.8256 (mmm) cc_final: 0.8027 (mmm) outliers start: 15 outliers final: 12 residues processed: 108 average time/residue: 0.1841 time to fit residues: 26.8416 Evaluate side-chains 109 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 59 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 17 optimal weight: 0.0270 chunk 65 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 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 = 0.3738 r_free = 0.3738 target = 0.163506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.129368 restraints weight = 6937.029| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.42 r_work: 0.3194 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6775 Z= 0.190 Angle : 0.482 6.767 9168 Z= 0.254 Chirality : 0.039 0.155 1103 Planarity : 0.004 0.045 1155 Dihedral : 3.731 19.785 916 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.14 % Allowed : 12.43 % Favored : 85.43 % 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: 2.16 (0.29), residues: 863 helix: 2.47 (0.24), residues: 480 sheet: -0.01 (0.57), residues: 82 loop : 0.22 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.002 0.000 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.013 0.001 TYR A 75 ARG 0.001 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.702 Fit side-chains REVERT: A 17 MET cc_start: 0.7246 (tpp) cc_final: 0.7009 (tpt) REVERT: A 25 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7322 (mttm) REVERT: A 28 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6673 (mm-30) REVERT: A 449 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8336 (mmtm) REVERT: A 464 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7565 (mtmm) REVERT: A 756 LYS cc_start: 0.7658 (mmmm) cc_final: 0.6796 (ptpp) REVERT: A 760 ARG cc_start: 0.8333 (mtm110) cc_final: 0.7698 (mmt180) REVERT: A 800 ASP cc_start: 0.6846 (t0) cc_final: 0.6422 (t0) REVERT: A 828 SER cc_start: 0.8748 (t) cc_final: 0.8454 (m) REVERT: A 853 MET cc_start: 0.8258 (mmm) cc_final: 0.8029 (mmm) outliers start: 16 outliers final: 16 residues processed: 106 average time/residue: 0.1882 time to fit residues: 26.9455 Evaluate side-chains 112 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 4 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 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 = 0.3721 r_free = 0.3721 target = 0.161852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.132413 restraints weight = 7031.706| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.24 r_work: 0.3166 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6775 Z= 0.266 Angle : 0.527 7.143 9168 Z= 0.277 Chirality : 0.041 0.164 1103 Planarity : 0.004 0.045 1155 Dihedral : 3.888 20.421 916 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.81 % Allowed : 12.30 % Favored : 84.89 % 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: 2.03 (0.29), residues: 863 helix: 2.33 (0.24), residues: 478 sheet: -0.01 (0.58), residues: 82 loop : 0.21 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.001 HIS A 140 PHE 0.022 0.002 PHE A 702 TYR 0.016 0.001 TYR A 75 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.728 Fit side-chains REVERT: A 17 MET cc_start: 0.7443 (tpp) cc_final: 0.7192 (tpt) REVERT: A 25 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7251 (mttm) REVERT: A 28 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6683 (mm-30) REVERT: A 449 LYS cc_start: 0.8964 (mmtp) cc_final: 0.8336 (mmtm) REVERT: A 464 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7561 (mtmm) REVERT: A 756 LYS cc_start: 0.7736 (mmmm) cc_final: 0.6911 (ptpp) REVERT: A 760 ARG cc_start: 0.8356 (mtm110) cc_final: 0.7792 (mmt180) REVERT: A 800 ASP cc_start: 0.6722 (t0) cc_final: 0.6278 (t0) REVERT: A 801 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7582 (t0) REVERT: A 828 SER cc_start: 0.8761 (t) cc_final: 0.8433 (m) outliers start: 21 outliers final: 17 residues processed: 106 average time/residue: 0.1939 time to fit residues: 27.5358 Evaluate side-chains 114 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 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 = 0.3735 r_free = 0.3735 target = 0.162836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.133277 restraints weight = 7045.496| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.24 r_work: 0.3183 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6775 Z= 0.220 Angle : 0.509 7.006 9168 Z= 0.265 Chirality : 0.040 0.157 1103 Planarity : 0.004 0.046 1155 Dihedral : 3.833 20.130 916 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.54 % Allowed : 12.83 % Favored : 84.63 % 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: 2.07 (0.29), residues: 863 helix: 2.40 (0.24), residues: 478 sheet: -0.05 (0.58), residues: 82 loop : 0.18 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.002 0.001 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.012 0.001 TYR A 75 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.728 Fit side-chains REVERT: A 17 MET cc_start: 0.7389 (tpp) cc_final: 0.7147 (tpt) REVERT: A 25 LYS cc_start: 0.7775 (mmmt) cc_final: 0.7322 (mttm) REVERT: A 28 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6690 (mm-30) REVERT: A 449 LYS cc_start: 0.8962 (mmtp) cc_final: 0.8330 (mmtm) REVERT: A 464 LYS cc_start: 0.8266 (mtmm) cc_final: 0.7568 (mtmm) REVERT: A 760 ARG cc_start: 0.8376 (mtm110) cc_final: 0.7778 (mmt180) REVERT: A 800 ASP cc_start: 0.6790 (t0) cc_final: 0.6378 (t0) REVERT: A 801 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7539 (t0) REVERT: A 853 MET cc_start: 0.8139 (mmm) cc_final: 0.7925 (mpp) outliers start: 19 outliers final: 16 residues processed: 107 average time/residue: 0.1873 time to fit residues: 27.0059 Evaluate side-chains 112 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 71 optimal weight: 0.1980 chunk 47 optimal weight: 0.0270 chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 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 = 0.3748 r_free = 0.3748 target = 0.164402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.134918 restraints weight = 7097.663| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.26 r_work: 0.3197 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6775 Z= 0.186 Angle : 0.500 7.208 9168 Z= 0.259 Chirality : 0.040 0.154 1103 Planarity : 0.004 0.046 1155 Dihedral : 3.764 19.764 916 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.14 % Allowed : 13.50 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.29), residues: 863 helix: 2.50 (0.23), residues: 478 sheet: -0.06 (0.58), residues: 82 loop : 0.20 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.002 0.000 HIS A 140 PHE 0.023 0.001 PHE A 702 TYR 0.008 0.001 TYR A 75 ARG 0.001 0.000 ARG A 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.791 Fit side-chains REVERT: A 17 MET cc_start: 0.7380 (tpp) cc_final: 0.7177 (tpt) REVERT: A 25 LYS cc_start: 0.7731 (mmmt) cc_final: 0.7300 (mttm) REVERT: A 28 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6785 (mm-30) REVERT: A 437 MET cc_start: 0.8110 (tpp) cc_final: 0.7857 (mmm) REVERT: A 449 LYS cc_start: 0.8960 (mmtp) cc_final: 0.8337 (mmtm) REVERT: A 464 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7602 (mtmm) REVERT: A 760 ARG cc_start: 0.8353 (mtm110) cc_final: 0.7772 (mmt180) REVERT: A 800 ASP cc_start: 0.6783 (t0) cc_final: 0.6408 (t0) REVERT: A 801 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7401 (t0) REVERT: A 828 SER cc_start: 0.8812 (t) cc_final: 0.8560 (m) REVERT: A 853 MET cc_start: 0.8145 (mmm) cc_final: 0.7940 (mpp) outliers start: 16 outliers final: 14 residues processed: 107 average time/residue: 0.1929 time to fit residues: 27.9468 Evaluate side-chains 108 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 0.0270 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 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 = 0.3814 r_free = 0.3814 target = 0.169313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.155852 restraints weight = 6855.970| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 0.45 r_work: 0.3418 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6775 Z= 0.194 Angle : 0.498 7.205 9168 Z= 0.259 Chirality : 0.040 0.158 1103 Planarity : 0.004 0.046 1155 Dihedral : 3.736 20.326 916 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.01 % Allowed : 13.50 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.29), residues: 863 helix: 2.51 (0.23), residues: 478 sheet: -0.09 (0.58), residues: 82 loop : 0.20 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.002 0.000 HIS A 140 PHE 0.023 0.001 PHE A 702 TYR 0.007 0.001 TYR A 483 ARG 0.001 0.000 ARG A 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3707.27 seconds wall clock time: 64 minutes 22.19 seconds (3862.19 seconds total)