Starting phenix.real_space_refine on Tue Mar 3 15:39:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yam_33717/03_2026/7yam_33717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yam_33717/03_2026/7yam_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_2026/7yam_33717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yam_33717/03_2026/7yam_33717.map" model { file = "/net/cci-nas-00/data/ceres_data/7yam_33717/03_2026/7yam_33717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yam_33717/03_2026/7yam_33717.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.63, per 1000 atoms: 0.24 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: 0.67 Conformation dependent library (CDL) restraints added in 233.4 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: 0.30 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: 1.32 Time building geometry restraints manager: 0.81 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.470 ------------------------------------------------------------------------------- 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 : 0.013 1.043 6776 Z= 1.276 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 623 TYR 0.006 0.001 TYR A 380 PHE 0.024 0.002 PHE A 702 TRP 0.007 0.001 TRP A 460 HIS 0.005 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6775) covalent geometry : angle 0.53453 ( 9168) hydrogen bonds : bond 0.13061 ( 401) hydrogen bonds : angle 5.85751 ( 1209) Misc. bond : bond 1.04287 ( 1) *********************** 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 : 0.242 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: 0.0859 time to fit residues: 14.5751 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 : 0.233 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 0.0670 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.209119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.181289 restraints weight = 6863.442| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.32 r_work: 0.3618 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6776 Z= 0.129 Angle : 0.495 6.498 9168 Z= 0.263 Chirality : 0.040 0.158 1103 Planarity : 0.004 0.042 1155 Dihedral : 4.369 56.102 919 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.09 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.29), residues: 863 helix: 2.43 (0.24), residues: 479 sheet: 0.32 (0.58), residues: 82 loop : 0.15 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 123 TYR 0.021 0.001 TYR A 75 PHE 0.023 0.001 PHE A 702 TRP 0.006 0.001 TRP A 736 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6775) covalent geometry : angle 0.49536 ( 9168) hydrogen bonds : bond 0.04118 ( 401) hydrogen bonds : angle 4.74017 ( 1209) Misc. bond : bond 0.00181 ( 1) *********************** 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 : 0.200 Fit side-chains REVERT: A 17 MET cc_start: 0.7725 (tpp) cc_final: 0.7437 (tpt) REVERT: A 25 LYS cc_start: 0.7582 (mmmt) cc_final: 0.6523 (mttm) REVERT: A 28 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6927 (mp0) REVERT: A 121 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7143 (tm-30) REVERT: A 464 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8094 (mtmm) REVERT: A 756 LYS cc_start: 0.7923 (mmmm) cc_final: 0.7341 (ptpp) REVERT: A 760 ARG cc_start: 0.8251 (mtm110) cc_final: 0.7884 (mmt-90) REVERT: A 828 SER cc_start: 0.8788 (t) cc_final: 0.8456 (m) outliers start: 7 outliers final: 6 residues processed: 108 average time/residue: 0.0890 time to fit residues: 12.7016 Evaluate side-chains 103 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 46 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 0.0030 overall best weight: 0.3108 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.165293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.131667 restraints weight = 6973.040| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.39 r_work: 0.3426 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 6776 Z= 0.104 Angle : 0.456 6.256 9168 Z= 0.240 Chirality : 0.039 0.152 1103 Planarity : 0.004 0.042 1155 Dihedral : 3.702 19.660 916 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.60 % Allowed : 9.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.29), residues: 863 helix: 2.56 (0.24), residues: 480 sheet: -0.05 (0.52), residues: 97 loop : 0.17 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 900 TYR 0.016 0.001 TYR A 75 PHE 0.024 0.001 PHE A 702 TRP 0.006 0.001 TRP A 460 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6775) covalent geometry : angle 0.45556 ( 9168) hydrogen bonds : bond 0.03614 ( 401) hydrogen bonds : angle 4.46968 ( 1209) Misc. bond : bond 0.00084 ( 1) *********************** 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 117 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.257 Fit side-chains REVERT: A 25 LYS cc_start: 0.7644 (mmmt) cc_final: 0.6573 (mttm) REVERT: A 28 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6832 (mp0) REVERT: A 54 ARG cc_start: 0.7284 (mtt90) cc_final: 0.6937 (mtt90) REVERT: A 449 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8270 (mmtm) REVERT: A 464 LYS cc_start: 0.8471 (mtmm) cc_final: 0.7965 (mtmm) REVERT: A 657 ILE cc_start: 0.7334 (mp) cc_final: 0.7064 (mp) REVERT: A 756 LYS cc_start: 0.7878 (mmmm) cc_final: 0.7188 (ptpp) REVERT: A 760 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7843 (mmt180) REVERT: A 828 SER cc_start: 0.8743 (t) cc_final: 0.8417 (m) outliers start: 12 outliers final: 9 residues processed: 112 average time/residue: 0.0809 time to fit residues: 12.0664 Evaluate side-chains 102 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 895 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.161628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.127928 restraints weight = 6982.211| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.46 r_work: 0.3186 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6776 Z= 0.166 Angle : 0.516 6.569 9168 Z= 0.270 Chirality : 0.041 0.165 1103 Planarity : 0.004 0.044 1155 Dihedral : 3.876 20.309 916 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.01 % Allowed : 10.70 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.29), residues: 863 helix: 2.31 (0.24), residues: 480 sheet: -0.16 (0.52), residues: 97 loop : 0.16 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.015 0.001 TYR A 75 PHE 0.022 0.002 PHE A 702 TRP 0.007 0.001 TRP A 736 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6775) covalent geometry : angle 0.51576 ( 9168) hydrogen bonds : bond 0.04163 ( 401) hydrogen bonds : angle 4.51133 ( 1209) Misc. bond : bond 0.00170 ( 1) *********************** 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 : 0.212 Fit side-chains REVERT: A 17 MET cc_start: 0.7408 (tpp) cc_final: 0.7103 (tpt) REVERT: A 25 LYS cc_start: 0.7568 (mmmt) cc_final: 0.6557 (mttm) REVERT: A 28 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6840 (mp0) REVERT: A 449 LYS cc_start: 0.8990 (mmtp) cc_final: 0.8274 (mmtm) REVERT: A 464 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8084 (mttm) REVERT: A 756 LYS cc_start: 0.7705 (mmmm) cc_final: 0.6989 (ptpp) REVERT: A 828 SER cc_start: 0.8779 (t) cc_final: 0.8430 (m) REVERT: A 853 MET cc_start: 0.8263 (mmm) cc_final: 0.8029 (mmm) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 0.0872 time to fit residues: 12.7189 Evaluate side-chains 110 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 13 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 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 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 = 0.3709 r_free = 0.3709 target = 0.160285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.126436 restraints weight = 7065.175| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.45 r_work: 0.3285 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6776 Z= 0.186 Angle : 0.530 6.602 9168 Z= 0.280 Chirality : 0.041 0.168 1103 Planarity : 0.004 0.047 1155 Dihedral : 4.045 21.189 916 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.41 % Allowed : 11.76 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.29), residues: 863 helix: 2.13 (0.23), residues: 485 sheet: -0.21 (0.58), residues: 77 loop : 0.19 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.016 0.002 TYR A 75 PHE 0.022 0.002 PHE A 702 TRP 0.008 0.001 TRP A 736 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 6775) covalent geometry : angle 0.53048 ( 9168) hydrogen bonds : bond 0.04351 ( 401) hydrogen bonds : angle 4.57339 ( 1209) Misc. bond : bond 0.00190 ( 1) *********************** 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 117 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.180 Fit side-chains REVERT: A 17 MET cc_start: 0.7489 (tpp) cc_final: 0.7209 (tpt) REVERT: A 25 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7371 (mttm) REVERT: A 449 LYS cc_start: 0.8966 (mmtp) cc_final: 0.8307 (mmtm) REVERT: A 756 LYS cc_start: 0.7812 (mmmm) cc_final: 0.7196 (ptpp) REVERT: A 760 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7908 (mmt180) REVERT: A 800 ASP cc_start: 0.6586 (t0) cc_final: 0.6036 (t0) REVERT: A 828 SER cc_start: 0.8780 (t) cc_final: 0.8440 (m) outliers start: 18 outliers final: 13 residues processed: 111 average time/residue: 0.0826 time to fit residues: 12.1247 Evaluate side-chains 107 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 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 82 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.163307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.129090 restraints weight = 7075.152| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.46 r_work: 0.3186 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6776 Z= 0.113 Angle : 0.474 6.697 9168 Z= 0.250 Chirality : 0.039 0.152 1103 Planarity : 0.004 0.045 1155 Dihedral : 3.810 20.377 916 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.74 % Allowed : 12.43 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.29), residues: 863 helix: 2.42 (0.24), residues: 479 sheet: -0.03 (0.57), residues: 82 loop : 0.16 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.018 0.001 TYR A 75 PHE 0.023 0.001 PHE A 702 TRP 0.007 0.001 TRP A 736 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6775) covalent geometry : angle 0.47430 ( 9168) hydrogen bonds : bond 0.03650 ( 401) hydrogen bonds : angle 4.36786 ( 1209) Misc. bond : bond 0.00072 ( 1) *********************** 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 112 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.233 Fit side-chains REVERT: A 17 MET cc_start: 0.7407 (tpp) cc_final: 0.7098 (tpt) REVERT: A 25 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7285 (mttm) REVERT: A 54 ARG cc_start: 0.7362 (mtt90) cc_final: 0.6980 (mtt90) REVERT: A 449 LYS cc_start: 0.9045 (mmtp) cc_final: 0.8379 (mmtm) REVERT: A 464 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7540 (mtmm) REVERT: A 756 LYS cc_start: 0.7634 (mmmm) cc_final: 0.6797 (ptpp) REVERT: A 760 ARG cc_start: 0.8343 (mtm110) cc_final: 0.7703 (mmt180) REVERT: A 800 ASP cc_start: 0.6872 (t0) cc_final: 0.6438 (t0) REVERT: A 801 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7599 (t0) REVERT: A 828 SER cc_start: 0.8719 (t) cc_final: 0.8428 (m) REVERT: A 853 MET cc_start: 0.8058 (mmm) cc_final: 0.7799 (mmm) outliers start: 13 outliers final: 10 residues processed: 107 average time/residue: 0.0826 time to fit residues: 11.8236 Evaluate side-chains 106 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR 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 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 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 606 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.160991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.127179 restraints weight = 6990.199| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.44 r_work: 0.3168 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6776 Z= 0.163 Angle : 0.515 6.722 9168 Z= 0.271 Chirality : 0.041 0.164 1103 Planarity : 0.004 0.046 1155 Dihedral : 3.928 20.967 916 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.14 % Allowed : 13.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.29), residues: 863 helix: 2.26 (0.24), residues: 484 sheet: -0.32 (0.57), residues: 77 loop : 0.16 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.015 0.001 TYR A 75 PHE 0.022 0.002 PHE A 702 TRP 0.007 0.001 TRP A 736 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6775) covalent geometry : angle 0.51526 ( 9168) hydrogen bonds : bond 0.04110 ( 401) hydrogen bonds : angle 4.46167 ( 1209) Misc. bond : bond 0.00154 ( 1) *********************** 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 113 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.269 Fit side-chains REVERT: A 17 MET cc_start: 0.7494 (tpp) cc_final: 0.7210 (tpt) REVERT: A 25 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7218 (mttm) REVERT: A 54 ARG cc_start: 0.7316 (mtt90) cc_final: 0.6921 (mtt90) REVERT: A 449 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8272 (mmtm) REVERT: A 464 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7563 (mtmm) REVERT: A 606 GLN cc_start: 0.7693 (tp40) cc_final: 0.7445 (mm-40) REVERT: A 760 ARG cc_start: 0.8313 (mtm110) cc_final: 0.7751 (mmt180) REVERT: A 800 ASP cc_start: 0.6816 (t0) cc_final: 0.6349 (t0) REVERT: A 801 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7528 (t0) REVERT: A 828 SER cc_start: 0.8782 (t) cc_final: 0.8447 (m) REVERT: A 853 MET cc_start: 0.8154 (mmm) cc_final: 0.7917 (mmm) outliers start: 16 outliers final: 14 residues processed: 106 average time/residue: 0.0845 time to fit residues: 11.9328 Evaluate side-chains 112 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.162585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.126437 restraints weight = 7012.672| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.49 r_work: 0.3154 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6776 Z= 0.142 Angle : 0.517 7.054 9168 Z= 0.269 Chirality : 0.040 0.157 1103 Planarity : 0.004 0.047 1155 Dihedral : 3.893 20.801 916 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.67 % Allowed : 13.64 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.29), residues: 863 helix: 2.34 (0.24), residues: 478 sheet: -0.03 (0.58), residues: 82 loop : 0.13 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.014 0.001 TYR A 75 PHE 0.022 0.001 PHE A 702 TRP 0.007 0.001 TRP A 736 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6775) covalent geometry : angle 0.51679 ( 9168) hydrogen bonds : bond 0.03915 ( 401) hydrogen bonds : angle 4.41777 ( 1209) Misc. bond : bond 0.00109 ( 1) *********************** 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: 20 poor density : 98 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 17 MET cc_start: 0.7536 (tpp) cc_final: 0.7280 (tpt) REVERT: A 25 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7127 (mttm) REVERT: A 449 LYS cc_start: 0.9000 (mmtp) cc_final: 0.8308 (mmtm) REVERT: A 464 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7414 (mtmm) REVERT: A 606 GLN cc_start: 0.7500 (tp40) cc_final: 0.7236 (mm-40) REVERT: A 760 ARG cc_start: 0.8330 (mtm110) cc_final: 0.7663 (mmt180) REVERT: A 800 ASP cc_start: 0.6815 (t0) cc_final: 0.6341 (t0) REVERT: A 801 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7466 (t0) REVERT: A 828 SER cc_start: 0.8687 (t) cc_final: 0.8341 (m) REVERT: A 853 MET cc_start: 0.7943 (mmm) cc_final: 0.7706 (mmm) outliers start: 20 outliers final: 18 residues processed: 109 average time/residue: 0.0781 time to fit residues: 11.3888 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 : 0.209 ------------------------------------------------------------------------------- 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 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 611 VAL 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 804 THR 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 50 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 58 optimal weight: 0.0570 chunk 5 optimal weight: 2.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.164599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.135463 restraints weight = 7013.955| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.24 r_work: 0.3196 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6776 Z= 0.115 Angle : 0.493 7.151 9168 Z= 0.256 Chirality : 0.039 0.153 1103 Planarity : 0.004 0.049 1155 Dihedral : 3.752 20.180 916 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.27 % Allowed : 14.04 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.29), residues: 863 helix: 2.49 (0.24), residues: 478 sheet: -0.04 (0.58), residues: 82 loop : 0.16 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.012 0.001 TYR A 75 PHE 0.024 0.001 PHE A 702 TRP 0.007 0.001 TRP A 460 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6775) covalent geometry : angle 0.49327 ( 9168) hydrogen bonds : bond 0.03591 ( 401) hydrogen bonds : angle 4.30585 ( 1209) Misc. bond : bond 0.00063 ( 1) *********************** 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 114 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 17 MET cc_start: 0.7479 (tpp) cc_final: 0.7253 (tpt) REVERT: A 25 LYS cc_start: 0.7686 (mmmt) cc_final: 0.7208 (mttm) REVERT: A 54 ARG cc_start: 0.7281 (mtt90) cc_final: 0.6895 (mtt180) REVERT: A 449 LYS cc_start: 0.9018 (mmtp) cc_final: 0.8367 (mmtm) REVERT: A 464 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7518 (mtmm) REVERT: A 606 GLN cc_start: 0.7558 (tp40) cc_final: 0.7339 (mm-40) REVERT: A 760 ARG cc_start: 0.8385 (mtm110) cc_final: 0.7766 (mmt180) REVERT: A 800 ASP cc_start: 0.6728 (t0) cc_final: 0.6347 (t0) REVERT: A 801 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7534 (t0) REVERT: A 828 SER cc_start: 0.8691 (t) cc_final: 0.8408 (m) REVERT: A 853 MET cc_start: 0.8008 (mmm) cc_final: 0.7784 (mmm) outliers start: 17 outliers final: 14 residues processed: 107 average time/residue: 0.0831 time to fit residues: 12.0006 Evaluate side-chains 110 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 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 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 = 0.3716 r_free = 0.3716 target = 0.161210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.130933 restraints weight = 7090.116| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.33 r_work: 0.3275 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6776 Z= 0.179 Angle : 0.541 6.995 9168 Z= 0.283 Chirality : 0.041 0.165 1103 Planarity : 0.004 0.048 1155 Dihedral : 3.962 20.960 916 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.27 % Allowed : 13.90 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.29), residues: 863 helix: 2.24 (0.23), residues: 484 sheet: -0.41 (0.58), residues: 77 loop : 0.17 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.010 0.001 TYR A 380 PHE 0.023 0.002 PHE A 702 TRP 0.008 0.001 TRP A 736 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 6775) covalent geometry : angle 0.54127 ( 9168) hydrogen bonds : bond 0.04263 ( 401) hydrogen bonds : angle 4.48142 ( 1209) Misc. bond : bond 0.00174 ( 1) ********************** 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 115 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7755 (mmmt) cc_final: 0.7240 (mttm) REVERT: A 54 ARG cc_start: 0.7457 (mtt90) cc_final: 0.7135 (mtt90) REVERT: A 437 MET cc_start: 0.8262 (tpp) cc_final: 0.8019 (mmm) REVERT: A 449 LYS cc_start: 0.9038 (mmtp) cc_final: 0.8400 (mmtm) REVERT: A 464 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7733 (mtmm) REVERT: A 760 ARG cc_start: 0.8392 (mtm110) cc_final: 0.7857 (mmt180) REVERT: A 800 ASP cc_start: 0.6752 (t0) cc_final: 0.6362 (t0) REVERT: A 801 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7633 (t0) REVERT: A 828 SER cc_start: 0.8780 (t) cc_final: 0.8462 (m) REVERT: A 853 MET cc_start: 0.8106 (mmm) cc_final: 0.7873 (mmm) outliers start: 17 outliers final: 15 residues processed: 108 average time/residue: 0.0808 time to fit residues: 11.7984 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 : 0.229 ------------------------------------------------------------------------------- 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 611 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: 0.5980 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 0.0170 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.163343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133983 restraints weight = 6990.026| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.25 r_work: 0.3176 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6776 Z= 0.127 Angle : 0.499 7.221 9168 Z= 0.260 Chirality : 0.040 0.153 1103 Planarity : 0.004 0.049 1155 Dihedral : 3.832 20.661 916 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.41 % Allowed : 13.77 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.29), residues: 863 helix: 2.45 (0.24), residues: 478 sheet: -0.14 (0.58), residues: 82 loop : 0.13 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.007 0.001 TYR A 380 PHE 0.023 0.001 PHE A 702 TRP 0.007 0.001 TRP A 736 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6775) covalent geometry : angle 0.49913 ( 9168) hydrogen bonds : bond 0.03795 ( 401) hydrogen bonds : angle 4.36451 ( 1209) Misc. bond : bond 0.00105 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1697.49 seconds wall clock time: 29 minutes 45.02 seconds (1785.02 seconds total)