Starting phenix.real_space_refine on Sat Apr 4 22:49:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lm0_63211/04_2026/9lm0_63211.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lm0_63211/04_2026/9lm0_63211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lm0_63211/04_2026/9lm0_63211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lm0_63211/04_2026/9lm0_63211.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lm0_63211/04_2026/9lm0_63211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lm0_63211/04_2026/9lm0_63211.map" } resolution = 3.82 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= -0.001 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 3349 2.51 5 N 852 2.21 5 O 926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5171 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2590 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 25, 'TRANS': 311} Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2581 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 25, 'TRANS': 310} Time building chain proxies: 1.09, per 1000 atoms: 0.21 Number of scatterers: 5171 At special positions: 0 Unit cell: (83.104, 62.752, 123.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 926 8.00 N 852 7.00 C 3349 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 522 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 650 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 522 " - pdb=" SG CYS A 540 " distance=2.04 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 744 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 319.9 milliseconds 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1258 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 63.6% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 586 through 610 removed outlier: 3.826A pdb=" N VAL B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 618 removed outlier: 3.634A pdb=" N ALA B 618 " --> pdb=" O PRO B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 642 removed outlier: 3.642A pdb=" N LEU B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 638 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE B 639 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 681 removed outlier: 3.976A pdb=" N ARG B 654 " --> pdb=" O CYS B 650 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 719 removed outlier: 3.717A pdb=" N GLN B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL B 699 " --> pdb=" O THR B 695 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 738 removed outlier: 3.615A pdb=" N GLN B 737 " --> pdb=" O ASP B 734 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 738 " --> pdb=" O PRO B 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 734 through 738' Processing helix chain 'B' and resid 747 through 772 removed outlier: 3.804A pdb=" N ILE B 752 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER B 758 " --> pdb=" O CYS B 754 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 760 " --> pdb=" O GLY B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 806 removed outlier: 3.764A pdb=" N ILE B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 789 " --> pdb=" O ILE B 785 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 794 " --> pdb=" O TYR B 790 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 795 " --> pdb=" O THR B 791 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 800 " --> pdb=" O TRP B 796 " (cutoff:3.500A) Proline residue: B 801 - end of helix Processing helix chain 'B' and resid 811 through 836 removed outlier: 3.642A pdb=" N THR B 817 " --> pdb=" O ILE B 813 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 831 " --> pdb=" O SER B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 846 removed outlier: 3.621A pdb=" N VAL B 842 " --> pdb=" O PRO B 838 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 843 " --> pdb=" O LYS B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 851 removed outlier: 3.603A pdb=" N VAL B 851 " --> pdb=" O PRO B 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 585 No H-bonds generated for 'chain 'A' and resid 583 through 585' Processing helix chain 'A' and resid 586 through 610 removed outlier: 3.757A pdb=" N VAL A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 620 removed outlier: 3.709A pdb=" N ARG A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 636 Processing helix chain 'A' and resid 636 through 642 removed outlier: 3.858A pdb=" N LEU A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 681 removed outlier: 3.907A pdb=" N ARG A 654 " --> pdb=" O CYS A 650 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 684 No H-bonds generated for 'chain 'A' and resid 682 through 684' Processing helix chain 'A' and resid 693 through 719 removed outlier: 3.591A pdb=" N GLN A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 738 Processing helix chain 'A' and resid 749 through 754 removed outlier: 3.649A pdb=" N CYS A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 772 Processing helix chain 'A' and resid 782 through 806 removed outlier: 3.515A pdb=" N MET A 789 " --> pdb=" O ILE A 785 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 790 " --> pdb=" O GLY A 786 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 800 " --> pdb=" O TRP A 796 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 812 through 836 removed outlier: 4.308A pdb=" N THR A 818 " --> pdb=" O TYR A 814 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 846 Processing helix chain 'A' and resid 847 through 850 Processing sheet with id=AA1, first strand: chain 'B' and resid 526 through 530 removed outlier: 3.548A pdb=" N GLU B 541 " --> pdb=" O ARG B 527 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 548 through 549 removed outlier: 3.534A pdb=" N GLU B 556 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 562 through 564 Processing sheet with id=AA4, first strand: chain 'B' and resid 576 through 577 removed outlier: 3.524A pdb=" N LEU B 742 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 741 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B 726 " --> pdb=" O VAL B 741 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 526 through 527 Processing sheet with id=AA6, first strand: chain 'A' and resid 547 through 549 removed outlier: 3.745A pdb=" N GLU A 556 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 562 through 564 Processing sheet with id=AA8, first strand: chain 'A' and resid 724 through 726 289 hydrogen bonds defined for protein. 846 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: 0.60 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1602 1.35 - 1.46: 1238 1.46 - 1.58: 2403 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 5303 Sorted by residual: bond pdb=" CB PRO A 584 " pdb=" CG PRO A 584 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.80e+00 bond pdb=" C PRO B 689 " pdb=" N PRO B 690 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.15e+00 bond pdb=" CB PHE B 803 " pdb=" CG PHE B 803 " ideal model delta sigma weight residual 1.502 1.526 -0.024 2.30e-02 1.89e+03 1.09e+00 bond pdb=" C PRO A 689 " pdb=" N PRO A 690 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.08e+00 bond pdb=" CB ASP B 561 " pdb=" CG ASP B 561 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.06e+00 ... (remaining 5298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 7080 1.59 - 3.18: 131 3.18 - 4.78: 24 4.78 - 6.37: 9 6.37 - 7.96: 4 Bond angle restraints: 7248 Sorted by residual: angle pdb=" N ILE A 815 " pdb=" CA ILE A 815 " pdb=" C ILE A 815 " ideal model delta sigma weight residual 111.81 108.63 3.18 8.60e-01 1.35e+00 1.37e+01 angle pdb=" CG1 ILE A 692 " pdb=" CB ILE A 692 " pdb=" CG2 ILE A 692 " ideal model delta sigma weight residual 110.70 102.74 7.96 3.00e+00 1.11e-01 7.04e+00 angle pdb=" CA LYS B 683 " pdb=" CB LYS B 683 " pdb=" CG LYS B 683 " ideal model delta sigma weight residual 114.10 119.34 -5.24 2.00e+00 2.50e-01 6.87e+00 angle pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" CD PRO A 584 " ideal model delta sigma weight residual 112.00 108.39 3.61 1.40e+00 5.10e-01 6.66e+00 angle pdb=" C HIS A 722 " pdb=" CA HIS A 722 " pdb=" CB HIS A 722 " ideal model delta sigma weight residual 112.27 116.50 -4.23 1.75e+00 3.27e-01 5.83e+00 ... (remaining 7243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 2705 18.08 - 36.16: 369 36.16 - 54.23: 104 54.23 - 72.31: 16 72.31 - 90.39: 4 Dihedral angle restraints: 3198 sinusoidal: 1243 harmonic: 1955 Sorted by residual: dihedral pdb=" CB CYS A 522 " pdb=" SG CYS A 522 " pdb=" SG CYS A 540 " pdb=" CB CYS A 540 " ideal model delta sinusoidal sigma weight residual -86.00 -176.39 90.39 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CA CYS A 522 " pdb=" C CYS A 522 " pdb=" N GLY A 523 " pdb=" CA GLY A 523 " ideal model delta harmonic sigma weight residual 180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CB CYS B 518 " pdb=" SG CYS B 518 " pdb=" SG CYS B 537 " pdb=" CB CYS B 537 " ideal model delta sinusoidal sigma weight residual -86.00 -56.34 -29.66 1 1.00e+01 1.00e-02 1.26e+01 ... (remaining 3195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 630 0.039 - 0.077: 177 0.077 - 0.116: 51 0.116 - 0.154: 5 0.154 - 0.193: 2 Chirality restraints: 865 Sorted by residual: chirality pdb=" CB ILE A 692 " pdb=" CA ILE A 692 " pdb=" CG1 ILE A 692 " pdb=" CG2 ILE A 692 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ILE B 692 " pdb=" N ILE B 692 " pdb=" C ILE B 692 " pdb=" CB ILE B 692 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA PRO B 694 " pdb=" N PRO B 694 " pdb=" C PRO B 694 " pdb=" CB PRO B 694 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 862 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 583 " 0.061 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO A 584 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 584 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 584 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 688 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 689 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 689 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 689 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 613 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO B 614 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 614 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 614 " -0.025 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2556 2.99 - 3.47: 5311 3.47 - 3.94: 7724 3.94 - 4.42: 8106 4.42 - 4.90: 13502 Nonbonded interactions: 37199 Sorted by model distance: nonbonded pdb=" O HIS A 722 " pdb=" ND1 HIS A 722 " model vdw 2.511 3.120 nonbonded pdb=" N ILE B 692 " pdb=" O ILE B 692 " model vdw 2.607 2.496 nonbonded pdb=" N ILE A 692 " pdb=" O ILE A 692 " model vdw 2.612 2.496 nonbonded pdb=" N THR B 791 " pdb=" OG1 THR B 791 " model vdw 2.628 2.496 nonbonded pdb=" C SER A 696 " pdb=" OG SER A 696 " model vdw 2.629 2.616 ... (remaining 37194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 516 through 851) } 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 group one per residue 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: 5.250 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.920 Find NCS groups from input model: 0.080 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 0.084 5313 Z= 0.119 Angle : 0.572 7.960 7268 Z= 0.291 Chirality : 0.040 0.193 865 Planarity : 0.006 0.091 902 Dihedral : 17.265 86.277 1910 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 35.23 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.65 (0.31), residues: 669 helix: 0.39 (0.27), residues: 373 sheet: -0.69 (0.95), residues: 30 loop : -1.54 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 654 TYR 0.005 0.001 TYR A 836 PHE 0.004 0.001 PHE A 803 TRP 0.015 0.001 TRP B 585 HIS 0.001 0.000 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5303) covalent geometry : angle 0.57215 ( 7248) SS BOND : bond 0.00240 ( 10) SS BOND : angle 0.59472 ( 20) hydrogen bonds : bond 0.27885 ( 289) hydrogen bonds : angle 7.08407 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0738 time to fit residues: 7.5261 Evaluate side-chains 75 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.173159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.141686 restraints weight = 7395.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144982 restraints weight = 5020.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.147242 restraints weight = 3959.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148421 restraints weight = 3417.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.149371 restraints weight = 3130.187| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5313 Z= 0.185 Angle : 0.649 6.971 7268 Z= 0.332 Chirality : 0.044 0.177 865 Planarity : 0.006 0.057 902 Dihedral : 3.961 18.984 731 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 6.04 % Allowed : 30.40 % Favored : 63.56 % 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: 0.13 (0.33), residues: 669 helix: 1.24 (0.27), residues: 381 sheet: -0.53 (1.05), residues: 30 loop : -1.63 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 654 TYR 0.012 0.001 TYR B 841 PHE 0.007 0.001 PHE B 803 TRP 0.012 0.001 TRP B 796 HIS 0.003 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 5303) covalent geometry : angle 0.64844 ( 7248) SS BOND : bond 0.00320 ( 10) SS BOND : angle 0.95294 ( 20) hydrogen bonds : bond 0.06656 ( 289) hydrogen bonds : angle 4.39887 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: B 623 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8370 (tt) REVERT: A 704 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8978 (mp) REVERT: A 795 ILE cc_start: 0.8533 (mt) cc_final: 0.8294 (tp) outliers start: 35 outliers final: 23 residues processed: 108 average time/residue: 0.0620 time to fit residues: 9.0331 Evaluate side-chains 101 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 837 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.167082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136886 restraints weight = 7377.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139845 restraints weight = 5266.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141646 restraints weight = 4288.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142982 restraints weight = 3775.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143878 restraints weight = 3455.016| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5313 Z= 0.140 Angle : 0.594 6.791 7268 Z= 0.297 Chirality : 0.043 0.158 865 Planarity : 0.006 0.051 902 Dihedral : 3.855 16.554 731 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.01 % Allowed : 31.78 % Favored : 63.21 % 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: 0.40 (0.33), residues: 669 helix: 1.53 (0.27), residues: 382 sheet: -0.34 (1.05), residues: 30 loop : -1.67 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 563 TYR 0.006 0.001 TYR B 790 PHE 0.006 0.001 PHE B 803 TRP 0.010 0.001 TRP B 796 HIS 0.002 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5303) covalent geometry : angle 0.59358 ( 7248) SS BOND : bond 0.00293 ( 10) SS BOND : angle 0.73718 ( 20) hydrogen bonds : bond 0.05142 ( 289) hydrogen bonds : angle 4.01701 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: B 739 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7431 (mmm-85) REVERT: B 746 MET cc_start: 0.8345 (pmm) cc_final: 0.8049 (pmm) REVERT: A 704 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8901 (mp) outliers start: 29 outliers final: 16 residues processed: 101 average time/residue: 0.0673 time to fit residues: 9.0672 Evaluate side-chains 90 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 739 ARG Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 850 ASN Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 762 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 37 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.167239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.137175 restraints weight = 7440.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139750 restraints weight = 5359.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141887 restraints weight = 4425.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.142967 restraints weight = 3884.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.143913 restraints weight = 3585.935| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5313 Z= 0.137 Angle : 0.587 6.747 7268 Z= 0.292 Chirality : 0.043 0.152 865 Planarity : 0.006 0.052 902 Dihedral : 3.839 16.504 731 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.04 % Allowed : 32.12 % Favored : 61.83 % 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: 0.57 (0.33), residues: 669 helix: 1.70 (0.28), residues: 381 sheet: -0.23 (1.08), residues: 30 loop : -1.64 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 563 TYR 0.007 0.001 TYR B 790 PHE 0.006 0.001 PHE B 691 TRP 0.007 0.001 TRP B 796 HIS 0.002 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5303) covalent geometry : angle 0.58607 ( 7248) SS BOND : bond 0.00255 ( 10) SS BOND : angle 0.72604 ( 20) hydrogen bonds : bond 0.04626 ( 289) hydrogen bonds : angle 3.89700 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 661 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7840 (m) REVERT: B 739 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7463 (mmm-85) REVERT: A 528 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6804 (ptmm) REVERT: A 704 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8923 (mp) outliers start: 35 outliers final: 22 residues processed: 102 average time/residue: 0.0639 time to fit residues: 8.6612 Evaluate side-chains 94 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 ARG Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 850 ASN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 762 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.166597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136175 restraints weight = 7547.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139024 restraints weight = 5404.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140780 restraints weight = 4393.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142201 restraints weight = 3890.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142201 restraints weight = 3576.510| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5313 Z= 0.147 Angle : 0.607 8.620 7268 Z= 0.301 Chirality : 0.044 0.237 865 Planarity : 0.006 0.052 902 Dihedral : 3.856 16.923 731 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.56 % Allowed : 32.47 % Favored : 60.97 % 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: 0.62 (0.34), residues: 669 helix: 1.76 (0.28), residues: 378 sheet: -0.35 (1.07), residues: 30 loop : -1.61 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 563 TYR 0.007 0.001 TYR A 790 PHE 0.006 0.001 PHE A 799 TRP 0.008 0.001 TRP B 585 HIS 0.002 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5303) covalent geometry : angle 0.60617 ( 7248) SS BOND : bond 0.00280 ( 10) SS BOND : angle 0.86251 ( 20) hydrogen bonds : bond 0.04643 ( 289) hydrogen bonds : angle 3.84303 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 526 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7034 (mm-30) REVERT: B 661 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7901 (m) REVERT: B 737 GLN cc_start: 0.8049 (pp30) cc_final: 0.7090 (pp30) REVERT: B 739 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7559 (mmm-85) REVERT: B 744 CYS cc_start: 0.6768 (m) cc_final: 0.6353 (m) REVERT: A 528 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6790 (ptmm) outliers start: 38 outliers final: 25 residues processed: 112 average time/residue: 0.0639 time to fit residues: 9.6933 Evaluate side-chains 102 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 ARG Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 850 ASN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 794 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.165988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.135639 restraints weight = 7520.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138594 restraints weight = 5343.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140235 restraints weight = 4312.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.141715 restraints weight = 3812.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142251 restraints weight = 3529.061| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5313 Z= 0.147 Angle : 0.620 7.209 7268 Z= 0.306 Chirality : 0.044 0.195 865 Planarity : 0.006 0.052 902 Dihedral : 3.904 20.341 731 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 7.08 % Allowed : 32.99 % Favored : 59.93 % 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: 0.66 (0.33), residues: 669 helix: 1.81 (0.28), residues: 377 sheet: -0.21 (1.09), residues: 30 loop : -1.61 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 563 TYR 0.007 0.001 TYR A 790 PHE 0.005 0.001 PHE A 799 TRP 0.009 0.001 TRP B 585 HIS 0.002 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5303) covalent geometry : angle 0.61784 ( 7248) SS BOND : bond 0.00334 ( 10) SS BOND : angle 1.09595 ( 20) hydrogen bonds : bond 0.04543 ( 289) hydrogen bonds : angle 3.80632 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 526 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 661 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7878 (m) REVERT: B 737 GLN cc_start: 0.8052 (pp30) cc_final: 0.7161 (pp30) REVERT: B 739 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7550 (mmm-85) REVERT: B 744 CYS cc_start: 0.6744 (m) cc_final: 0.6427 (m) REVERT: A 528 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6790 (ptmm) REVERT: A 768 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6311 (t80) outliers start: 41 outliers final: 30 residues processed: 112 average time/residue: 0.0580 time to fit residues: 8.9170 Evaluate side-chains 111 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 ARG Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 850 ASN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 794 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 0.0870 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.0270 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.170672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.140513 restraints weight = 7467.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.143521 restraints weight = 5272.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145243 restraints weight = 4265.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.146730 restraints weight = 3751.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147892 restraints weight = 3409.421| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5313 Z= 0.122 Angle : 0.590 6.625 7268 Z= 0.291 Chirality : 0.042 0.169 865 Planarity : 0.005 0.053 902 Dihedral : 3.795 17.651 731 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.01 % Allowed : 34.54 % Favored : 60.45 % 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: 0.76 (0.34), residues: 669 helix: 1.93 (0.28), residues: 375 sheet: 0.02 (1.12), residues: 30 loop : -1.63 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 563 TYR 0.007 0.001 TYR B 790 PHE 0.013 0.001 PHE B 691 TRP 0.010 0.001 TRP B 585 HIS 0.001 0.000 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5303) covalent geometry : angle 0.58919 ( 7248) SS BOND : bond 0.00234 ( 10) SS BOND : angle 0.73080 ( 20) hydrogen bonds : bond 0.03938 ( 289) hydrogen bonds : angle 3.65824 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 526 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 661 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7775 (m) REVERT: B 737 GLN cc_start: 0.8022 (pp30) cc_final: 0.7238 (pp30) REVERT: B 739 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7892 (mmm-85) REVERT: A 528 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6703 (ptmm) REVERT: A 768 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.6293 (t80) outliers start: 29 outliers final: 18 residues processed: 104 average time/residue: 0.0648 time to fit residues: 8.9122 Evaluate side-chains 99 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 ARG Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 850 ASN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 768 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 12 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.0000 chunk 48 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138214 restraints weight = 7441.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141122 restraints weight = 5286.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143151 restraints weight = 4300.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144162 restraints weight = 3767.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.145115 restraints weight = 3483.687| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5313 Z= 0.132 Angle : 0.607 6.703 7268 Z= 0.297 Chirality : 0.043 0.166 865 Planarity : 0.005 0.053 902 Dihedral : 3.797 17.513 731 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.01 % Allowed : 35.06 % Favored : 59.93 % 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: 0.81 (0.34), residues: 669 helix: 1.96 (0.28), residues: 376 sheet: -0.02 (1.11), residues: 30 loop : -1.60 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 563 TYR 0.008 0.001 TYR A 790 PHE 0.009 0.001 PHE B 691 TRP 0.009 0.001 TRP B 585 HIS 0.002 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5303) covalent geometry : angle 0.60623 ( 7248) SS BOND : bond 0.00240 ( 10) SS BOND : angle 0.76408 ( 20) hydrogen bonds : bond 0.04106 ( 289) hydrogen bonds : angle 3.66055 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 526 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7267 (mm-30) REVERT: B 661 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7845 (m) REVERT: B 737 GLN cc_start: 0.8030 (pp30) cc_final: 0.7221 (pp30) REVERT: B 739 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7886 (mmm-85) REVERT: A 528 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6777 (ptmm) REVERT: A 768 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.6377 (t80) outliers start: 29 outliers final: 23 residues processed: 105 average time/residue: 0.0637 time to fit residues: 8.9959 Evaluate side-chains 108 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 722 HIS Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 ARG Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 850 ASN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 820 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 0.0370 chunk 51 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138364 restraints weight = 7438.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141611 restraints weight = 5183.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143767 restraints weight = 4157.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.144567 restraints weight = 3619.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.145661 restraints weight = 3371.513| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5313 Z= 0.132 Angle : 0.602 6.671 7268 Z= 0.296 Chirality : 0.043 0.161 865 Planarity : 0.006 0.053 902 Dihedral : 3.775 16.953 731 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.35 % Allowed : 34.89 % Favored : 59.76 % 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: 0.73 (0.34), residues: 669 helix: 1.88 (0.28), residues: 375 sheet: 0.02 (1.11), residues: 30 loop : -1.61 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 563 TYR 0.008 0.001 TYR A 790 PHE 0.008 0.001 PHE B 691 TRP 0.009 0.001 TRP B 585 HIS 0.002 0.000 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5303) covalent geometry : angle 0.60169 ( 7248) SS BOND : bond 0.00248 ( 10) SS BOND : angle 0.75083 ( 20) hydrogen bonds : bond 0.04075 ( 289) hydrogen bonds : angle 3.66622 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 526 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 661 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7831 (m) REVERT: B 737 GLN cc_start: 0.8022 (pp30) cc_final: 0.7242 (pp30) REVERT: B 739 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7573 (mmm-85) REVERT: A 528 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6712 (ptmm) REVERT: A 768 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.6362 (t80) outliers start: 31 outliers final: 25 residues processed: 107 average time/residue: 0.0533 time to fit residues: 7.9114 Evaluate side-chains 109 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 ARG Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 850 ASN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 820 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.2980 chunk 17 optimal weight: 0.0060 chunk 61 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.169157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138476 restraints weight = 7503.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.141570 restraints weight = 5303.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143312 restraints weight = 4292.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144856 restraints weight = 3782.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145619 restraints weight = 3461.933| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5313 Z= 0.130 Angle : 0.606 6.645 7268 Z= 0.296 Chirality : 0.043 0.162 865 Planarity : 0.006 0.053 902 Dihedral : 3.759 16.725 731 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.53 % Allowed : 34.37 % Favored : 60.10 % 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: 0.85 (0.34), residues: 669 helix: 2.02 (0.28), residues: 375 sheet: 0.06 (1.11), residues: 30 loop : -1.63 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 572 TYR 0.008 0.001 TYR A 790 PHE 0.007 0.001 PHE B 691 TRP 0.010 0.001 TRP B 585 HIS 0.002 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5303) covalent geometry : angle 0.60563 ( 7248) SS BOND : bond 0.00258 ( 10) SS BOND : angle 0.76048 ( 20) hydrogen bonds : bond 0.04001 ( 289) hydrogen bonds : angle 3.62535 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 526 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 661 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7856 (m) REVERT: B 737 GLN cc_start: 0.7990 (pp30) cc_final: 0.7246 (pp30) REVERT: B 739 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7630 (mmm-85) REVERT: A 528 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6733 (ptmm) REVERT: A 768 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.6399 (t80) outliers start: 32 outliers final: 27 residues processed: 106 average time/residue: 0.0509 time to fit residues: 7.3825 Evaluate side-chains 110 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 ARG Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 850 ASN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 820 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138267 restraints weight = 7562.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.141375 restraints weight = 5340.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143468 restraints weight = 4318.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144626 restraints weight = 3770.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144627 restraints weight = 3462.170| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5313 Z= 0.132 Angle : 0.603 6.672 7268 Z= 0.295 Chirality : 0.043 0.161 865 Planarity : 0.006 0.053 902 Dihedral : 3.756 16.579 731 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.53 % Allowed : 34.37 % Favored : 60.10 % 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: 0.86 (0.34), residues: 669 helix: 2.03 (0.28), residues: 375 sheet: 0.08 (1.11), residues: 30 loop : -1.63 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 563 TYR 0.008 0.001 TYR A 790 PHE 0.007 0.001 PHE B 691 TRP 0.010 0.001 TRP B 585 HIS 0.002 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5303) covalent geometry : angle 0.60258 ( 7248) SS BOND : bond 0.00243 ( 10) SS BOND : angle 0.74993 ( 20) hydrogen bonds : bond 0.04046 ( 289) hydrogen bonds : angle 3.62851 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 974.11 seconds wall clock time: 17 minutes 26.03 seconds (1046.03 seconds total)