Starting phenix.real_space_refine on Wed Aug 5 20:40:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10eq_75115/08_2026/10eq_75115.cif Found real_map, /net/cci-nas-00/data/ceres_data/10eq_75115/08_2026/10eq_75115.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 { model { file = "/net/cci-nas-00/data/ceres_data/10eq_75115/08_2026/10eq_75115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10eq_75115/08_2026/10eq_75115.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10eq_75115/08_2026/10eq_75115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10eq_75115/08_2026/10eq_75115.map" } 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= 0.000 sd= 0.009 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 37 5.16 5 C 7155 2.51 5 N 1918 2.21 5 O 2112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11222 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4860 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 48, 'TRANS': 567} Chain breaks: 12 Chain: "B" Number of atoms: 6362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6362 Classifications: {'peptide': 806} Link IDs: {'PTRANS': 57, 'TRANS': 748} Time building chain proxies: 2.22, per 1000 atoms: 0.20 Number of scatterers: 11222 At special positions: 0 Unit cell: (101.38, 147.96, 94.53, 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 37 16.00 O 2112 8.00 N 1918 7.00 C 7155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 651.4 milliseconds 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 20 sheets defined 17.7% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.626A pdb=" N ILE A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 718 through 726 removed outlier: 4.481A pdb=" N ALA A 724 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 726 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 747 removed outlier: 3.667A pdb=" N ASP A 747 " --> pdb=" O GLU A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 744 through 747' Processing helix chain 'A' and resid 748 through 768 removed outlier: 3.600A pdb=" N VAL A 764 " --> pdb=" O ALA A 760 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 765 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.831A pdb=" N PHE A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 786 " --> pdb=" O TYR A 782 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.719A pdb=" N LEU A 812 " --> pdb=" O ASN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'A' and resid 839 through 843 removed outlier: 3.619A pdb=" N ILE A 843 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 875 removed outlier: 4.206A pdb=" N SER A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 912 removed outlier: 3.666A pdb=" N HIS A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 900 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.674A pdb=" N ILE B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 315 through 326 removed outlier: 3.544A pdb=" N ALA B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.623A pdb=" N ARG B 377 " --> pdb=" O PRO B 374 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 378 " --> pdb=" O CYS B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 378' Processing helix chain 'B' and resid 718 through 723 removed outlier: 3.693A pdb=" N TRP B 722 " --> pdb=" O ALA B 719 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 723 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.724A pdb=" N ASP B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 removed outlier: 4.141A pdb=" N ALA B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 782 through 794 removed outlier: 3.750A pdb=" N MET B 786 " --> pdb=" O TYR B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 813 removed outlier: 3.773A pdb=" N LEU B 812 " --> pdb=" O ASN B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 834 Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.765A pdb=" N ALA B 840 " --> pdb=" O PHE B 837 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASN B 841 " --> pdb=" O MET B 838 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 842 " --> pdb=" O SER B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 875 removed outlier: 3.710A pdb=" N SER B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 912 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 159 removed outlier: 4.025A pdb=" N GLU A 157 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 207 removed outlier: 3.581A pdb=" N ASN A 207 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE A 220 " --> pdb=" O TRP A 236 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP A 236 " --> pdb=" O PHE A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 275 removed outlier: 4.062A pdb=" N VAL A 273 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA6, first strand: chain 'A' and resid 589 through 590 removed outlier: 4.983A pdb=" N SER A 618 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASN A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 659 removed outlier: 3.775A pdb=" N GLN A 652 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 669 " --> pdb=" O SER A 731 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 729 " --> pdb=" O TYR A 671 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU A 730 " --> pdb=" O PRO A 685 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 687 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU A 684 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ALA A 776 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N CYS A 686 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY A 778 " --> pdb=" O CYS A 686 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE A 688 " --> pdb=" O GLY A 778 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 801 through 804 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.751A pdb=" N LYS B 195 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AB2, first strand: chain 'B' and resid 205 through 211 removed outlier: 4.599A pdb=" N VAL B 209 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA B 219 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TRP B 211 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N HIS B 217 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 263 through 265 removed outlier: 4.991A pdb=" N SER B 334 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N THR B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 348 through 351 removed outlier: 7.147A pdb=" N SER B 363 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 384 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 394 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 416 through 420 removed outlier: 4.227A pdb=" N ILE B 418 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR B 429 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TRP B 420 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR B 427 " --> pdb=" O TRP B 420 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP B 447 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS B 467 " --> pdb=" O ASP B 447 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 449 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 471 through 479 removed outlier: 5.482A pdb=" N TYR B 472 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER B 488 " --> pdb=" O TYR B 472 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 482 " --> pdb=" O CYS B 478 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR B 495 " --> pdb=" O ASP B 514 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP B 514 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B 497 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 526 through 527 removed outlier: 6.853A pdb=" N LEU B 570 " --> pdb=" O ARG B 580 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG B 580 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ASP B 572 " --> pdb=" O LYS B 578 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS B 578 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 529 through 531 Processing sheet with id=AB9, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AC1, first strand: chain 'B' and resid 590 through 596 removed outlier: 6.613A pdb=" N LEU B 613 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU B 596 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LYS B 611 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 652 through 659 removed outlier: 3.626A pdb=" N GLN B 652 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU B 730 " --> pdb=" O PRO B 685 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B 687 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 10.875A pdb=" N LEU B 684 " --> pdb=" O ARG B 772 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LYS B 774 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 778 " --> pdb=" O PHE B 688 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N CYS B 800 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 775 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ILE B 802 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 777 " --> pdb=" O ILE B 802 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ARG B 804 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY B 779 " --> pdb=" O ARG B 804 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 847 " --> pdb=" O ARG B 880 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL B 882 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 849 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU B 884 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS B 851 " --> pdb=" O LEU B 884 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 753 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: 1.99 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3659 1.34 - 1.46: 2335 1.46 - 1.58: 5456 1.58 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 11509 Sorted by residual: bond pdb=" N SER A 718 " pdb=" CA SER A 718 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.33e-02 5.65e+03 5.52e+00 bond pdb=" N MET A 898 " pdb=" CA MET A 898 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.29e+00 bond pdb=" N ILE A 897 " pdb=" CA ILE A 897 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.25e-02 6.40e+03 5.12e+00 bond pdb=" N LEU A 720 " pdb=" CA LEU A 720 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.27e-02 6.20e+03 4.70e+00 bond pdb=" N ALA A 719 " pdb=" CA ALA A 719 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.72e+00 ... (remaining 11504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 15352 1.16 - 2.33: 168 2.33 - 3.49: 112 3.49 - 4.65: 10 4.65 - 5.81: 5 Bond angle restraints: 15647 Sorted by residual: angle pdb=" N THR A 717 " pdb=" CA THR A 717 " pdb=" C THR A 717 " ideal model delta sigma weight residual 112.86 108.85 4.01 1.22e+00 6.72e-01 1.08e+01 angle pdb=" N ILE A 897 " pdb=" CA ILE A 897 " pdb=" C ILE A 897 " ideal model delta sigma weight residual 109.34 103.53 5.81 2.08e+00 2.31e-01 7.81e+00 angle pdb=" C SER A 896 " pdb=" N ILE A 897 " pdb=" CA ILE A 897 " ideal model delta sigma weight residual 121.97 117.15 4.82 1.80e+00 3.09e-01 7.18e+00 angle pdb=" CA SER A 718 " pdb=" C SER A 718 " pdb=" O SER A 718 " ideal model delta sigma weight residual 120.92 118.09 2.83 1.15e+00 7.56e-01 6.06e+00 angle pdb=" CA LEU A 720 " pdb=" C LEU A 720 " pdb=" O LEU A 720 " ideal model delta sigma weight residual 120.20 117.45 2.75 1.12e+00 7.97e-01 6.04e+00 ... (remaining 15642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 6233 17.60 - 35.19: 537 35.19 - 52.79: 112 52.79 - 70.39: 19 70.39 - 87.98: 7 Dihedral angle restraints: 6908 sinusoidal: 2797 harmonic: 4111 Sorted by residual: dihedral pdb=" CA LYS B 491 " pdb=" C LYS B 491 " pdb=" N THR B 492 " pdb=" CA THR B 492 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA VAL A 240 " pdb=" C VAL A 240 " pdb=" N GLU A 241 " pdb=" CA GLU A 241 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP B 523 " pdb=" CB ASP B 523 " pdb=" CG ASP B 523 " pdb=" OD1 ASP B 523 " ideal model delta sinusoidal sigma weight residual -30.00 -88.55 58.55 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 6905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1395 0.046 - 0.093: 222 0.093 - 0.139: 94 0.139 - 0.185: 0 0.185 - 0.232: 1 Chirality restraints: 1712 Sorted by residual: chirality pdb=" CA ILE A 897 " pdb=" N ILE A 897 " pdb=" C ILE A 897 " pdb=" CB ILE A 897 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE B 276 " pdb=" N ILE B 276 " pdb=" C ILE B 276 " pdb=" CB ILE B 276 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE A 276 " pdb=" N ILE A 276 " pdb=" C ILE A 276 " pdb=" CB ILE A 276 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1709 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 292 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 293 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 373 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 374 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 374 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 374 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 113 " 0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 114 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " 0.018 5.00e-02 4.00e+02 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.94: 4460 2.94 - 3.43: 9909 3.43 - 3.92: 16856 3.92 - 4.41: 17766 4.41 - 4.90: 31271 Nonbonded interactions: 80262 Sorted by model distance: nonbonded pdb=" O SER A 716 " pdb=" OG1 THR A 717 " model vdw 2.455 3.040 nonbonded pdb=" O MET A 898 " pdb=" N LEU A 901 " model vdw 2.525 3.120 nonbonded pdb=" N ILE A 897 " pdb=" N MET A 898 " model vdw 2.584 2.560 nonbonded pdb=" O MET A 898 " pdb=" C HIS A 899 " model vdw 2.589 3.270 nonbonded pdb=" O LEU A 720 " pdb=" N TRP A 722 " model vdw 2.591 3.120 ... (remaining 80257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.830 Find NCS groups from input model: 0.060 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: 0.000 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: 13.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 0.002 0.031 11509 Z= 0.096 Angle : 0.418 5.813 15647 Z= 0.210 Chirality : 0.040 0.232 1712 Planarity : 0.003 0.042 2028 Dihedral : 13.834 87.982 4260 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.94 % Favored : 96.99 % Rotamer: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.93 % 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: 0.02 (0.23), residues: 1394 helix: 0.72 (0.38), residues: 200 sheet: 1.17 (0.31), residues: 311 loop : -0.59 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 660 TYR 0.007 0.000 TYR A 645 PHE 0.004 0.000 PHE A 263 TRP 0.003 0.000 TRP B 902 HIS 0.001 0.000 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.10 (11509) covalent geometry : angle 0.41768 / 0.21 (15647) hydrogen bonds : bond 0.23149 / 15.58 ( 290) hydrogen bonds : angle 6.51713 / 4.71 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 SER cc_start: 0.7813 (m) cc_final: 0.7253 (p) REVERT: A 450 TYR cc_start: 0.7938 (m-80) cc_final: 0.7620 (m-80) REVERT: A 589 TYR cc_start: 0.7606 (m-80) cc_final: 0.7287 (m-10) REVERT: A 856 ASN cc_start: 0.8735 (t0) cc_final: 0.7993 (p0) REVERT: B 167 TYR cc_start: 0.7177 (t80) cc_final: 0.6830 (t80) REVERT: B 184 GLN cc_start: 0.8647 (pp30) cc_final: 0.8263 (pp30) REVERT: B 186 LEU cc_start: 0.8180 (mp) cc_final: 0.7905 (mp) REVERT: B 484 LEU cc_start: 0.8025 (mm) cc_final: 0.7594 (mm) REVERT: B 656 ILE cc_start: 0.7883 (pt) cc_final: 0.7601 (pt) REVERT: B 786 MET cc_start: 0.6629 (ppp) cc_final: 0.5597 (mtt) REVERT: B 819 ASN cc_start: 0.8335 (t0) cc_final: 0.7818 (t0) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1029 time to fit residues: 25.1179 Evaluate side-chains 102 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 HIS A 394 GLN A 564 ASN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS A 899 HIS B 183 HIS B 703 GLN B 780 HIS ** B 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094582 restraints weight = 20171.281| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.95 r_work: 0.3123 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 11509 Z= 0.205 Angle : 0.625 7.652 15647 Z= 0.317 Chirality : 0.046 0.180 1712 Planarity : 0.005 0.058 2028 Dihedral : 3.554 19.557 1546 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.54 % Allowed : 10.73 % Favored : 87.72 % 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: -0.21 (0.23), residues: 1394 helix: 0.55 (0.37), residues: 210 sheet: 1.09 (0.31), residues: 301 loop : -0.78 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 810 TYR 0.013 0.002 TYR A 167 PHE 0.020 0.002 PHE A 727 TRP 0.018 0.002 TRP A 236 HIS 0.006 0.001 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (11509) covalent geometry : angle 0.62479 / 0.32 (15647) hydrogen bonds : bond 0.04982 / 3.32 ( 290) hydrogen bonds : angle 4.91190 / 3.49 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 SER cc_start: 0.8097 (m) cc_final: 0.7415 (p) REVERT: A 348 TYR cc_start: 0.7307 (m-80) cc_final: 0.6952 (m-10) REVERT: A 364 SER cc_start: 0.8273 (p) cc_final: 0.7861 (m) REVERT: A 450 TYR cc_start: 0.7965 (m-80) cc_final: 0.7256 (m-80) REVERT: A 589 TYR cc_start: 0.7242 (m-80) cc_final: 0.6870 (m-10) REVERT: A 856 ASN cc_start: 0.8783 (t0) cc_final: 0.7752 (p0) REVERT: B 167 TYR cc_start: 0.7423 (t80) cc_final: 0.7073 (t80) REVERT: B 184 GLN cc_start: 0.8739 (pp30) cc_final: 0.8080 (pp30) REVERT: B 186 LEU cc_start: 0.8330 (mp) cc_final: 0.8105 (mp) REVERT: B 656 ILE cc_start: 0.8374 (pt) cc_final: 0.8156 (pt) REVERT: B 786 MET cc_start: 0.6932 (ppp) cc_final: 0.6056 (mtt) outliers start: 19 outliers final: 11 residues processed: 106 average time/residue: 0.1036 time to fit residues: 15.6847 Evaluate side-chains 87 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 830 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 123 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 HIS ** B 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.090876 restraints weight = 20306.169| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.91 r_work: 0.3063 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11509 Z= 0.156 Angle : 0.533 5.897 15647 Z= 0.270 Chirality : 0.043 0.150 1712 Planarity : 0.004 0.050 2028 Dihedral : 3.682 20.332 1546 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.95 % Allowed : 12.76 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.26 (0.23), residues: 1394 helix: 0.87 (0.39), residues: 208 sheet: 1.07 (0.31), residues: 301 loop : -0.92 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.010 0.001 TYR B 486 PHE 0.035 0.002 PHE B 695 TRP 0.010 0.001 TRP B 420 HIS 0.007 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11509) covalent geometry : angle 0.53347 / 0.27 (15647) hydrogen bonds : bond 0.05109 / 3.36 ( 290) hydrogen bonds : angle 4.63735 / 3.26 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.423 Fit side-chains REVERT: A 217 HIS cc_start: 0.7170 (p-80) cc_final: 0.6558 (p-80) REVERT: A 348 TYR cc_start: 0.7460 (m-80) cc_final: 0.7227 (m-10) REVERT: A 364 SER cc_start: 0.8317 (p) cc_final: 0.8098 (m) REVERT: A 450 TYR cc_start: 0.7902 (m-80) cc_final: 0.7218 (m-80) REVERT: A 589 TYR cc_start: 0.7131 (m-80) cc_final: 0.6758 (m-10) REVERT: B 152 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8047 (tt) REVERT: B 167 TYR cc_start: 0.7494 (t80) cc_final: 0.7230 (t80) REVERT: B 184 GLN cc_start: 0.8810 (pp30) cc_final: 0.8141 (pp30) REVERT: B 186 LEU cc_start: 0.8241 (mp) cc_final: 0.7958 (mp) REVERT: B 316 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6791 (tm-30) REVERT: B 656 ILE cc_start: 0.8298 (pt) cc_final: 0.8070 (pt) REVERT: B 786 MET cc_start: 0.7049 (ppp) cc_final: 0.6326 (mtt) outliers start: 24 outliers final: 15 residues processed: 96 average time/residue: 0.1061 time to fit residues: 14.5285 Evaluate side-chains 84 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 TRP Chi-restraints excluded: chain B residue 686 CYS Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 ASN ** B 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.091677 restraints weight = 20243.725| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.91 r_work: 0.3077 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11509 Z= 0.099 Angle : 0.482 5.904 15647 Z= 0.240 Chirality : 0.042 0.137 1712 Planarity : 0.004 0.045 2028 Dihedral : 3.529 20.805 1546 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.30 % Allowed : 14.15 % Favored : 84.55 % 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: -0.20 (0.23), residues: 1394 helix: 1.13 (0.40), residues: 202 sheet: 1.07 (0.32), residues: 291 loop : -0.89 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 154 TYR 0.009 0.001 TYR A 167 PHE 0.013 0.001 PHE B 695 TRP 0.009 0.001 TRP A 722 HIS 0.005 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (11509) covalent geometry : angle 0.48203 / 0.24 (15647) hydrogen bonds : bond 0.03379 / 2.21 ( 290) hydrogen bonds : angle 4.36526 / 3.06 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.349 Fit side-chains REVERT: A 217 HIS cc_start: 0.7367 (p-80) cc_final: 0.6719 (p-80) REVERT: A 348 TYR cc_start: 0.7325 (m-80) cc_final: 0.6982 (m-10) REVERT: A 364 SER cc_start: 0.8310 (p) cc_final: 0.7913 (m) REVERT: A 450 TYR cc_start: 0.7907 (m-80) cc_final: 0.7221 (m-80) REVERT: A 589 TYR cc_start: 0.7089 (m-80) cc_final: 0.6708 (m-10) REVERT: B 152 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7927 (tt) REVERT: B 184 GLN cc_start: 0.8677 (pp30) cc_final: 0.8088 (pp30) REVERT: B 186 LEU cc_start: 0.8281 (mp) cc_final: 0.8010 (mp) REVERT: B 316 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6601 (tm-30) REVERT: B 786 MET cc_start: 0.7011 (ppp) cc_final: 0.6215 (mtt) outliers start: 16 outliers final: 10 residues processed: 88 average time/residue: 0.1000 time to fit residues: 12.7172 Evaluate side-chains 81 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 737 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 HIS ** 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 = 0.3629 r_free = 0.3629 target = 0.121835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.089225 restraints weight = 20391.864| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.88 r_work: 0.3021 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11509 Z= 0.170 Angle : 0.536 6.230 15647 Z= 0.271 Chirality : 0.043 0.162 1712 Planarity : 0.004 0.049 2028 Dihedral : 3.744 20.369 1546 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.95 % Allowed : 14.47 % Favored : 83.58 % 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: -0.37 (0.23), residues: 1394 helix: 0.95 (0.39), residues: 209 sheet: 0.91 (0.31), residues: 299 loop : -1.01 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 223 TYR 0.010 0.001 TYR B 671 PHE 0.017 0.002 PHE A 391 TRP 0.012 0.001 TRP A 722 HIS 0.006 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (11509) covalent geometry : angle 0.53613 / 0.27 (15647) hydrogen bonds : bond 0.04389 / 2.89 ( 290) hydrogen bonds : angle 4.47478 / 3.16 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.305 Fit side-chains REVERT: A 217 HIS cc_start: 0.7238 (p-80) cc_final: 0.6769 (p-80) REVERT: A 348 TYR cc_start: 0.7537 (m-10) cc_final: 0.7187 (m-10) REVERT: A 364 SER cc_start: 0.8278 (p) cc_final: 0.7899 (m) REVERT: A 450 TYR cc_start: 0.7744 (m-80) cc_final: 0.7396 (m-80) REVERT: A 490 TYR cc_start: 0.5006 (OUTLIER) cc_final: 0.4416 (p90) REVERT: B 152 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7984 (tt) REVERT: B 184 GLN cc_start: 0.8696 (pp30) cc_final: 0.8087 (pp30) REVERT: B 186 LEU cc_start: 0.8338 (mp) cc_final: 0.8008 (mp) REVERT: B 316 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6737 (tm-30) REVERT: B 786 MET cc_start: 0.7127 (ppp) cc_final: 0.6336 (mtt) REVERT: B 866 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7831 (t70) outliers start: 24 outliers final: 14 residues processed: 87 average time/residue: 0.0998 time to fit residues: 12.5351 Evaluate side-chains 83 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 TRP Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 90 optimal weight: 0.0970 chunk 26 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 851 HIS ** 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 = 0.3640 r_free = 0.3640 target = 0.123038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090623 restraints weight = 20223.278| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.88 r_work: 0.3050 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11509 Z= 0.087 Angle : 0.475 6.165 15647 Z= 0.236 Chirality : 0.041 0.140 1712 Planarity : 0.004 0.045 2028 Dihedral : 3.548 19.584 1546 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.46 % Allowed : 15.45 % Favored : 83.09 % 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: -0.24 (0.23), residues: 1394 helix: 1.22 (0.40), residues: 199 sheet: 0.98 (0.31), residues: 298 loop : -0.93 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 377 TYR 0.008 0.001 TYR B 486 PHE 0.012 0.001 PHE B 695 TRP 0.009 0.001 TRP A 722 HIS 0.005 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (11509) covalent geometry : angle 0.47491 / 0.24 (15647) hydrogen bonds : bond 0.03138 / 2.05 ( 290) hydrogen bonds : angle 4.23736 / 2.97 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 217 HIS cc_start: 0.7093 (p-80) cc_final: 0.6612 (p-80) REVERT: A 348 TYR cc_start: 0.7429 (m-80) cc_final: 0.7076 (m-10) REVERT: A 364 SER cc_start: 0.8280 (p) cc_final: 0.7909 (m) REVERT: A 450 TYR cc_start: 0.7722 (m-80) cc_final: 0.6989 (m-80) REVERT: A 490 TYR cc_start: 0.5035 (OUTLIER) cc_final: 0.4341 (p90) REVERT: A 589 TYR cc_start: 0.7242 (m-10) cc_final: 0.6885 (m-10) REVERT: B 152 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7990 (tt) REVERT: B 184 GLN cc_start: 0.8688 (pp30) cc_final: 0.8066 (pp30) REVERT: B 186 LEU cc_start: 0.8237 (mp) cc_final: 0.7919 (mp) REVERT: B 316 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6593 (tm-30) REVERT: B 786 MET cc_start: 0.7099 (ppp) cc_final: 0.6248 (mtt) REVERT: B 866 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7759 (t70) outliers start: 18 outliers final: 13 residues processed: 82 average time/residue: 0.0988 time to fit residues: 11.5662 Evaluate side-chains 84 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 122 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 796 HIS ** B 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.118980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.086402 restraints weight = 20539.036| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.89 r_work: 0.2989 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11509 Z= 0.179 Angle : 0.553 6.660 15647 Z= 0.281 Chirality : 0.044 0.147 1712 Planarity : 0.004 0.049 2028 Dihedral : 3.911 19.722 1546 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.44 % Allowed : 14.47 % Favored : 83.09 % 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: -0.41 (0.22), residues: 1394 helix: 1.20 (0.39), residues: 200 sheet: 0.77 (0.31), residues: 301 loop : -1.04 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 377 TYR 0.009 0.001 TYR B 671 PHE 0.012 0.002 PHE A 391 TRP 0.011 0.001 TRP A 722 HIS 0.004 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (11509) covalent geometry : angle 0.55304 / 0.28 (15647) hydrogen bonds : bond 0.04701 / 3.10 ( 290) hydrogen bonds : angle 4.53672 / 3.22 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 217 HIS cc_start: 0.7340 (p-80) cc_final: 0.6693 (p90) REVERT: A 348 TYR cc_start: 0.7627 (m-10) cc_final: 0.7276 (m-10) REVERT: A 364 SER cc_start: 0.8278 (p) cc_final: 0.7919 (m) REVERT: A 450 TYR cc_start: 0.7707 (m-80) cc_final: 0.7366 (m-80) REVERT: A 490 TYR cc_start: 0.4920 (OUTLIER) cc_final: 0.2976 (p90) REVERT: A 589 TYR cc_start: 0.7270 (m-10) cc_final: 0.6869 (m-10) REVERT: B 152 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8155 (tt) REVERT: B 184 GLN cc_start: 0.8652 (pp30) cc_final: 0.8018 (pp30) REVERT: B 186 LEU cc_start: 0.8313 (mp) cc_final: 0.7897 (mp) REVERT: B 316 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6734 (tm-30) REVERT: B 866 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7807 (t70) outliers start: 30 outliers final: 21 residues processed: 94 average time/residue: 0.0947 time to fit residues: 12.8866 Evaluate side-chains 93 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 TRP Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 851 HIS ** 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 = 0.3616 r_free = 0.3616 target = 0.120967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.088417 restraints weight = 20248.622| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.89 r_work: 0.3023 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11509 Z= 0.100 Angle : 0.489 6.067 15647 Z= 0.246 Chirality : 0.042 0.142 1712 Planarity : 0.004 0.045 2028 Dihedral : 3.714 19.693 1546 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.95 % Allowed : 15.61 % Favored : 82.44 % 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: -0.30 (0.23), residues: 1394 helix: 1.46 (0.40), residues: 191 sheet: 0.81 (0.31), residues: 298 loop : -0.96 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.008 0.001 TYR B 671 PHE 0.011 0.001 PHE B 695 TRP 0.018 0.001 TRP A 211 HIS 0.005 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (11509) covalent geometry : angle 0.48920 / 0.25 (15647) hydrogen bonds : bond 0.03403 / 2.23 ( 290) hydrogen bonds : angle 4.29640 / 3.03 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 137 LYS cc_start: 0.7859 (mmtt) cc_final: 0.7442 (mmtt) REVERT: A 144 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7805 (ptm-80) REVERT: A 217 HIS cc_start: 0.7238 (p-80) cc_final: 0.6742 (p-80) REVERT: A 348 TYR cc_start: 0.7609 (m-10) cc_final: 0.7249 (m-10) REVERT: A 364 SER cc_start: 0.8292 (p) cc_final: 0.7933 (m) REVERT: A 450 TYR cc_start: 0.7682 (m-80) cc_final: 0.7341 (m-80) REVERT: A 490 TYR cc_start: 0.5115 (OUTLIER) cc_final: 0.3192 (p90) REVERT: A 589 TYR cc_start: 0.7156 (m-10) cc_final: 0.6825 (m-10) REVERT: B 184 GLN cc_start: 0.8655 (pp30) cc_final: 0.8017 (pp30) REVERT: B 186 LEU cc_start: 0.8258 (mp) cc_final: 0.7841 (mp) REVERT: B 786 MET cc_start: 0.7134 (ppp) cc_final: 0.6297 (mtt) REVERT: B 866 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7724 (t70) outliers start: 24 outliers final: 17 residues processed: 88 average time/residue: 0.0851 time to fit residues: 10.8624 Evaluate side-chains 92 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 87 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 851 HIS ** 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 = 0.3682 r_free = 0.3682 target = 0.119918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.090123 restraints weight = 20394.067| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.47 r_work: 0.3122 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11509 Z= 0.147 Angle : 0.530 7.395 15647 Z= 0.268 Chirality : 0.043 0.143 1712 Planarity : 0.004 0.048 2028 Dihedral : 3.840 19.192 1546 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.03 % Allowed : 15.45 % Favored : 82.52 % 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: -0.42 (0.23), residues: 1394 helix: 1.29 (0.39), residues: 200 sheet: 0.74 (0.31), residues: 291 loop : -1.05 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.009 0.001 TYR B 671 PHE 0.015 0.001 PHE A 391 TRP 0.011 0.001 TRP A 722 HIS 0.003 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (11509) covalent geometry : angle 0.53045 / 0.27 (15647) hydrogen bonds : bond 0.04176 / 2.74 ( 290) hydrogen bonds : angle 4.41105 / 3.12 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 217 HIS cc_start: 0.7245 (p-80) cc_final: 0.6653 (p90) REVERT: A 348 TYR cc_start: 0.7745 (m-10) cc_final: 0.7408 (m-10) REVERT: A 364 SER cc_start: 0.8426 (p) cc_final: 0.8142 (m) REVERT: A 450 TYR cc_start: 0.7646 (m-80) cc_final: 0.7338 (m-80) REVERT: A 490 TYR cc_start: 0.5479 (OUTLIER) cc_final: 0.3157 (p90) REVERT: A 589 TYR cc_start: 0.7440 (m-10) cc_final: 0.7089 (m-10) REVERT: B 184 GLN cc_start: 0.8723 (pp30) cc_final: 0.8130 (pp30) REVERT: B 186 LEU cc_start: 0.8306 (mp) cc_final: 0.7891 (mp) REVERT: B 316 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6744 (tm-30) REVERT: B 790 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7739 (mp) outliers start: 25 outliers final: 18 residues processed: 92 average time/residue: 0.1002 time to fit residues: 13.1888 Evaluate side-chains 91 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 100 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 90 optimal weight: 0.0000 chunk 119 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 659 GLN ** B 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088721 restraints weight = 20258.673| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.87 r_work: 0.3033 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11509 Z= 0.091 Angle : 0.492 7.608 15647 Z= 0.246 Chirality : 0.041 0.142 1712 Planarity : 0.004 0.045 2028 Dihedral : 3.663 19.143 1546 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.38 % Allowed : 16.59 % Favored : 82.03 % 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: -0.27 (0.23), residues: 1394 helix: 1.59 (0.40), residues: 190 sheet: 0.82 (0.31), residues: 291 loop : -0.96 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.009 0.001 TYR A 691 PHE 0.009 0.001 PHE A 263 TRP 0.014 0.001 TRP A 211 HIS 0.004 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (11509) covalent geometry : angle 0.49240 / 0.25 (15647) hydrogen bonds : bond 0.03131 / 2.06 ( 290) hydrogen bonds : angle 4.23469 / 2.99 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 156 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7193 (tm-30) REVERT: A 159 LEU cc_start: 0.7249 (mm) cc_final: 0.7006 (mp) REVERT: A 217 HIS cc_start: 0.7198 (p-80) cc_final: 0.6703 (p-80) REVERT: A 348 TYR cc_start: 0.7588 (m-10) cc_final: 0.7224 (m-10) REVERT: A 364 SER cc_start: 0.8507 (p) cc_final: 0.8080 (m) REVERT: A 450 TYR cc_start: 0.7687 (m-80) cc_final: 0.7330 (m-80) REVERT: A 490 TYR cc_start: 0.5137 (OUTLIER) cc_final: 0.3153 (p90) REVERT: A 589 TYR cc_start: 0.7164 (m-10) cc_final: 0.6899 (m-10) REVERT: B 184 GLN cc_start: 0.8627 (pp30) cc_final: 0.7973 (pp30) REVERT: B 186 LEU cc_start: 0.8309 (mp) cc_final: 0.7882 (mp) REVERT: B 316 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6211 (tm-30) REVERT: B 786 MET cc_start: 0.7099 (ppp) cc_final: 0.6140 (mtt) outliers start: 17 outliers final: 14 residues processed: 87 average time/residue: 0.0958 time to fit residues: 12.0244 Evaluate side-chains 89 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 769 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 123 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 overall best weight: 0.8338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 851 HIS ** 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 = 0.3612 r_free = 0.3612 target = 0.120646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.088286 restraints weight = 20404.545| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.89 r_work: 0.3024 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11509 Z= 0.101 Angle : 0.498 7.509 15647 Z= 0.248 Chirality : 0.042 0.141 1712 Planarity : 0.004 0.045 2028 Dihedral : 3.628 18.619 1546 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.22 % Allowed : 16.75 % Favored : 82.03 % 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: -0.27 (0.23), residues: 1394 helix: 1.50 (0.39), residues: 198 sheet: 0.80 (0.31), residues: 291 loop : -0.95 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 367 TYR 0.008 0.001 TYR B 486 PHE 0.015 0.001 PHE A 391 TRP 0.011 0.001 TRP A 211 HIS 0.003 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (11509) covalent geometry : angle 0.49849 / 0.25 (15647) hydrogen bonds : bond 0.03309 / 2.18 ( 290) hydrogen bonds : angle 4.20352 / 2.97 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2141.56 seconds wall clock time: 37 minutes 17.81 seconds (2237.81 seconds total)