Starting phenix.real_space_refine on Sat Oct 24 22:26:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e8i_31020/10_2026/7e8i_31020.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8i_31020/10_2026/7e8i_31020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e8i_31020/10_2026/7e8i_31020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8i_31020/10_2026/7e8i_31020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e8i_31020/10_2026/7e8i_31020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8i_31020/10_2026/7e8i_31020.map" } resolution = 3.1 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= 0.037 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 30 5.16 5 C 8711 2.51 5 N 2830 2.21 5 O 3410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15271 Number of models: 1 Model: "" Number of chains: 12 Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 711 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2653 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 18, 'TRANS': 315} Chain breaks: 1 Chain: "L" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 3.45, per 1000 atoms: 0.23 Number of scatterers: 15271 At special positions: 0 Unit cell: (110, 116, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 290 15.00 O 3410 8.00 N 2830 7.00 C 8711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 461.2 milliseconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 60.5% alpha, 4.6% beta 132 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.508A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 114 removed outlier: 3.729A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.782A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.884A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.985A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.234A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.501A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.891A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.726A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.579A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.914A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.781A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.216A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.982A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.527A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.371A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.707A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.511A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.549A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 99 removed outlier: 3.942A pdb=" N ALA H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.733A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 430 through 438 Processing helix chain 'K' and resid 440 through 449 Processing helix chain 'K' and resid 463 through 472 Processing helix chain 'K' and resid 474 through 483 Processing helix chain 'K' and resid 496 through 504 removed outlier: 3.535A pdb=" N ASP K 500 " --> pdb=" O SER K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 506 through 515 Processing helix chain 'K' and resid 530 through 535 removed outlier: 3.606A pdb=" N THR K 534 " --> pdb=" O PRO K 530 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP K 535 " --> pdb=" O VAL K 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 530 through 535' Processing helix chain 'K' and resid 536 through 544 removed outlier: 3.965A pdb=" N LEU K 544 " --> pdb=" O LYS K 540 " (cutoff:3.500A) Processing helix chain 'K' and resid 578 through 592 Processing helix chain 'K' and resid 617 through 627 Processing helix chain 'K' and resid 633 through 643 removed outlier: 3.938A pdb=" N LYS K 637 " --> pdb=" O PHE K 633 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG K 641 " --> pdb=" O LYS K 637 " (cutoff:3.500A) Processing helix chain 'K' and resid 655 through 666 Processing helix chain 'K' and resid 687 through 698 Processing helix chain 'K' and resid 711 through 716 removed outlier: 3.851A pdb=" N GLN K 715 " --> pdb=" O SER K 711 " (cutoff:3.500A) Processing helix chain 'K' and resid 760 through 770 removed outlier: 3.557A pdb=" N VAL K 767 " --> pdb=" O PHE K 763 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 30 removed outlier: 4.155A pdb=" N VAL L 26 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE L 30 " --> pdb=" O VAL L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 35 Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.503A pdb=" N GLN L 41 " --> pdb=" O PRO L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.691A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.652A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.386A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.993A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 572 through 574 removed outlier: 3.963A pdb=" N ILE K 573 " --> pdb=" O HIS K 606 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL K 608 " --> pdb=" O ILE K 573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 701 through 702 removed outlier: 6.271A pdb=" N TYR K 676 " --> pdb=" O TYR K 736 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE K 738 " --> pdb=" O TYR K 676 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR K 678 " --> pdb=" O ILE K 738 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR K 739 " --> pdb=" O ALA K 758 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL K 755 " --> pdb=" O GLN K 752 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.749A pdb=" N LEU L 15 " --> pdb=" O ILE L 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE L 3 " --> pdb=" O LEU L 15 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU L 67 " --> pdb=" O GLN L 2 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE L 4 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU L 69 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS L 6 " --> pdb=" O LEU L 69 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2016 1.32 - 1.44: 5597 1.44 - 1.57: 7908 1.57 - 1.69: 578 1.69 - 1.81: 46 Bond restraints: 16145 Sorted by residual: bond pdb=" CA SER D 61 " pdb=" CB SER D 61 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.59e-02 3.96e+03 1.15e+01 bond pdb=" N ILE K 717 " pdb=" CA ILE K 717 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" CA SER D 57 " pdb=" CB SER D 57 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" CA SER D 53 " pdb=" CB SER D 53 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.05e+01 ... (remaining 16140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 21294 1.58 - 3.17: 1579 3.17 - 4.75: 153 4.75 - 6.33: 29 6.33 - 7.92: 5 Bond angle restraints: 23060 Sorted by residual: angle pdb=" N TYR D 34 " pdb=" CA TYR D 34 " pdb=" C TYR D 34 " ideal model delta sigma weight residual 112.93 106.60 6.33 1.12e+00 7.97e-01 3.19e+01 angle pdb=" N LYS K 438 " pdb=" CA LYS K 438 " pdb=" C LYS K 438 " ideal model delta sigma weight residual 113.20 107.20 6.00 1.21e+00 6.83e-01 2.46e+01 angle pdb=" N LYS K 688 " pdb=" CA LYS K 688 " pdb=" C LYS K 688 " ideal model delta sigma weight residual 111.28 105.96 5.32 1.09e+00 8.42e-01 2.38e+01 angle pdb=" C PRO H 100 " pdb=" CA PRO H 100 " pdb=" CB PRO H 100 " ideal model delta sigma weight residual 111.56 104.00 7.56 1.65e+00 3.67e-01 2.10e+01 angle pdb=" N LEU H 103 " pdb=" CA LEU H 103 " pdb=" C LEU H 103 " ideal model delta sigma weight residual 111.07 106.24 4.83 1.07e+00 8.73e-01 2.04e+01 ... (remaining 23055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 7728 35.96 - 71.91: 1233 71.91 - 107.87: 12 107.87 - 143.82: 0 143.82 - 179.78: 4 Dihedral angle restraints: 8977 sinusoidal: 5571 harmonic: 3406 Sorted by residual: dihedral pdb=" CA HIS A 39 " pdb=" C HIS A 39 " pdb=" N ARG A 40 " pdb=" CA ARG A 40 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA ARG L 72 " pdb=" C ARG L 72 " pdb=" N LEU L 73 " pdb=" CA LEU L 73 " ideal model delta harmonic sigma weight residual 180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 39.78 -179.78 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2128 0.061 - 0.123: 407 0.123 - 0.184: 59 0.184 - 0.246: 20 0.246 - 0.307: 7 Chirality restraints: 2621 Sorted by residual: chirality pdb=" CA ILE K 737 " pdb=" N ILE K 737 " pdb=" C ILE K 737 " pdb=" CB ILE K 737 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA ILE C 102 " pdb=" N ILE C 102 " pdb=" C ILE C 102 " pdb=" CB ILE C 102 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA VAL B 21 " pdb=" N VAL B 21 " pdb=" C VAL B 21 " pdb=" CB VAL B 21 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2618 not shown) Planarity restraints: 1919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 33 " -0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C SER D 33 " 0.070 2.00e-02 2.50e+03 pdb=" O SER D 33 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR D 34 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 98 " 0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLY C 98 " -0.067 2.00e-02 2.50e+03 pdb=" O GLY C 98 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG C 99 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER K 711 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C SER K 711 " -0.047 2.00e-02 2.50e+03 pdb=" O SER K 711 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP K 712 " 0.015 2.00e-02 2.50e+03 ... (remaining 1916 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1862 2.75 - 3.29: 13878 3.29 - 3.83: 29395 3.83 - 4.36: 35218 4.36 - 4.90: 50984 Nonbonded interactions: 131337 Sorted by model distance: nonbonded pdb=" OP2 DA J 21 " pdb=" OH TYR H 39 " model vdw 2.216 3.040 nonbonded pdb=" O LEU K 512 " pdb=" OG SER K 515 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.239 3.040 nonbonded pdb=" OP2 DG I 50 " pdb=" OG SER A 86 " model vdw 2.260 3.040 nonbonded pdb=" O SER D 120 " pdb=" OG SER D 120 " model vdw 2.311 3.040 ... (remaining 131332 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 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 19 through 101) selection = (chain 'F' and resid 19 through 101) } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.900 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16145 Z= 0.530 Angle : 0.848 7.917 23060 Z= 0.704 Chirality : 0.054 0.307 2621 Planarity : 0.004 0.040 1919 Dihedral : 24.649 179.777 6779 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.21), residues: 1154 helix: -1.38 (0.17), residues: 681 sheet: -2.67 (0.66), residues: 40 loop : -2.46 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 42 TYR 0.010 0.001 TYR K 736 PHE 0.012 0.001 PHE D 62 TRP 0.003 0.001 TRP K 756 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.53 (16145) covalent geometry : angle 0.84812 / 0.70 (23060) hydrogen bonds : bond 0.14036 / 15.13 ( 812) hydrogen bonds : angle 5.96138 / 7.85 ( 2075) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7874 (ttm110) REVERT: A 59 GLU cc_start: 0.8010 (pp20) cc_final: 0.7778 (pp20) REVERT: A 80 THR cc_start: 0.8939 (m) cc_final: 0.8732 (p) REVERT: C 99 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7532 (mmm160) REVERT: E 56 LYS cc_start: 0.8493 (pttt) cc_final: 0.8147 (ptpt) REVERT: F 25 ASN cc_start: 0.7522 (m110) cc_final: 0.6969 (m110) REVERT: G 36 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7734 (ttpt) REVERT: G 73 ASN cc_start: 0.8599 (t0) cc_final: 0.7731 (t0) REVERT: G 74 LYS cc_start: 0.8703 (mptt) cc_final: 0.8213 (mtmt) REVERT: H 102 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7331 (mm-30) REVERT: K 618 LEU cc_start: 0.6517 (tt) cc_final: 0.5447 (pp) REVERT: L 40 GLN cc_start: 0.8031 (pt0) cc_final: 0.7062 (pp30) REVERT: L 63 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7634 (ptpp) REVERT: L 64 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8234 (mt-10) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1697 time to fit residues: 51.4537 Evaluate side-chains 167 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 104 GLN H 81 ASN K 521 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.167256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105466 restraints weight = 20765.339| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.05 r_work: 0.3188 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16145 Z= 0.182 Angle : 0.622 8.443 23060 Z= 0.357 Chirality : 0.043 0.288 2621 Planarity : 0.005 0.046 1919 Dihedral : 28.803 175.226 4459 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.20 % Allowed : 10.00 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.23), residues: 1154 helix: -0.06 (0.19), residues: 698 sheet: -2.41 (0.66), residues: 40 loop : -2.18 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 520 TYR 0.013 0.001 TYR H 37 PHE 0.012 0.001 PHE A 67 TRP 0.015 0.002 TRP K 629 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (16145) covalent geometry : angle 0.62155 / 0.36 (23060) hydrogen bonds : bond 0.04655 / 5.05 ( 812) hydrogen bonds : angle 3.93078 / 5.12 ( 2075) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8482 (mtt90) cc_final: 0.8099 (ttm110) REVERT: A 59 GLU cc_start: 0.7946 (pp20) cc_final: 0.7625 (pp20) REVERT: B 77 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8392 (mmmt) REVERT: E 56 LYS cc_start: 0.8608 (pttt) cc_final: 0.8192 (ptpt) REVERT: G 36 LYS cc_start: 0.8633 (ttmt) cc_final: 0.7895 (ttpt) REVERT: G 73 ASN cc_start: 0.8590 (t0) cc_final: 0.7611 (t0) REVERT: G 74 LYS cc_start: 0.8753 (mptt) cc_final: 0.8217 (mtmt) REVERT: H 102 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7563 (mm-30) REVERT: H 105 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8210 (ttmm) REVERT: K 486 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7869 (mp) REVERT: K 704 SER cc_start: 0.9291 (m) cc_final: 0.8931 (t) REVERT: L 40 GLN cc_start: 0.8365 (pt0) cc_final: 0.7318 (pp30) REVERT: L 64 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8150 (mt-10) outliers start: 12 outliers final: 8 residues processed: 181 average time/residue: 0.1391 time to fit residues: 36.0091 Evaluate side-chains 165 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 49 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [87, 93, 139, 92, 82, 38, 16, 0, 100, 6, 112] chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.167237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105007 restraints weight = 20899.859| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.08 r_work: 0.3183 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16145 Z= 0.144 Angle : 0.582 5.986 23060 Z= 0.333 Chirality : 0.042 0.308 2621 Planarity : 0.004 0.042 1919 Dihedral : 29.195 173.704 4459 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.20 % Allowed : 12.90 % Favored : 85.90 % 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: -0.52 (0.24), residues: 1154 helix: 0.65 (0.20), residues: 701 sheet: -2.24 (0.65), residues: 40 loop : -1.87 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 52 TYR 0.011 0.001 TYR D 37 PHE 0.011 0.001 PHE K 672 TRP 0.014 0.001 TRP K 629 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (16145) covalent geometry : angle 0.58202 / 0.33 (23060) hydrogen bonds : bond 0.03987 / 4.31 ( 812) hydrogen bonds : angle 3.56482 / 4.67 ( 2075) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8032 (ttm110) REVERT: B 77 LYS cc_start: 0.8726 (mmmt) cc_final: 0.8336 (mmmt) REVERT: C 36 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8425 (tmtt) REVERT: E 56 LYS cc_start: 0.8575 (pttt) cc_final: 0.8127 (ptpt) REVERT: G 36 LYS cc_start: 0.8625 (ttmt) cc_final: 0.7871 (ttpt) REVERT: G 73 ASN cc_start: 0.8562 (t0) cc_final: 0.7562 (t0) REVERT: G 74 LYS cc_start: 0.8747 (mptt) cc_final: 0.8194 (mtmt) REVERT: H 102 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7914 (mm-30) REVERT: H 105 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8108 (ttmm) REVERT: K 621 MET cc_start: 0.7587 (mmt) cc_final: 0.7373 (mmp) REVERT: K 704 SER cc_start: 0.9264 (m) cc_final: 0.8841 (t) REVERT: L 40 GLN cc_start: 0.8393 (pt0) cc_final: 0.7766 (pp30) REVERT: L 64 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8150 (mt-10) outliers start: 12 outliers final: 10 residues processed: 171 average time/residue: 0.1291 time to fit residues: 32.0752 Evaluate side-chains 167 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 710 ASP Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 49 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [60, 71, 6, 102, 3, 101, 57, 20, 116, 93, 22] chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 102 optimal weight: 0.4980 chunk 3 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS H 81 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.163584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100480 restraints weight = 20858.944| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.07 r_work: 0.3115 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16145 Z= 0.206 Angle : 0.631 6.228 23060 Z= 0.349 Chirality : 0.045 0.321 2621 Planarity : 0.004 0.043 1919 Dihedral : 29.663 173.424 4459 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.00 % Allowed : 14.20 % Favored : 83.80 % 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: -0.29 (0.24), residues: 1154 helix: 0.81 (0.20), residues: 701 sheet: -2.26 (0.65), residues: 39 loop : -1.72 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.013 0.001 TYR K 446 PHE 0.012 0.002 PHE A 67 TRP 0.014 0.002 TRP K 629 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (16145) covalent geometry : angle 0.63110 / 0.35 (23060) hydrogen bonds : bond 0.04118 / 4.45 ( 812) hydrogen bonds : angle 3.55163 / 4.64 ( 2075) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8042 (m-80) cc_final: 0.7718 (m-80) REVERT: A 52 ARG cc_start: 0.8464 (mtt90) cc_final: 0.8047 (ttm110) REVERT: B 77 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8404 (mmtm) REVERT: C 36 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8478 (tmtt) REVERT: C 99 ARG cc_start: 0.8142 (mmt180) cc_final: 0.7588 (mmm160) REVERT: E 56 LYS cc_start: 0.8647 (pttt) cc_final: 0.8233 (ptpt) REVERT: G 36 LYS cc_start: 0.8698 (ttmt) cc_final: 0.7971 (ttpt) REVERT: G 73 ASN cc_start: 0.8599 (t0) cc_final: 0.7602 (t0) REVERT: G 74 LYS cc_start: 0.8784 (mptt) cc_final: 0.8258 (mtmt) REVERT: H 105 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8230 (ttmm) REVERT: K 425 ASN cc_start: 0.8482 (t0) cc_final: 0.7899 (t0) REVERT: K 539 MET cc_start: 0.8560 (mtt) cc_final: 0.8319 (mtt) REVERT: K 621 MET cc_start: 0.7694 (mmt) cc_final: 0.7274 (mmp) REVERT: K 701 GLN cc_start: 0.8521 (mp10) cc_final: 0.8174 (mp10) REVERT: K 704 SER cc_start: 0.9267 (m) cc_final: 0.8811 (t) REVERT: L 40 GLN cc_start: 0.8217 (pt0) cc_final: 0.7713 (pp30) REVERT: L 41 GLN cc_start: 0.7688 (tt0) cc_final: 0.7304 (mt0) REVERT: L 64 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8172 (mt-10) outliers start: 20 outliers final: 15 residues processed: 177 average time/residue: 0.1403 time to fit residues: 35.6120 Evaluate side-chains 173 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 49 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [12, 1, 45, 47, 72, 13, 107, 15, 32, 132, 30] chunk 12 optimal weight: 20.0000 chunk 1 optimal weight: 40.0000 chunk 45 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 32 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 64 ASN L 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.164260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102007 restraints weight = 20698.469| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.05 r_work: 0.3134 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16145 Z= 0.146 Angle : 0.593 6.983 23060 Z= 0.331 Chirality : 0.043 0.318 2621 Planarity : 0.004 0.043 1919 Dihedral : 29.704 173.848 4459 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.00 % Allowed : 14.70 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1154 helix: 1.06 (0.20), residues: 703 sheet: -2.17 (0.66), residues: 39 loop : -1.54 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.012 0.001 TYR K 651 PHE 0.009 0.001 PHE A 67 TRP 0.008 0.001 TRP K 629 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (16145) covalent geometry : angle 0.59288 / 0.33 (23060) hydrogen bonds : bond 0.03667 / 3.96 ( 812) hydrogen bonds : angle 3.42008 / 4.50 ( 2075) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7942 (m-80) cc_final: 0.7651 (m-80) REVERT: A 52 ARG cc_start: 0.8396 (mtt90) cc_final: 0.8042 (ttm110) REVERT: B 77 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8352 (mmmt) REVERT: C 99 ARG cc_start: 0.8057 (mmt180) cc_final: 0.7469 (mmm160) REVERT: E 56 LYS cc_start: 0.8598 (pttt) cc_final: 0.8153 (ptpt) REVERT: G 36 LYS cc_start: 0.8655 (ttmt) cc_final: 0.7906 (ttpt) REVERT: G 73 ASN cc_start: 0.8575 (t0) cc_final: 0.7584 (t0) REVERT: G 74 LYS cc_start: 0.8770 (mptt) cc_final: 0.8241 (mtmt) REVERT: H 102 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8148 (mm-30) REVERT: H 105 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8125 (ttmm) REVERT: K 425 ASN cc_start: 0.8469 (t0) cc_final: 0.7884 (t0) REVERT: K 486 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7961 (mp) REVERT: K 701 GLN cc_start: 0.8432 (mp10) cc_final: 0.8027 (mp10) REVERT: K 704 SER cc_start: 0.9244 (m) cc_final: 0.8780 (t) REVERT: L 40 GLN cc_start: 0.8252 (pt0) cc_final: 0.7779 (pp30) REVERT: L 64 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8150 (mt-10) outliers start: 20 outliers final: 16 residues processed: 179 average time/residue: 0.1367 time to fit residues: 34.8408 Evaluate side-chains 175 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 49 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [69, 131, 22, 111, 80, 73, 5, 18, 12, 41, 84] chunk 69 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 81 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.164506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102580 restraints weight = 20638.104| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.05 r_work: 0.3144 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16145 Z= 0.132 Angle : 0.582 7.250 23060 Z= 0.326 Chirality : 0.042 0.315 2621 Planarity : 0.004 0.043 1919 Dihedral : 29.702 174.140 4459 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.90 % Allowed : 15.80 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1154 helix: 1.27 (0.20), residues: 704 sheet: -2.15 (0.65), residues: 39 loop : -1.49 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.015 0.001 TYR K 446 PHE 0.008 0.001 PHE K 633 TRP 0.019 0.002 TRP K 629 HIS 0.002 0.000 HIS K 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (16145) covalent geometry : angle 0.58186 / 0.33 (23060) hydrogen bonds : bond 0.03531 / 3.80 ( 812) hydrogen bonds : angle 3.33566 / 4.40 ( 2075) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8438 (mtt90) cc_final: 0.8094 (ttm110) REVERT: A 123 ASP cc_start: 0.8518 (m-30) cc_final: 0.7887 (m-30) REVERT: B 77 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8368 (mmmt) REVERT: C 99 ARG cc_start: 0.8032 (mmt180) cc_final: 0.7465 (mmm160) REVERT: E 56 LYS cc_start: 0.8602 (pttt) cc_final: 0.8156 (ptpt) REVERT: G 36 LYS cc_start: 0.8651 (ttmt) cc_final: 0.7904 (ttpt) REVERT: G 73 ASN cc_start: 0.8578 (t0) cc_final: 0.7576 (t0) REVERT: G 74 LYS cc_start: 0.8766 (mptt) cc_final: 0.8234 (mtmt) REVERT: H 102 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8142 (mm-30) REVERT: H 105 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8097 (ttmm) REVERT: K 425 ASN cc_start: 0.8474 (t0) cc_final: 0.7878 (t0) REVERT: K 486 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7954 (mp) REVERT: K 701 GLN cc_start: 0.8438 (mp10) cc_final: 0.7992 (mp10) REVERT: K 704 SER cc_start: 0.9229 (m) cc_final: 0.8642 (t) REVERT: L 40 GLN cc_start: 0.8244 (pt0) cc_final: 0.7838 (pp30) REVERT: L 60 ASN cc_start: 0.7788 (m110) cc_final: 0.7155 (p0) REVERT: L 64 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8142 (mt-10) outliers start: 19 outliers final: 18 residues processed: 174 average time/residue: 0.1431 time to fit residues: 35.3383 Evaluate side-chains 176 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 49 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [21, 8, 93, 2, 49, 77, 11, 122, 136, 33, 106] chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.164623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102469 restraints weight = 20538.003| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.03 r_work: 0.3151 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16145 Z= 0.133 Angle : 0.578 6.635 23060 Z= 0.324 Chirality : 0.042 0.315 2621 Planarity : 0.004 0.043 1919 Dihedral : 29.728 174.522 4459 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.10 % Allowed : 15.80 % Favored : 82.10 % 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: 0.43 (0.25), residues: 1154 helix: 1.39 (0.20), residues: 706 sheet: -2.06 (0.66), residues: 39 loop : -1.46 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.010 0.001 TYR H 37 PHE 0.010 0.001 PHE C 25 TRP 0.021 0.002 TRP K 629 HIS 0.002 0.000 HIS K 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (16145) covalent geometry : angle 0.57801 / 0.32 (23060) hydrogen bonds : bond 0.03510 / 3.78 ( 812) hydrogen bonds : angle 3.29187 / 4.34 ( 2075) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8376 (mtt90) cc_final: 0.8037 (ttm110) REVERT: B 77 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8375 (mmmt) REVERT: C 99 ARG cc_start: 0.8030 (mmt180) cc_final: 0.7451 (mmm160) REVERT: E 56 LYS cc_start: 0.8585 (pttt) cc_final: 0.8131 (ptpt) REVERT: G 36 LYS cc_start: 0.8653 (ttmt) cc_final: 0.7916 (ttpt) REVERT: G 73 ASN cc_start: 0.8571 (t0) cc_final: 0.7654 (t0) REVERT: G 74 LYS cc_start: 0.8768 (mptt) cc_final: 0.8227 (mtmt) REVERT: H 102 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8146 (mm-30) REVERT: H 105 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8132 (ttmm) REVERT: K 425 ASN cc_start: 0.8476 (t0) cc_final: 0.7972 (t0) REVERT: K 486 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7956 (mp) REVERT: K 701 GLN cc_start: 0.8454 (mp10) cc_final: 0.7971 (mp10) REVERT: K 704 SER cc_start: 0.9220 (m) cc_final: 0.8623 (t) REVERT: L 40 GLN cc_start: 0.8216 (pt0) cc_final: 0.7765 (pp30) REVERT: L 60 ASN cc_start: 0.7776 (m110) cc_final: 0.7180 (p0) REVERT: L 64 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8144 (mt-10) outliers start: 21 outliers final: 18 residues processed: 170 average time/residue: 0.1338 time to fit residues: 32.4151 Evaluate side-chains 175 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 49 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [139, 59, 114, 11, 55, 28, 1, 20, 80, 36, 60] chunk 139 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 40.0000 chunk 20 optimal weight: 8.9990 chunk 80 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.162023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099305 restraints weight = 20695.662| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.05 r_work: 0.3093 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16145 Z= 0.200 Angle : 0.627 7.151 23060 Z= 0.343 Chirality : 0.044 0.325 2621 Planarity : 0.004 0.044 1919 Dihedral : 29.958 175.442 4459 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.40 % Allowed : 15.50 % Favored : 82.10 % 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: 0.31 (0.25), residues: 1154 helix: 1.28 (0.20), residues: 705 sheet: -2.08 (0.65), residues: 39 loop : -1.45 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 52 TYR 0.016 0.001 TYR K 446 PHE 0.013 0.002 PHE C 25 TRP 0.016 0.002 TRP K 629 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (16145) covalent geometry : angle 0.62675 / 0.34 (23060) hydrogen bonds : bond 0.03897 / 4.20 ( 812) hydrogen bonds : angle 3.38192 / 4.44 ( 2075) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8370 (mtt90) cc_final: 0.8008 (ttm110) REVERT: B 77 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8385 (mmmt) REVERT: C 99 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7479 (mmm160) REVERT: D 60 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7953 (t0) REVERT: E 42 ARG cc_start: 0.7483 (mtp85) cc_final: 0.6796 (mtp-110) REVERT: G 36 LYS cc_start: 0.8667 (ttmt) cc_final: 0.7936 (ttpt) REVERT: G 73 ASN cc_start: 0.8582 (t0) cc_final: 0.7696 (t0) REVERT: G 74 LYS cc_start: 0.8784 (mptt) cc_final: 0.8253 (mtmt) REVERT: H 43 LYS cc_start: 0.8245 (mttt) cc_final: 0.7665 (mptt) REVERT: H 102 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8207 (mm-30) REVERT: H 105 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8099 (ttmm) REVERT: K 425 ASN cc_start: 0.8466 (t0) cc_final: 0.7953 (t0) REVERT: K 701 GLN cc_start: 0.8436 (mp10) cc_final: 0.7898 (mp10) REVERT: K 704 SER cc_start: 0.9245 (m) cc_final: 0.8646 (t) REVERT: L 40 GLN cc_start: 0.8251 (pt0) cc_final: 0.7832 (pp30) REVERT: L 60 ASN cc_start: 0.7696 (m110) cc_final: 0.7075 (p0) REVERT: L 64 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8096 (mt-10) outliers start: 24 outliers final: 19 residues processed: 175 average time/residue: 0.1446 time to fit residues: 35.8725 Evaluate side-chains 177 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 710 ASP Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 49 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [14, 70, 100, 127, 28, 112, 38, 97, 2, 106, 120] chunk 14 optimal weight: 50.0000 chunk 70 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 112 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.164153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101722 restraints weight = 20544.335| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.09 r_work: 0.3130 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16145 Z= 0.127 Angle : 0.588 7.964 23060 Z= 0.328 Chirality : 0.042 0.319 2621 Planarity : 0.004 0.044 1919 Dihedral : 29.875 175.327 4459 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.00 % Allowed : 16.60 % Favored : 81.40 % 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: 0.50 (0.25), residues: 1154 helix: 1.45 (0.20), residues: 708 sheet: -2.42 (0.61), residues: 46 loop : -1.37 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 42 TYR 0.011 0.001 TYR D 37 PHE 0.010 0.001 PHE K 633 TRP 0.014 0.001 TRP K 629 HIS 0.002 0.001 HIS K 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (16145) covalent geometry : angle 0.58840 / 0.33 (23060) hydrogen bonds : bond 0.03476 / 3.74 ( 812) hydrogen bonds : angle 3.29180 / 4.33 ( 2075) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8326 (mtt90) cc_final: 0.7970 (ttm110) REVERT: A 123 ASP cc_start: 0.8580 (m-30) cc_final: 0.7843 (m-30) REVERT: B 77 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8349 (mmmt) REVERT: C 99 ARG cc_start: 0.8046 (mmt180) cc_final: 0.7427 (mmm160) REVERT: G 36 LYS cc_start: 0.8635 (ttmt) cc_final: 0.7898 (ttpt) REVERT: G 73 ASN cc_start: 0.8548 (t0) cc_final: 0.7634 (t0) REVERT: G 74 LYS cc_start: 0.8750 (mptt) cc_final: 0.8204 (mtmt) REVERT: H 102 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8163 (mm-30) REVERT: H 105 LYS cc_start: 0.8262 (mtpt) cc_final: 0.8039 (ttmm) REVERT: K 425 ASN cc_start: 0.8437 (t0) cc_final: 0.7930 (t0) REVERT: K 701 GLN cc_start: 0.8405 (mp10) cc_final: 0.7895 (mp10) REVERT: K 704 SER cc_start: 0.9230 (m) cc_final: 0.8630 (t) REVERT: L 40 GLN cc_start: 0.8267 (pt0) cc_final: 0.7457 (pp30) REVERT: L 59 TYR cc_start: 0.7585 (m-80) cc_final: 0.7318 (m-80) REVERT: L 60 ASN cc_start: 0.7677 (m110) cc_final: 0.7052 (p0) REVERT: L 64 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8069 (mt-10) outliers start: 20 outliers final: 17 residues processed: 175 average time/residue: 0.1363 time to fit residues: 34.1243 Evaluate side-chains 177 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 49 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [108, 59, 77, 125, 10, 139, 121, 9, 11, 101, 135] chunk 108 optimal weight: 0.0970 chunk 59 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.162288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099318 restraints weight = 20706.126| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.06 r_work: 0.3099 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16145 Z= 0.184 Angle : 0.617 8.370 23060 Z= 0.339 Chirality : 0.044 0.324 2621 Planarity : 0.004 0.060 1919 Dihedral : 29.982 175.874 4459 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.80 % Allowed : 17.20 % Favored : 81.00 % 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: 0.44 (0.25), residues: 1154 helix: 1.38 (0.20), residues: 707 sheet: -2.52 (0.61), residues: 46 loop : -1.31 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 52 TYR 0.011 0.001 TYR G 57 PHE 0.013 0.001 PHE C 25 TRP 0.014 0.002 TRP K 629 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (16145) covalent geometry : angle 0.61747 / 0.34 (23060) hydrogen bonds : bond 0.03790 / 4.07 ( 812) hydrogen bonds : angle 3.35205 / 4.39 ( 2075) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8357 (mtt90) cc_final: 0.7983 (ttm110) REVERT: B 77 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8372 (mmmt) REVERT: C 99 ARG cc_start: 0.8069 (mmt180) cc_final: 0.7483 (mmm160) REVERT: E 42 ARG cc_start: 0.7518 (mtp85) cc_final: 0.6809 (mtp-110) REVERT: G 36 LYS cc_start: 0.8666 (ttmt) cc_final: 0.7938 (ttpt) REVERT: G 73 ASN cc_start: 0.8575 (t0) cc_final: 0.7675 (t0) REVERT: G 74 LYS cc_start: 0.8770 (mptt) cc_final: 0.8235 (mtmt) REVERT: H 43 LYS cc_start: 0.8253 (mttt) cc_final: 0.7675 (mptt) REVERT: H 102 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8210 (mm-30) REVERT: H 105 LYS cc_start: 0.8328 (mtpt) cc_final: 0.8093 (ttmm) REVERT: K 425 ASN cc_start: 0.8469 (t0) cc_final: 0.7958 (t0) REVERT: K 701 GLN cc_start: 0.8448 (mp10) cc_final: 0.7893 (mp10) REVERT: K 704 SER cc_start: 0.9221 (m) cc_final: 0.8635 (t) REVERT: L 40 GLN cc_start: 0.8131 (pt0) cc_final: 0.7507 (pp30) REVERT: L 60 ASN cc_start: 0.7690 (m110) cc_final: 0.7063 (p0) REVERT: L 64 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8076 (mt-10) outliers start: 18 outliers final: 17 residues processed: 174 average time/residue: 0.1475 time to fit residues: 36.2893 Evaluate side-chains 178 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 49 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [43, 32, 48, 2, 37, 55, 135, 0, 89, 14, 54] chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 89 optimal weight: 0.9980 chunk 14 optimal weight: 40.0000 chunk 54 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 41 GLN ** 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 = 0.4117 r_free = 0.4117 target = 0.162426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099763 restraints weight = 20461.769| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.02 r_work: 0.3104 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16145 Z= 0.168 Angle : 0.613 8.397 23060 Z= 0.338 Chirality : 0.044 0.324 2621 Planarity : 0.004 0.044 1919 Dihedral : 30.022 176.210 4459 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.90 % Allowed : 17.10 % Favored : 81.00 % 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: 0.46 (0.25), residues: 1154 helix: 1.38 (0.20), residues: 708 sheet: -2.52 (0.62), residues: 46 loop : -1.29 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 52 TYR 0.010 0.001 TYR G 57 PHE 0.012 0.001 PHE K 633 TRP 0.014 0.001 TRP K 629 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (16145) covalent geometry : angle 0.61295 / 0.34 (23060) hydrogen bonds : bond 0.03689 / 3.96 ( 812) hydrogen bonds : angle 3.33144 / 4.36 ( 2075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3826.19 seconds wall clock time: 65 minutes 58.56 seconds (3958.56 seconds total)