Starting phenix.real_space_refine on Wed Mar 4 16:42:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e8i_31020/03_2026/7e8i_31020.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8i_31020/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7e8i_31020/03_2026/7e8i_31020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8i_31020/03_2026/7e8i_31020.map" model { file = "/net/cci-nas-00/data/ceres_data/7e8i_31020/03_2026/7e8i_31020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8i_31020/03_2026/7e8i_31020.cif" } 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-dev-5986/lib/python3.9/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: 3.07, per 1000 atoms: 0.20 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: 1.17 Conformation dependent library (CDL) restraints added in 471.3 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: 2.16 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: 2.77 Time building geometry restraints manager: 1.61 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=" 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 bond pdb=" CA SER H 75 " pdb=" CB SER H 75 " ideal model delta sigma weight residual 1.530 1.480 0.049 1.56e-02 4.11e+03 9.99e+00 ... (remaining 16140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 21807 1.58 - 3.17: 1075 3.17 - 4.75: 144 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: 2331 0.061 - 0.123: 207 0.123 - 0.184: 56 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.130 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.005 0.054 16145 Z= 0.318 Angle : 0.737 7.917 23060 Z= 0.511 Chirality : 0.047 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 covalent geometry : bond 0.00478 (16145) covalent geometry : angle 0.73744 (23060) hydrogen bonds : bond 0.14036 ( 812) hydrogen bonds : angle 5.96138 ( 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 : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7875 (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: 0.7531 (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: 0.7735 (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: 0.8214 (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: 0.5446 (pp) REVERT: L 40 GLN cc_start: 0.8031 (pt0) cc_final: 0.7061 (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: 0.1827 time to fit residues: 54.5069 Evaluate side-chains 168 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 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: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN 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 = 0.4174 r_free = 0.4174 target = 0.166213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104171 restraints weight = 20829.378| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.08 r_work: 0.3168 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16145 Z= 0.205 Angle : 0.589 8.411 23060 Z= 0.335 Chirality : 0.037 0.173 2621 Planarity : 0.005 0.055 1919 Dihedral : 28.642 177.829 4459 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.00 % Allowed : 10.80 % Favored : 88.20 % 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: -1.38 (0.23), residues: 1154 helix: -0.08 (0.19), residues: 698 sheet: -2.36 (0.67), residues: 40 loop : -2.13 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 520 TYR 0.013 0.001 TYR G 57 PHE 0.011 0.001 PHE A 67 TRP 0.012 0.002 TRP K 629 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00472 (16145) covalent geometry : angle 0.58883 (23060) hydrogen bonds : bond 0.03898 ( 812) hydrogen bonds : angle 3.83450 ( 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 184 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8487 (mtt90) cc_final: 0.8094 (ttm110) REVERT: A 59 GLU cc_start: 0.7961 (pp20) cc_final: 0.7621 (pp20) REVERT: B 77 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8400 (mmmt) REVERT: C 99 ARG cc_start: 0.8158 (mmt180) cc_final: 0.7565 (mmm160) REVERT: E 56 LYS cc_start: 0.8641 (pttt) cc_final: 0.8218 (ptpt) REVERT: G 36 LYS cc_start: 0.8665 (ttmt) cc_final: 0.7919 (ttpt) REVERT: G 73 ASN cc_start: 0.8600 (t0) cc_final: 0.7612 (t0) REVERT: G 74 LYS cc_start: 0.8753 (mptt) cc_final: 0.8197 (mtmt) REVERT: H 102 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7583 (mm-30) REVERT: H 105 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8191 (ttmm) REVERT: K 486 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7892 (mp) REVERT: K 704 SER cc_start: 0.9289 (m) cc_final: 0.8928 (t) REVERT: L 40 GLN cc_start: 0.8343 (pt0) cc_final: 0.7745 (pp30) REVERT: L 64 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8136 (mt-10) outliers start: 10 outliers final: 8 residues processed: 181 average time/residue: 0.1489 time to fit residues: 37.5098 Evaluate side-chains 170 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 30 THR Chi-restraints excluded: chain F residue 80 THR 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: chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** 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 = 0.4167 r_free = 0.4167 target = 0.165733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103342 restraints weight = 20954.595| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.09 r_work: 0.3157 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16145 Z= 0.173 Angle : 0.551 6.067 23060 Z= 0.318 Chirality : 0.036 0.155 2621 Planarity : 0.004 0.046 1919 Dihedral : 28.978 178.006 4459 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.50 % Allowed : 12.70 % Favored : 85.80 % 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: -0.55 (0.24), residues: 1154 helix: 0.59 (0.19), residues: 702 sheet: -2.38 (0.65), residues: 39 loop : -1.78 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 54 TYR 0.010 0.001 TYR B 72 PHE 0.011 0.001 PHE A 67 TRP 0.015 0.001 TRP K 629 HIS 0.004 0.001 HIS K 471 Details of bonding type rmsd covalent geometry : bond 0.00397 (16145) covalent geometry : angle 0.55122 (23060) hydrogen bonds : bond 0.03342 ( 812) hydrogen bonds : angle 3.49132 ( 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 183 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8458 (mtt90) cc_final: 0.8038 (ttm110) REVERT: B 77 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8380 (mmmt) REVERT: C 36 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8442 (tmtt) REVERT: E 56 LYS cc_start: 0.8546 (pttt) cc_final: 0.8133 (ptpt) REVERT: G 36 LYS cc_start: 0.8653 (ttmt) cc_final: 0.7897 (ttpt) REVERT: G 73 ASN cc_start: 0.8571 (t0) cc_final: 0.7570 (t0) REVERT: G 74 LYS cc_start: 0.8779 (mptt) cc_final: 0.8235 (mtmt) REVERT: H 102 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7947 (mm-30) REVERT: H 105 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8132 (ttmm) REVERT: K 704 SER cc_start: 0.9270 (m) cc_final: 0.8820 (t) REVERT: L 40 GLN cc_start: 0.8316 (pt0) cc_final: 0.7778 (pp30) REVERT: L 64 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8131 (mt-10) outliers start: 15 outliers final: 11 residues processed: 174 average time/residue: 0.1478 time to fit residues: 36.0503 Evaluate side-chains 167 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 86 SER 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 727 ASP Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.161728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098733 restraints weight = 20819.670| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.06 r_work: 0.3081 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16145 Z= 0.226 Angle : 0.586 6.193 23060 Z= 0.336 Chirality : 0.038 0.168 2621 Planarity : 0.004 0.043 1919 Dihedral : 29.451 179.883 4459 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.50 % Allowed : 13.90 % Favored : 83.60 % 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 (0.25), residues: 1154 helix: 0.78 (0.20), residues: 705 sheet: -2.39 (0.63), residues: 39 loop : -1.54 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 52 TYR 0.012 0.001 TYR G 57 PHE 0.012 0.002 PHE C 25 TRP 0.017 0.002 TRP K 629 HIS 0.005 0.001 HIS K 471 Details of bonding type rmsd covalent geometry : bond 0.00531 (16145) covalent geometry : angle 0.58598 (23060) hydrogen bonds : bond 0.03601 ( 812) hydrogen bonds : angle 3.47952 ( 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 192 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8451 (mtt90) cc_final: 0.8068 (ttm110) REVERT: B 77 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8398 (mmmt) REVERT: C 33 LEU cc_start: 0.8890 (mt) cc_final: 0.8649 (mt) REVERT: C 36 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8491 (tmtt) REVERT: C 74 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8386 (mmtm) REVERT: C 99 ARG cc_start: 0.8054 (mmt180) cc_final: 0.7490 (mmm160) REVERT: E 56 LYS cc_start: 0.8672 (pttt) cc_final: 0.8209 (ptpt) REVERT: G 36 LYS cc_start: 0.8663 (ttmt) cc_final: 0.7936 (ttpt) REVERT: G 73 ASN cc_start: 0.8599 (t0) cc_final: 0.7607 (t0) REVERT: G 74 LYS cc_start: 0.8792 (mptt) cc_final: 0.8269 (mtmt) REVERT: H 102 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8084 (mm-30) REVERT: H 105 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8161 (ttmm) REVERT: K 425 ASN cc_start: 0.8457 (t0) cc_final: 0.7850 (t0) REVERT: K 486 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7946 (mp) REVERT: K 701 GLN cc_start: 0.8463 (mp10) cc_final: 0.7994 (mp10) REVERT: K 704 SER cc_start: 0.9249 (m) cc_final: 0.8671 (t) REVERT: L 40 GLN cc_start: 0.8312 (pt0) cc_final: 0.7816 (pp30) REVERT: L 64 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8178 (mt-10) outliers start: 25 outliers final: 16 residues processed: 184 average time/residue: 0.1425 time to fit residues: 36.7638 Evaluate side-chains 176 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 B residue 73 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain E residue 86 SER 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 486 LEU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 514 LEU Chi-restraints excluded: chain K residue 710 ASP Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 64 ASN C 84 GLN D 44 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.161265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098641 restraints weight = 20779.527| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.06 r_work: 0.3090 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16145 Z= 0.199 Angle : 0.566 6.744 23060 Z= 0.325 Chirality : 0.037 0.152 2621 Planarity : 0.004 0.044 1919 Dihedral : 29.598 179.408 4459 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.10 % Allowed : 15.70 % Favored : 82.20 % 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: 0.03 (0.25), residues: 1154 helix: 0.98 (0.20), residues: 706 sheet: -2.26 (0.64), residues: 39 loop : -1.42 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 52 TYR 0.013 0.001 TYR K 446 PHE 0.009 0.001 PHE A 67 TRP 0.015 0.002 TRP K 629 HIS 0.005 0.001 HIS K 471 Details of bonding type rmsd covalent geometry : bond 0.00463 (16145) covalent geometry : angle 0.56639 (23060) hydrogen bonds : bond 0.03329 ( 812) hydrogen bonds : angle 3.35973 ( 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 193 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8067 (ttm110) REVERT: B 77 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8371 (mmmt) REVERT: C 99 ARG cc_start: 0.8050 (mmt180) cc_final: 0.7465 (mmm160) REVERT: D 60 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7935 (t0) REVERT: D 105 LYS cc_start: 0.8350 (ttpt) cc_final: 0.8034 (ttmm) REVERT: F 52 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7861 (mm-30) REVERT: G 36 LYS cc_start: 0.8661 (ttmt) cc_final: 0.7940 (ttpt) REVERT: G 73 ASN cc_start: 0.8584 (t0) cc_final: 0.7592 (t0) REVERT: G 74 LYS cc_start: 0.8768 (mptt) cc_final: 0.8232 (mtmt) REVERT: H 102 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8141 (mm-30) REVERT: H 105 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8140 (ttmm) REVERT: K 425 ASN cc_start: 0.8470 (t0) cc_final: 0.7952 (t0) REVERT: K 704 SER cc_start: 0.9244 (m) cc_final: 0.8625 (t) REVERT: L 40 GLN cc_start: 0.8311 (pt0) cc_final: 0.7923 (pp30) REVERT: L 60 ASN cc_start: 0.7701 (m110) cc_final: 0.7070 (p0) REVERT: L 64 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8072 (mt-10) outliers start: 21 outliers final: 12 residues processed: 186 average time/residue: 0.1350 time to fit residues: 35.3730 Evaluate side-chains 174 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 60 ASN 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 489 THR Chi-restraints excluded: chain K residue 514 LEU Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 0.6980 chunk 131 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN K 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.161499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098759 restraints weight = 20761.543| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.06 r_work: 0.3088 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16145 Z= 0.188 Angle : 0.563 6.325 23060 Z= 0.324 Chirality : 0.037 0.153 2621 Planarity : 0.004 0.045 1919 Dihedral : 29.674 178.020 4459 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.10 % Allowed : 16.20 % Favored : 81.70 % 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: 0.18 (0.25), residues: 1154 helix: 1.11 (0.20), residues: 711 sheet: -2.15 (0.65), residues: 39 loop : -1.40 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.012 0.001 TYR H 37 PHE 0.010 0.001 PHE A 67 TRP 0.009 0.001 TRP K 629 HIS 0.005 0.001 HIS K 471 Details of bonding type rmsd covalent geometry : bond 0.00436 (16145) covalent geometry : angle 0.56282 (23060) hydrogen bonds : bond 0.03285 ( 812) hydrogen bonds : angle 3.32972 ( 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 192 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8398 (mtt90) cc_final: 0.8000 (ttm110) REVERT: B 77 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8389 (mmmt) REVERT: C 99 ARG cc_start: 0.8035 (mmt180) cc_final: 0.7460 (mmm160) REVERT: D 60 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7951 (t0) REVERT: D 105 LYS cc_start: 0.8365 (ttpt) cc_final: 0.8050 (ttmm) REVERT: E 94 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8201 (mm-30) REVERT: F 52 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7810 (mm-30) REVERT: G 36 LYS cc_start: 0.8677 (ttmt) cc_final: 0.7956 (ttpt) REVERT: G 73 ASN cc_start: 0.8585 (t0) cc_final: 0.7674 (t0) REVERT: G 74 LYS cc_start: 0.8767 (mptt) cc_final: 0.8213 (mtmt) REVERT: H 43 LYS cc_start: 0.8286 (mttt) cc_final: 0.7717 (mptt) REVERT: H 102 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7677 (mm-30) REVERT: H 105 LYS cc_start: 0.8383 (mtpt) cc_final: 0.8122 (ttmm) REVERT: K 425 ASN cc_start: 0.8458 (t0) cc_final: 0.7970 (t0) REVERT: K 704 SER cc_start: 0.9225 (m) cc_final: 0.8640 (t) REVERT: L 40 GLN cc_start: 0.8327 (pt0) cc_final: 0.8063 (pp30) REVERT: L 49 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7852 (mm-40) REVERT: L 60 ASN cc_start: 0.7600 (m110) cc_final: 0.6998 (p0) outliers start: 21 outliers final: 15 residues processed: 184 average time/residue: 0.1485 time to fit residues: 38.2486 Evaluate side-chains 179 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 124 ILE 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 727 ASP Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN K 521 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.159492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096228 restraints weight = 20705.997| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.05 r_work: 0.3049 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16145 Z= 0.235 Angle : 0.589 6.309 23060 Z= 0.337 Chirality : 0.039 0.175 2621 Planarity : 0.004 0.044 1919 Dihedral : 29.897 176.852 4459 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.90 % Allowed : 16.10 % 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: 0.11 (0.25), residues: 1154 helix: 1.03 (0.20), residues: 712 sheet: -1.98 (0.67), residues: 39 loop : -1.42 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 52 TYR 0.012 0.001 TYR G 57 PHE 0.012 0.002 PHE A 67 TRP 0.007 0.002 TRP K 629 HIS 0.004 0.001 HIS K 471 Details of bonding type rmsd covalent geometry : bond 0.00553 (16145) covalent geometry : angle 0.58871 (23060) hydrogen bonds : bond 0.03532 ( 812) hydrogen bonds : angle 3.39163 ( 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 195 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8402 (mtt90) cc_final: 0.8006 (ttm110) REVERT: B 77 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8376 (mmmt) REVERT: C 99 ARG cc_start: 0.8071 (mmt180) cc_final: 0.7492 (mmm160) REVERT: D 60 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7951 (t0) REVERT: D 105 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8127 (ttmm) REVERT: E 94 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8384 (mm-30) REVERT: G 36 LYS cc_start: 0.8687 (ttmt) cc_final: 0.7959 (ttpt) REVERT: G 73 ASN cc_start: 0.8569 (t0) cc_final: 0.7569 (t0) REVERT: G 74 LYS cc_start: 0.8775 (mptt) cc_final: 0.8221 (mtmt) REVERT: H 43 LYS cc_start: 0.8316 (mttt) cc_final: 0.7746 (mptt) REVERT: H 102 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8153 (mm-30) REVERT: H 105 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8220 (ttmm) REVERT: K 425 ASN cc_start: 0.8485 (t0) cc_final: 0.7967 (t0) REVERT: K 704 SER cc_start: 0.9247 (m) cc_final: 0.8657 (t) REVERT: L 40 GLN cc_start: 0.8354 (pt0) cc_final: 0.7442 (pp30) REVERT: L 41 GLN cc_start: 0.7646 (tt0) cc_final: 0.7420 (tt0) REVERT: L 64 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8194 (mt-10) outliers start: 29 outliers final: 17 residues processed: 186 average time/residue: 0.1464 time to fit residues: 37.9170 Evaluate side-chains 178 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 124 ILE 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 H residue 36 ILE Chi-restraints excluded: chain K residue 487 VAL Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 609 VAL Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 139 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN E 113 HIS K 663 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.163051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100351 restraints weight = 21028.831| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.15 r_work: 0.3080 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16145 Z= 0.156 Angle : 0.550 8.704 23060 Z= 0.317 Chirality : 0.036 0.153 2621 Planarity : 0.004 0.045 1919 Dihedral : 29.617 177.293 4459 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % 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: 0.47 (0.25), residues: 1154 helix: 1.37 (0.20), residues: 713 sheet: -2.37 (0.63), residues: 46 loop : -1.30 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 52 TYR 0.010 0.001 TYR H 118 PHE 0.012 0.001 PHE K 633 TRP 0.007 0.001 TRP K 629 HIS 0.003 0.001 HIS K 471 Details of bonding type rmsd covalent geometry : bond 0.00354 (16145) covalent geometry : angle 0.55048 (23060) hydrogen bonds : bond 0.03109 ( 812) hydrogen bonds : angle 3.19411 ( 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 193 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8347 (mtt90) cc_final: 0.7943 (ttm110) REVERT: B 77 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8371 (mmmt) REVERT: C 99 ARG cc_start: 0.8062 (mmt180) cc_final: 0.7428 (mmm160) REVERT: D 60 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7849 (t0) REVERT: D 105 LYS cc_start: 0.8350 (ttpt) cc_final: 0.8023 (ttmm) REVERT: E 94 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8179 (mm-30) REVERT: F 52 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7809 (mm-30) REVERT: G 36 LYS cc_start: 0.8628 (ttmt) cc_final: 0.7892 (ttpt) REVERT: G 73 ASN cc_start: 0.8545 (t0) cc_final: 0.7610 (t0) REVERT: G 74 LYS cc_start: 0.8737 (mptt) cc_final: 0.8156 (mtmt) REVERT: H 43 LYS cc_start: 0.8257 (mttt) cc_final: 0.7677 (mptt) REVERT: H 102 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8166 (mm-30) REVERT: H 105 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8106 (ttmm) REVERT: K 425 ASN cc_start: 0.8443 (t0) cc_final: 0.8069 (t0) REVERT: K 704 SER cc_start: 0.9164 (m) cc_final: 0.8771 (p) REVERT: K 710 ASP cc_start: 0.8173 (m-30) cc_final: 0.7615 (p0) REVERT: L 42 ARG cc_start: 0.6772 (mtm-85) cc_final: 0.6365 (mtm-85) REVERT: L 49 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7631 (mm-40) REVERT: L 60 ASN cc_start: 0.7623 (m110) cc_final: 0.7071 (p0) REVERT: L 64 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8154 (mt-10) outliers start: 20 outliers final: 15 residues processed: 186 average time/residue: 0.1517 time to fit residues: 39.1953 Evaluate side-chains 170 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 124 ILE 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 H residue 36 ILE Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 609 VAL Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 14 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 38 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN K 521 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.163748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101362 restraints weight = 20985.996| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.15 r_work: 0.3092 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16145 Z= 0.149 Angle : 0.558 8.000 23060 Z= 0.320 Chirality : 0.035 0.153 2621 Planarity : 0.004 0.044 1919 Dihedral : 29.588 176.926 4459 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: 0.69 (0.25), residues: 1154 helix: 1.57 (0.20), residues: 705 sheet: -1.78 (0.70), residues: 39 loop : -1.30 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.011 0.001 TYR H 37 PHE 0.013 0.001 PHE C 25 TRP 0.021 0.002 TRP K 629 HIS 0.003 0.001 HIS K 471 Details of bonding type rmsd covalent geometry : bond 0.00335 (16145) covalent geometry : angle 0.55814 (23060) hydrogen bonds : bond 0.03082 ( 812) hydrogen bonds : angle 3.15981 ( 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 178 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7931 (ttm110) REVERT: A 123 ASP cc_start: 0.8568 (m-30) cc_final: 0.7801 (m-30) REVERT: B 77 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8342 (mmmt) REVERT: C 99 ARG cc_start: 0.8047 (mmt180) cc_final: 0.7340 (mmm160) REVERT: D 60 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7852 (t0) REVERT: E 94 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8184 (mm-30) REVERT: F 52 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7770 (mm-30) REVERT: G 36 LYS cc_start: 0.8624 (ttmt) cc_final: 0.7875 (ttpt) REVERT: G 73 ASN cc_start: 0.8542 (t0) cc_final: 0.7614 (t0) REVERT: G 74 LYS cc_start: 0.8800 (mptt) cc_final: 0.8214 (mtmt) REVERT: H 43 LYS cc_start: 0.8253 (mttt) cc_final: 0.7682 (mptt) REVERT: H 102 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8154 (mm-30) REVERT: H 105 LYS cc_start: 0.8324 (mtpt) cc_final: 0.8095 (ttmm) REVERT: K 425 ASN cc_start: 0.8454 (t0) cc_final: 0.8096 (t0) REVERT: K 537 GLU cc_start: 0.8500 (tp30) cc_final: 0.8152 (pm20) REVERT: K 704 SER cc_start: 0.9133 (m) cc_final: 0.8545 (t) REVERT: K 710 ASP cc_start: 0.8164 (m-30) cc_final: 0.7628 (p0) REVERT: L 49 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7697 (mm-40) REVERT: L 60 ASN cc_start: 0.7618 (m110) cc_final: 0.7073 (p0) outliers start: 19 outliers final: 16 residues processed: 174 average time/residue: 0.1427 time to fit residues: 34.9877 Evaluate side-chains 174 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 124 ILE 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 H residue 36 ILE Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 609 VAL Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN H 81 ASN K 521 ASN K 746 HIS ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.159466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095845 restraints weight = 21135.431| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.18 r_work: 0.3004 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16145 Z= 0.255 Angle : 0.628 11.860 23060 Z= 0.355 Chirality : 0.040 0.214 2621 Planarity : 0.004 0.044 1919 Dihedral : 30.015 175.332 4459 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.00 % Allowed : 17.70 % Favored : 80.30 % 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: 0.31 (0.25), residues: 1154 helix: 1.19 (0.20), residues: 712 sheet: -1.78 (0.70), residues: 39 loop : -1.36 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 42 TYR 0.017 0.002 TYR K 446 PHE 0.015 0.002 PHE K 633 TRP 0.017 0.002 TRP K 629 HIS 0.004 0.001 HIS K 471 Details of bonding type rmsd covalent geometry : bond 0.00600 (16145) covalent geometry : angle 0.62830 (23060) hydrogen bonds : bond 0.03720 ( 812) hydrogen bonds : angle 3.38648 ( 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 178 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8340 (mtt90) cc_final: 0.7929 (ttm110) REVERT: B 77 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8330 (mmmt) REVERT: C 99 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7412 (mmm160) REVERT: D 60 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7926 (t0) REVERT: D 105 LYS cc_start: 0.8381 (ttpt) cc_final: 0.8066 (ttmm) REVERT: E 94 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8256 (mm-30) REVERT: G 36 LYS cc_start: 0.8644 (ttmt) cc_final: 0.7895 (ttpt) REVERT: G 73 ASN cc_start: 0.8525 (t0) cc_final: 0.7630 (t0) REVERT: G 74 LYS cc_start: 0.8743 (mptt) cc_final: 0.8173 (mtmt) REVERT: H 43 LYS cc_start: 0.8282 (mttt) cc_final: 0.7694 (mptt) REVERT: H 102 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8184 (mm-30) REVERT: H 105 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8200 (ttmm) REVERT: K 425 ASN cc_start: 0.8483 (t0) cc_final: 0.8018 (t0) REVERT: K 537 GLU cc_start: 0.8520 (tp30) cc_final: 0.8165 (pm20) REVERT: K 704 SER cc_start: 0.9220 (m) cc_final: 0.8647 (t) REVERT: K 710 ASP cc_start: 0.8322 (m-30) cc_final: 0.7738 (p0) outliers start: 20 outliers final: 17 residues processed: 174 average time/residue: 0.1475 time to fit residues: 35.7425 Evaluate side-chains 174 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 124 ILE 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 H residue 36 ILE Chi-restraints excluded: chain K residue 487 VAL Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 609 VAL Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 521 ASN L 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.161145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098239 restraints weight = 20903.613| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.14 r_work: 0.3044 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 16145 Z= 0.195 Angle : 0.591 13.116 23060 Z= 0.338 Chirality : 0.037 0.227 2621 Planarity : 0.004 0.047 1919 Dihedral : 29.856 175.589 4459 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.10 % Allowed : 17.20 % Favored : 80.70 % 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: 0.50 (0.25), residues: 1154 helix: 1.38 (0.20), residues: 708 sheet: -1.73 (0.70), residues: 39 loop : -1.33 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 52 TYR 0.018 0.001 TYR K 446 PHE 0.022 0.001 PHE K 633 TRP 0.013 0.001 TRP K 629 HIS 0.004 0.001 HIS K 471 Details of bonding type rmsd covalent geometry : bond 0.00454 (16145) covalent geometry : angle 0.59141 (23060) hydrogen bonds : bond 0.03321 ( 812) hydrogen bonds : angle 3.25042 ( 2075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3913.49 seconds wall clock time: 67 minutes 22.00 seconds (4042.00 seconds total)