Starting phenix.real_space_refine on Sun Jul 5 00:54:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9v_64889/07_2026/9v9v_64889.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9v_64889/07_2026/9v9v_64889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v9v_64889/07_2026/9v9v_64889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9v_64889/07_2026/9v9v_64889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v9v_64889/07_2026/9v9v_64889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9v_64889/07_2026/9v9v_64889.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12582 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 264 5.49 5 S 42 5.16 5 C 8254 2.51 5 N 2669 2.21 5 O 3206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14440 Number of models: 1 Model: "" Number of chains: 18 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: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "D" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 711 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} 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: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2688 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "J" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2724 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "M" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 812 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "N" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "L" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 252 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "K" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11493 SG CYS M 18 58.673 113.891 52.555 1.00 93.44 S ATOM 11514 SG CYS M 21 60.020 117.159 51.576 1.00 95.76 S ATOM 11652 SG CYS M 39 60.711 114.199 49.117 1.00 94.77 S ATOM 11674 SG CYS M 42 62.431 114.465 52.434 1.00 90.06 S ATOM 11611 SG CYS M 34 54.732 101.883 58.253 1.00 81.99 S ATOM 11769 SG CYS M 53 57.622 104.188 59.317 1.00 74.08 S ATOM 11790 SG CYS M 56 55.736 102.069 61.893 1.00 78.00 S ATOM 12473 SG CYS N 51 38.160 95.382 43.463 1.00130.37 S ATOM 12494 SG CYS N 54 34.528 95.501 43.612 1.00138.19 S ATOM 12642 SG CYS N 72 36.465 94.958 46.982 1.00119.30 S ATOM 12661 SG CYS N 75 36.155 92.219 44.492 1.00113.60 S ATOM 12596 SG CYS N 67 51.337 94.332 42.829 1.00 95.39 S ATOM 12750 SG CYS N 87 49.170 91.477 41.497 1.00100.08 S ATOM 12770 SG CYS N 90 52.558 92.131 39.927 1.00104.57 S ATOM 13619 SG CYS L 27 83.550 33.095 52.987 1.00121.56 S ATOM 13638 SG CYS L 30 82.483 30.844 50.078 1.00125.47 S ATOM 13726 SG CYS L 41 85.382 33.336 49.692 1.00116.63 S ATOM 13746 SG CYS L 44 81.781 34.523 49.924 1.00122.41 S Time building chain proxies: 2.97, per 1000 atoms: 0.21 Number of scatterers: 14440 At special positions: 0 Unit cell: (125.4, 144.1, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 42 16.00 P 264 15.00 O 3206 8.00 N 2669 7.00 C 8254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 464.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 44 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 27 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 30 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 42 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 21 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 39 " pdb=" ZN M 402 " pdb="ZN ZN M 402 " - pdb=" ND1 HIS M 36 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 56 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 53 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 72 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " Number of angles added : 24 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 17 sheets defined 57.8% alpha, 5.6% beta 130 base pairs and 208 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.978A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.533A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 removed outlier: 3.561A pdb=" N ALA C 21 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 18 through 22' Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.404A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.093A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.590A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.508A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.568A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.089A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.469A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.902A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 12 removed outlier: 3.739A pdb=" N GLU M 11 " --> pdb=" O LYS M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 50 removed outlier: 3.627A pdb=" N GLU M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR M 49 " --> pdb=" O ARG M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 72 through 83 removed outlier: 3.773A pdb=" N GLN M 76 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 101 removed outlier: 3.571A pdb=" N ASN M 89 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU M 90 " --> pdb=" O LEU M 86 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET M 91 " --> pdb=" O PHE M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 25 removed outlier: 4.551A pdb=" N GLN N 25 " --> pdb=" O LEU N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 83 Processing helix chain 'N' and resid 96 through 98 No H-bonds generated for 'chain 'N' and resid 96 through 98' Processing helix chain 'N' and resid 103 through 114 Processing helix chain 'O' and resid 22 through 34 Processing helix chain 'O' and resid 55 through 59 Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 55 through 59 removed outlier: 3.674A pdb=" N TYR K 59 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.790A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.606A 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 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.806A 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 42 through 43 removed outlier: 7.231A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.807A pdb=" N VAL N 40 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE M 7 " --> pdb=" O ILE N 38 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE N 38 " --> pdb=" O ILE M 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 17 through 18 removed outlier: 3.507A pdb=" N GLY M 23 " --> pdb=" O CYS M 18 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 37 through 38 Processing sheet with id=AB5, first strand: chain 'N' and resid 70 through 72 Processing sheet with id=AB6, first strand: chain 'O' and resid 12 through 14 removed outlier: 3.740A pdb=" N ILE O 13 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS O 68 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL O 70 " --> pdb=" O ARG O 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG O 42 " --> pdb=" O VAL O 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'K' and resid 48 through 49 removed outlier: 3.802A pdb=" N PHE K 45 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG K 42 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL K 70 " --> pdb=" O ARG K 42 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS K 68 " --> pdb=" O ILE K 44 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 331 hydrogen bonds 658 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 208 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3396 1.34 - 1.46: 4110 1.46 - 1.57: 7128 1.57 - 1.69: 526 1.69 - 1.81: 59 Bond restraints: 15219 Sorted by residual: bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DC J 77 " pdb=" C2' DC J 77 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DT J 57 " pdb=" C2' DT J 57 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG I 44 " pdb=" C2' DG I 44 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC I 23 " pdb=" C2' DC I 23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.99e+00 ... (remaining 15214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 20381 1.37 - 2.75: 1214 2.75 - 4.12: 67 4.12 - 5.50: 13 5.50 - 6.87: 2 Bond angle restraints: 21677 Sorted by residual: angle pdb=" N ILE M 32 " pdb=" CA ILE M 32 " pdb=" C ILE M 32 " ideal model delta sigma weight residual 106.21 111.04 -4.83 1.07e+00 8.73e-01 2.03e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J 87 " pdb=" C4 DT J 87 " pdb=" O4 DT J 87 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 35 " pdb=" C4 DT I 35 " pdb=" O4 DT I 35 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I 142 " pdb=" C4 DT I 142 " pdb=" O4 DT I 142 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 ... (remaining 21672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 7312 35.12 - 70.25: 1220 70.25 - 105.37: 18 105.37 - 140.50: 0 140.50 - 175.62: 2 Dihedral angle restraints: 8552 sinusoidal: 5246 harmonic: 3306 Sorted by residual: dihedral pdb=" CA ILE M 32 " pdb=" C ILE M 32 " pdb=" N GLU M 33 " pdb=" CA GLU M 33 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" C4' DT J 57 " pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " pdb=" P DT J 58 " ideal model delta sinusoidal sigma weight residual -140.00 35.62 -175.62 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 79.11 140.89 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 8549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1739 0.039 - 0.078: 540 0.078 - 0.116: 200 0.116 - 0.155: 10 0.155 - 0.194: 1 Chirality restraints: 2490 Sorted by residual: chirality pdb=" CA ASN M 13 " pdb=" N ASN M 13 " pdb=" C ASN M 13 " pdb=" CB ASN M 13 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CA ILE K 36 " pdb=" N ILE K 36 " pdb=" C ILE K 36 " pdb=" CB ILE K 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" C3' DG J 82 " pdb=" C4' DG J 82 " pdb=" O3' DG J 82 " pdb=" C2' DG J 82 " both_signs ideal model delta sigma weight residual False -2.73 -2.61 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 2487 not shown) Planarity restraints: 1825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL M 83 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO M 84 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO M 84 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 84 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 74 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" CD GLU F 74 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU F 74 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU F 74 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE K 36 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO K 37 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO K 37 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO K 37 " -0.019 5.00e-02 4.00e+02 ... (remaining 1822 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 386 2.69 - 3.24: 12676 3.24 - 3.79: 25155 3.79 - 4.35: 30888 4.35 - 4.90: 46837 Nonbonded interactions: 115942 Sorted by model distance: nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.133 2.496 nonbonded pdb=" O ASP O 39 " pdb=" NH2 ARG O 72 " model vdw 2.231 3.120 nonbonded pdb=" NE2 GLN O 31 " pdb=" O ILE O 36 " model vdw 2.249 3.120 nonbonded pdb=" NH1 ARG A 72 " pdb=" OP1 DC I 51 " model vdw 2.261 3.120 nonbonded pdb=" O THR N 78 " pdb=" OG SER N 82 " model vdw 2.267 3.040 ... (remaining 115937 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' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) selection = (chain 'F' and resid 21 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 116) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 120) } ncs_group { reference = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.030 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 0.037 15239 Z= 0.444 Angle : 0.664 8.242 21701 Z= 0.575 Chirality : 0.042 0.194 2490 Planarity : 0.003 0.042 1825 Dihedral : 25.005 175.619 6408 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.26), residues: 1110 helix: 2.64 (0.21), residues: 614 sheet: -0.12 (1.05), residues: 30 loop : -0.92 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.015 0.001 TYR H 80 PHE 0.021 0.001 PHE M 87 TRP 0.002 0.000 TRP L 25 HIS 0.002 0.000 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.44 (15219) covalent geometry : angle 0.65397 / 0.57 (21677) hydrogen bonds : bond 0.12253 / 8.11 ( 811) hydrogen bonds : angle 4.30008 / 3.08 ( 2062) metal coordination : bond 0.00811 / 0.53 ( 20) metal coordination : angle 3.49791 / 2.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9152 (m-80) cc_final: 0.8497 (m-80) REVERT: B 25 ASN cc_start: 0.7814 (m110) cc_final: 0.7490 (m110) REVERT: H 65 ASP cc_start: 0.7685 (t0) cc_final: 0.7408 (t0) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1231 time to fit residues: 32.9214 Evaluate side-chains 155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 GLN O 2 GLN K 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.134645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.108644 restraints weight = 32196.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108175 restraints weight = 49002.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108521 restraints weight = 48171.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108304 restraints weight = 41814.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108443 restraints weight = 38224.329| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15239 Z= 0.226 Angle : 0.696 10.175 21701 Z= 0.391 Chirality : 0.046 0.232 2490 Planarity : 0.006 0.056 1825 Dihedral : 28.684 171.465 4137 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.34 % Allowed : 9.88 % Favored : 87.78 % 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: 1.18 (0.25), residues: 1110 helix: 2.15 (0.21), residues: 624 sheet: -0.29 (1.01), residues: 30 loop : -1.14 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.033 0.003 TYR D 80 PHE 0.021 0.002 PHE M 87 TRP 0.007 0.001 TRP L 25 HIS 0.007 0.002 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.23 (15219) covalent geometry : angle 0.68650 / 0.39 (21677) hydrogen bonds : bond 0.06782 / 4.65 ( 811) hydrogen bonds : angle 3.59741 / 2.59 ( 2062) metal coordination : bond 0.00931 / 0.63 ( 20) metal coordination : angle 3.56335 / 2.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.523 Fit side-chains REVERT: B 63 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7465 (mp0) REVERT: G 35 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7930 (mpp80) REVERT: M 79 VAL cc_start: 0.7757 (m) cc_final: 0.7388 (t) outliers start: 23 outliers final: 13 residues processed: 181 average time/residue: 0.1190 time to fit residues: 31.3392 Evaluate side-chains 167 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 122 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 95 optimal weight: 40.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.136468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110315 restraints weight = 32324.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109864 restraints weight = 49558.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110131 restraints weight = 44651.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110119 restraints weight = 37859.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110192 restraints weight = 35730.444| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15239 Z= 0.134 Angle : 0.565 11.108 21701 Z= 0.334 Chirality : 0.041 0.184 2490 Planarity : 0.004 0.042 1825 Dihedral : 28.694 172.117 4137 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.93 % Allowed : 13.34 % Favored : 84.73 % 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: 1.62 (0.26), residues: 1110 helix: 2.54 (0.21), residues: 628 sheet: -0.62 (0.94), residues: 35 loop : -1.01 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.014 0.001 TYR D 80 PHE 0.015 0.001 PHE O 45 TRP 0.005 0.001 TRP L 25 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (15219) covalent geometry : angle 0.55453 / 0.33 (21677) hydrogen bonds : bond 0.05217 / 3.57 ( 811) hydrogen bonds : angle 3.28464 / 2.37 ( 2062) metal coordination : bond 0.00591 / 0.42 ( 20) metal coordination : angle 3.25026 / 2.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9093 (m-10) cc_final: 0.8845 (m-80) REVERT: A 73 GLU cc_start: 0.7114 (tt0) cc_final: 0.6827 (tt0) REVERT: M 91 MET cc_start: 0.5193 (mmt) cc_final: 0.4895 (mmt) outliers start: 19 outliers final: 11 residues processed: 167 average time/residue: 0.1101 time to fit residues: 27.0692 Evaluate side-chains 157 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 43 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 115 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.131765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105406 restraints weight = 32089.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104681 restraints weight = 47745.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104816 restraints weight = 48300.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104732 restraints weight = 38703.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104803 restraints weight = 35643.014| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15239 Z= 0.227 Angle : 0.688 10.782 21701 Z= 0.382 Chirality : 0.045 0.192 2490 Planarity : 0.005 0.069 1825 Dihedral : 29.133 169.181 4137 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.95 % Allowed : 15.89 % Favored : 81.16 % 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: 0.99 (0.25), residues: 1110 helix: 2.04 (0.20), residues: 629 sheet: 0.03 (1.17), residues: 20 loop : -1.35 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 96 TYR 0.022 0.002 TYR D 80 PHE 0.034 0.002 PHE L 32 TRP 0.009 0.001 TRP L 25 HIS 0.005 0.002 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (15219) covalent geometry : angle 0.67808 / 0.38 (21677) hydrogen bonds : bond 0.07044 / 4.79 ( 811) hydrogen bonds : angle 3.56981 / 2.55 ( 2062) metal coordination : bond 0.01067 / 0.71 ( 20) metal coordination : angle 3.48686 / 2.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: G 35 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8030 (mpp80) REVERT: H 73 GLU cc_start: 0.8063 (tp30) cc_final: 0.7836 (tp30) outliers start: 29 outliers final: 22 residues processed: 177 average time/residue: 0.1128 time to fit residues: 28.9685 Evaluate side-chains 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain K residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN N 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.134148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.107672 restraints weight = 31939.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107059 restraints weight = 47971.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.107352 restraints weight = 44343.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107280 restraints weight = 37042.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107413 restraints weight = 33899.948| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15239 Z= 0.137 Angle : 0.585 10.161 21701 Z= 0.338 Chirality : 0.042 0.191 2490 Planarity : 0.004 0.049 1825 Dihedral : 29.026 171.040 4137 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.04 % Allowed : 18.53 % Favored : 79.43 % 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: 1.37 (0.26), residues: 1110 helix: 2.39 (0.21), residues: 628 sheet: -0.09 (1.18), residues: 20 loop : -1.25 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.015 0.001 TYR D 37 PHE 0.024 0.001 PHE M 87 TRP 0.006 0.001 TRP L 25 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (15219) covalent geometry : angle 0.57581 / 0.34 (21677) hydrogen bonds : bond 0.05334 / 3.65 ( 811) hydrogen bonds : angle 3.25334 / 2.34 ( 2062) metal coordination : bond 0.00527 / 0.38 ( 20) metal coordination : angle 3.21181 / 2.41 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7484 (tp30) cc_final: 0.7283 (tp30) REVERT: A 54 TYR cc_start: 0.9127 (m-10) cc_final: 0.8865 (m-80) REVERT: F 84 MET cc_start: 0.7823 (tpt) cc_final: 0.7582 (mmm) REVERT: N 81 ARG cc_start: 0.7363 (ttp-170) cc_final: 0.7131 (ttp-170) REVERT: O 13 ILE cc_start: 0.6454 (mm) cc_final: 0.6062 (mt) outliers start: 20 outliers final: 14 residues processed: 164 average time/residue: 0.1203 time to fit residues: 28.8065 Evaluate side-chains 161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain M residue 15 HIS Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 40 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 89 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN K 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.131244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.104612 restraints weight = 31867.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104032 restraints weight = 47685.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104092 restraints weight = 49711.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104049 restraints weight = 38977.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104118 restraints weight = 35523.336| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15239 Z= 0.230 Angle : 0.693 11.714 21701 Z= 0.383 Chirality : 0.046 0.195 2490 Planarity : 0.005 0.067 1825 Dihedral : 29.307 169.458 4137 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.85 % Allowed : 18.74 % Favored : 78.41 % 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: 0.88 (0.25), residues: 1110 helix: 1.98 (0.20), residues: 629 sheet: -0.56 (1.17), residues: 20 loop : -1.43 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 116 TYR 0.018 0.002 TYR D 80 PHE 0.018 0.002 PHE C 25 TRP 0.009 0.001 TRP L 25 HIS 0.012 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.23 (15219) covalent geometry : angle 0.68337 / 0.38 (21677) hydrogen bonds : bond 0.07009 / 4.76 ( 811) hydrogen bonds : angle 3.53628 / 2.54 ( 2062) metal coordination : bond 0.01037 / 0.69 ( 20) metal coordination : angle 3.49049 / 2.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: G 35 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8027 (mpp80) REVERT: H 73 GLU cc_start: 0.7982 (tp30) cc_final: 0.7745 (tp30) REVERT: N 81 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.7233 (ttp-170) REVERT: N 114 TYR cc_start: 0.7118 (t80) cc_final: 0.6755 (t80) outliers start: 28 outliers final: 18 residues processed: 178 average time/residue: 0.1340 time to fit residues: 34.0424 Evaluate side-chains 175 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 83 optimal weight: 50.0000 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 125 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.132704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106348 restraints weight = 31686.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.105640 restraints weight = 52001.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105947 restraints weight = 47261.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106026 restraints weight = 37064.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106059 restraints weight = 37506.624| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15239 Z= 0.144 Angle : 0.607 10.912 21701 Z= 0.346 Chirality : 0.043 0.195 2490 Planarity : 0.004 0.064 1825 Dihedral : 29.198 171.120 4137 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.44 % Allowed : 19.65 % Favored : 77.90 % 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: 1.21 (0.26), residues: 1110 helix: 2.30 (0.21), residues: 628 sheet: -0.58 (1.21), residues: 20 loop : -1.34 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.014 0.001 TYR D 37 PHE 0.010 0.001 PHE O 4 TRP 0.004 0.001 TRP L 25 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (15219) covalent geometry : angle 0.59717 / 0.35 (21677) hydrogen bonds : bond 0.05452 / 3.72 ( 811) hydrogen bonds : angle 3.22617 / 2.32 ( 2062) metal coordination : bond 0.00544 / 0.41 ( 20) metal coordination : angle 3.28226 / 2.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9128 (m-10) cc_final: 0.8693 (m-80) REVERT: F 77 LYS cc_start: 0.7383 (mmtt) cc_final: 0.7025 (mmtt) REVERT: H 90 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6317 (mt-10) REVERT: N 114 TYR cc_start: 0.7001 (t80) cc_final: 0.6523 (t80) REVERT: O 18 GLU cc_start: 0.4902 (tp30) cc_final: 0.4581 (tp30) outliers start: 24 outliers final: 20 residues processed: 170 average time/residue: 0.1261 time to fit residues: 31.0517 Evaluate side-chains 173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 15 HIS Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain K residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 112 optimal weight: 20.0000 chunk 73 optimal weight: 40.0000 chunk 28 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.133350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107044 restraints weight = 31957.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.106433 restraints weight = 49120.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106722 restraints weight = 48793.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106631 restraints weight = 39322.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106741 restraints weight = 36029.450| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15239 Z= 0.135 Angle : 0.592 11.689 21701 Z= 0.340 Chirality : 0.041 0.201 2490 Planarity : 0.004 0.059 1825 Dihedral : 29.148 172.221 4137 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.34 % Allowed : 20.16 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.26), residues: 1110 helix: 2.49 (0.21), residues: 626 sheet: -0.42 (1.01), residues: 30 loop : -1.34 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.012 0.001 TYR D 37 PHE 0.023 0.001 PHE M 87 TRP 0.004 0.001 TRP L 25 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (15219) covalent geometry : angle 0.58507 / 0.34 (21677) hydrogen bonds : bond 0.05136 / 3.50 ( 811) hydrogen bonds : angle 3.16760 / 2.29 ( 2062) metal coordination : bond 0.00554 / 0.40 ( 20) metal coordination : angle 2.68149 / 1.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9111 (m-10) cc_final: 0.8688 (m-80) REVERT: H 90 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6283 (mt-10) REVERT: N 114 TYR cc_start: 0.6841 (t80) cc_final: 0.6310 (t80) REVERT: O 18 GLU cc_start: 0.4585 (tp30) cc_final: 0.4343 (tp30) REVERT: L 32 PHE cc_start: 0.5534 (t80) cc_final: 0.5229 (t80) outliers start: 23 outliers final: 17 residues processed: 167 average time/residue: 0.1231 time to fit residues: 30.0122 Evaluate side-chains 162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 15 HIS Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 89 optimal weight: 30.0000 chunk 109 optimal weight: 0.0770 chunk 77 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 overall best weight: 2.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 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 = 0.3900 r_free = 0.3900 target = 0.132969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106346 restraints weight = 32029.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105862 restraints weight = 48406.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106152 restraints weight = 44320.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106070 restraints weight = 37631.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106188 restraints weight = 35182.796| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15239 Z= 0.149 Angle : 0.610 11.973 21701 Z= 0.346 Chirality : 0.042 0.202 2490 Planarity : 0.004 0.058 1825 Dihedral : 29.180 172.086 4137 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.04 % Allowed : 20.16 % Favored : 77.80 % 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: 1.33 (0.26), residues: 1110 helix: 2.43 (0.21), residues: 627 sheet: -0.62 (1.00), residues: 30 loop : -1.34 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 74 TYR 0.012 0.001 TYR H 80 PHE 0.022 0.001 PHE M 87 TRP 0.004 0.001 TRP L 25 HIS 0.005 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (15219) covalent geometry : angle 0.60226 / 0.35 (21677) hydrogen bonds : bond 0.05272 / 3.59 ( 811) hydrogen bonds : angle 3.18893 / 2.30 ( 2062) metal coordination : bond 0.00537 / 0.40 ( 20) metal coordination : angle 2.96409 / 2.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9146 (m-10) cc_final: 0.8862 (m-80) REVERT: H 90 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6372 (mt-10) REVERT: N 77 ILE cc_start: 0.6926 (tp) cc_final: 0.6693 (tt) outliers start: 20 outliers final: 17 residues processed: 162 average time/residue: 0.1253 time to fit residues: 29.7421 Evaluate side-chains 163 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 15 HIS Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 85 optimal weight: 50.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.132818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106279 restraints weight = 31820.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105672 restraints weight = 48890.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.105962 restraints weight = 45923.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105903 restraints weight = 38600.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106061 restraints weight = 35757.252| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15239 Z= 0.149 Angle : 0.610 12.310 21701 Z= 0.346 Chirality : 0.042 0.204 2490 Planarity : 0.004 0.057 1825 Dihedral : 29.203 171.856 4137 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.93 % Allowed : 20.47 % Favored : 77.60 % 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: 1.33 (0.26), residues: 1110 helix: 2.43 (0.21), residues: 626 sheet: -0.63 (1.00), residues: 30 loop : -1.35 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 74 TYR 0.014 0.001 TYR H 80 PHE 0.023 0.001 PHE M 87 TRP 0.004 0.001 TRP L 25 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (15219) covalent geometry : angle 0.60261 / 0.35 (21677) hydrogen bonds : bond 0.05297 / 3.61 ( 811) hydrogen bonds : angle 3.18424 / 2.30 ( 2062) metal coordination : bond 0.00509 / 0.38 ( 20) metal coordination : angle 2.92247 / 2.24 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7444 (tp30) cc_final: 0.7226 (tp30) REVERT: A 54 TYR cc_start: 0.9173 (m-10) cc_final: 0.8884 (m-80) REVERT: H 90 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6319 (mt-10) REVERT: N 77 ILE cc_start: 0.6966 (tp) cc_final: 0.6718 (tt) REVERT: O 74 ARG cc_start: 0.5639 (mpt180) cc_final: 0.5230 (mmt90) REVERT: L 32 PHE cc_start: 0.5434 (t80) cc_final: 0.5125 (t80) outliers start: 19 outliers final: 18 residues processed: 163 average time/residue: 0.1276 time to fit residues: 30.3561 Evaluate side-chains 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 15 HIS Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 76 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 = 0.3912 r_free = 0.3912 target = 0.133825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107442 restraints weight = 32000.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106882 restraints weight = 50670.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107074 restraints weight = 46975.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107108 restraints weight = 37713.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107154 restraints weight = 35554.313| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15239 Z= 0.130 Angle : 0.592 11.945 21701 Z= 0.339 Chirality : 0.041 0.205 2490 Planarity : 0.004 0.059 1825 Dihedral : 29.142 172.490 4137 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.14 % Allowed : 20.77 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1110 helix: 2.59 (0.21), residues: 624 sheet: -0.50 (1.01), residues: 30 loop : -1.26 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 42 TYR 0.012 0.001 TYR N 22 PHE 0.024 0.001 PHE M 87 TRP 0.003 0.000 TRP L 25 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (15219) covalent geometry : angle 0.58471 / 0.34 (21677) hydrogen bonds : bond 0.04833 / 3.30 ( 811) hydrogen bonds : angle 3.08723 / 2.23 ( 2062) metal coordination : bond 0.00544 / 0.37 ( 20) metal coordination : angle 2.82729 / 2.16 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.19 seconds wall clock time: 33 minutes 43.34 seconds (2023.34 seconds total)