Starting phenix.real_space_refine on Sat Aug 8 11:08:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9q_64884/08_2026/9v9q_64884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9q_64884/08_2026/9v9q_64884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9q_64884/08_2026/9v9q_64884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9q_64884/08_2026/9v9q_64884.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9q_64884/08_2026/9v9q_64884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9q_64884/08_2026/9v9q_64884.cif" } resolution = 2.8 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= 0.006 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 14808 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 4 6.06 5 P 289 5.49 5 S 42 5.16 5 C 9162 2.51 5 N 2944 2.21 5 O 3555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15996 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} 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: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} 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: "P" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1171 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 130} 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: "R" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11978 SG CYS M 18 62.988 89.242 66.810 1.00 28.92 S ATOM 11999 SG CYS M 21 64.245 92.638 65.921 1.00 31.82 S ATOM 12137 SG CYS M 39 63.044 90.230 63.205 1.00 21.49 S ATOM 12159 SG CYS M 42 66.429 89.808 64.982 1.00 21.90 S ATOM 12096 SG CYS M 34 58.398 77.243 69.847 1.00 20.12 S ATOM 12254 SG CYS M 53 61.154 79.415 71.501 1.00 20.12 S ATOM 12275 SG CYS M 56 58.728 77.258 73.618 1.00 20.12 S ATOM 13113 SG CYS N 51 41.218 74.079 55.182 1.00 21.92 S ATOM 13134 SG CYS N 54 37.573 74.982 55.415 1.00 22.58 S ATOM 13282 SG CYS N 72 39.861 75.180 58.477 1.00 20.12 S ATOM 13301 SG CYS N 75 38.749 71.790 57.140 1.00 20.12 S ATOM 13236 SG CYS N 67 53.999 71.593 54.262 1.00 20.12 S ATOM 13390 SG CYS N 87 50.950 69.853 52.695 1.00 20.12 S ATOM 13410 SG CYS N 90 54.387 69.772 50.955 1.00 20.12 S Time building chain proxies: 2.27, per 1000 atoms: 0.14 Number of scatterers: 15996 At special positions: 0 Unit cell: (124.3, 116.6, 126.5, 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 4 29.99 S 42 16.00 P 289 15.00 O 3555 8.00 N 2944 7.00 C 9162 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: 0.96 Conformation dependent library (CDL) restraints added in 421.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 401 " 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 ZN M 401 " - pdb=" SG CYS M 42 " 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 72 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " Number of angles added : 18 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 15 sheets defined 56.6% alpha, 5.6% beta 139 base pairs and 232 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 45 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 24 through 29 removed outlier: 3.887A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.027A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.521A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.522A 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: 4.014A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.615A 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 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.047A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.616A 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 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.492A 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 'G' and resid 112 through 116 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: 3.868A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 16 Processing helix chain 'M' and resid 40 through 48 removed outlier: 3.651A pdb=" N GLU M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 72 through 83 Processing helix chain 'M' and resid 85 through 101 removed outlier: 3.629A pdb=" N ALA M 99 " --> pdb=" O ARG M 95 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA M 100 " --> pdb=" O ASP M 96 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS M 101 " --> pdb=" O PHE M 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 25 removed outlier: 3.936A 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 removed outlier: 3.501A pdb=" N ASP N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 16 Processing helix chain 'P' and resid 98 through 111 removed outlier: 3.662A pdb=" N CYS P 111 " --> pdb=" O CYS P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 130 removed outlier: 3.593A pdb=" N ALA P 124 " --> pdb=" O VAL P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 146 Processing helix chain 'O' and resid 22 through 34 Processing helix chain 'O' and resid 55 through 59 Processing helix chain 'R' and resid 22 through 34 removed outlier: 4.071A pdb=" N VAL R 26 " --> pdb=" O THR R 22 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP R 32 " --> pdb=" O ALA R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.842A 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 'B' and resid 96 through 98 removed outlier: 6.770A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.104A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.267A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.659A pdb=" N THR M 5 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL N 40 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE M 7 " --> pdb=" O ILE N 38 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE N 38 " --> pdb=" O ILE M 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AB3, first strand: chain 'N' and resid 70 through 72 Processing sheet with id=AB4, first strand: chain 'P' and resid 22 through 25 removed outlier: 3.640A pdb=" N ARG P 22 " --> pdb=" O THR P 36 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR P 53 " --> pdb=" O ALA P 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 12 through 14 removed outlier: 3.687A pdb=" N HIS O 68 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE O 44 " --> pdb=" O HIS O 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 3 through 5 529 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 710 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 232 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.39 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: 3861 1.34 - 1.46: 4460 1.46 - 1.57: 7912 1.57 - 1.69: 576 1.69 - 1.81: 62 Bond restraints: 16871 Sorted by residual: bond pdb=" C3' DG I 44 " pdb=" C2' DG I 44 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC J 77 " pdb=" C2' DC J 77 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DG J 97 " pdb=" C2' DG J 97 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG J 137 " pdb=" C2' DG J 137 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 16866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 23198 1.79 - 3.59: 810 3.59 - 5.38: 25 5.38 - 7.18: 6 7.18 - 8.97: 1 Bond angle restraints: 24040 Sorted by residual: angle pdb=" C ASP F 24 " pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 117.23 110.64 6.59 1.36e+00 5.41e-01 2.35e+01 angle pdb=" N3 DT J 143 " pdb=" C4 DT J 143 " pdb=" O4 DT J 143 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I 138 " pdb=" C4 DT I 138 " pdb=" O4 DT I 138 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 24035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.30: 8081 33.30 - 66.60: 1377 66.60 - 99.89: 25 99.89 - 133.19: 0 133.19 - 166.49: 3 Dihedral angle restraints: 9486 sinusoidal: 5796 harmonic: 3690 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 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA THR N 33 " pdb=" C THR N 33 " pdb=" N ASP N 34 " pdb=" CA ASP N 34 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+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 220.00 53.51 166.49 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 9483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1537 0.030 - 0.059: 788 0.059 - 0.089: 264 0.089 - 0.119: 144 0.119 - 0.149: 13 Chirality restraints: 2746 Sorted by residual: chirality pdb=" CA GLU D 68 " pdb=" N GLU D 68 " pdb=" C GLU D 68 " pdb=" CB GLU D 68 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE M 31 " pdb=" N ILE M 31 " pdb=" C ILE M 31 " pdb=" CB ILE M 31 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 2743 not shown) Planarity restraints: 2050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP P 16 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO P 17 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO P 17 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO P 17 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 64 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C ASN D 64 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN D 64 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP D 65 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP P 112 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO P 113 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO P 113 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO P 113 " -0.023 5.00e-02 4.00e+02 ... (remaining 2047 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 385 2.67 - 3.23: 13516 3.23 - 3.79: 27630 3.79 - 4.34: 36201 4.34 - 4.90: 53120 Nonbonded interactions: 130852 Sorted by model distance: nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.116 2.496 nonbonded pdb=" OD2 ASP G 72 " pdb=" NE ARG N 81 " model vdw 2.230 3.120 nonbonded pdb=" OE1 GLU G 64 " pdb=" NZ LYS N 97 " model vdw 2.231 3.120 nonbonded pdb=" NE2 GLN R 62 " pdb=" O GLU R 64 " model vdw 2.268 3.120 nonbonded pdb=" OG SER M 110 " pdb=" OD1 ASP M 113 " model vdw 2.274 3.040 ... (remaining 130847 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 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 100) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 120) } ncs_group { reference = (chain 'O' and resid 1 through 75) selection = (chain 'R' and resid 1 through 75) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.140 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 0.038 16887 Z= 0.443 Angle : 0.665 8.972 24058 Z= 0.571 Chirality : 0.042 0.149 2746 Planarity : 0.004 0.079 2050 Dihedral : 24.385 166.490 7094 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.25), residues: 1240 helix: 2.80 (0.20), residues: 673 sheet: -0.43 (0.84), residues: 45 loop : -0.99 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 89 TYR 0.015 0.001 TYR H 80 PHE 0.012 0.001 PHE P 31 TRP 0.002 0.001 TRP P 141 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.44 (16871) covalent geometry : angle 0.66145 / 0.57 (24040) hydrogen bonds : bond 0.11676 / 7.11 ( 886) hydrogen bonds : angle 4.08804 / 2.92 ( 2246) metal coordination : bond 0.00417 / 0.25 ( 16) metal coordination : angle 2.52422 / 1.42 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.317 Fit side-chains REVERT: F 93 GLN cc_start: 0.8225 (mt0) cc_final: 0.7959 (mt0) REVERT: P 73 ILE cc_start: 0.3519 (mm) cc_final: 0.2988 (tp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.6545 time to fit residues: 155.7883 Evaluate side-chains 172 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN F 27 GLN G 24 GLN H 60 ASN N 25 GLN N 84 ASN P 114 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.182697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.140323 restraints weight = 17890.659| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 0.97 r_work: 0.3319 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16887 Z= 0.148 Angle : 0.600 7.238 24058 Z= 0.350 Chirality : 0.043 0.282 2746 Planarity : 0.004 0.053 2050 Dihedral : 28.063 166.919 4551 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.55 % Allowed : 10.57 % Favored : 86.87 % 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: 1.68 (0.25), residues: 1240 helix: 2.72 (0.20), residues: 685 sheet: -0.31 (0.78), residues: 54 loop : -1.09 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 101 TYR 0.012 0.001 TYR G 50 PHE 0.019 0.002 PHE M 97 TRP 0.004 0.001 TRP N 17 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (16871) covalent geometry : angle 0.59680 / 0.35 (24040) hydrogen bonds : bond 0.05632 / 3.78 ( 886) hydrogen bonds : angle 3.11512 / 2.23 ( 2246) metal coordination : bond 0.00485 / 0.33 ( 16) metal coordination : angle 2.33602 / 1.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.366 Fit side-chains REVERT: C 92 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: C 104 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: E 123 ASP cc_start: 0.8893 (m-30) cc_final: 0.8582 (m-30) REVERT: G 74 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7361 (mppt) REVERT: H 109 SER cc_start: 0.8876 (t) cc_final: 0.8441 (m) REVERT: P 30 MET cc_start: 0.5814 (tpp) cc_final: 0.5535 (tpt) REVERT: P 34 GLN cc_start: 0.6473 (OUTLIER) cc_final: 0.6187 (tt0) REVERT: P 73 ILE cc_start: 0.3765 (mm) cc_final: 0.3316 (tp) outliers start: 28 outliers final: 6 residues processed: 204 average time/residue: 0.6662 time to fit residues: 147.3826 Evaluate side-chains 183 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain P residue 34 GLN Chi-restraints excluded: chain P residue 54 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 116 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN E 113 HIS H 81 ASN N 84 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131451 restraints weight = 17567.606| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 0.88 r_work: 0.3181 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16887 Z= 0.206 Angle : 0.719 7.807 24058 Z= 0.400 Chirality : 0.050 0.318 2746 Planarity : 0.006 0.048 2050 Dihedral : 28.656 163.449 4551 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.01 % Allowed : 13.31 % Favored : 83.68 % 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: 0.94 (0.24), residues: 1240 helix: 2.12 (0.19), residues: 681 sheet: -0.58 (0.78), residues: 54 loop : -1.42 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 101 TYR 0.015 0.003 TYR N 22 PHE 0.026 0.003 PHE M 38 TRP 0.007 0.002 TRP P 33 HIS 0.008 0.002 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (16871) covalent geometry : angle 0.71532 / 0.40 (24040) hydrogen bonds : bond 0.07960 / 5.21 ( 886) hydrogen bonds : angle 3.35675 / 2.40 ( 2246) metal coordination : bond 0.01153 / 0.86 ( 16) metal coordination : angle 2.86894 / 1.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: D 90 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: E 56 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8044 (ttpp) REVERT: E 123 ASP cc_start: 0.9027 (m-30) cc_final: 0.8744 (m-30) REVERT: H 73 GLU cc_start: 0.8266 (tp30) cc_final: 0.8002 (tp30) REVERT: H 109 SER cc_start: 0.8828 (t) cc_final: 0.8416 (m) REVERT: M 9 ILE cc_start: 0.7016 (pp) cc_final: 0.6766 (mm) REVERT: N 66 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: P 55 HIS cc_start: 0.5970 (OUTLIER) cc_final: 0.5426 (m-70) REVERT: P 110 LEU cc_start: 0.4162 (mt) cc_final: 0.3960 (mt) outliers start: 33 outliers final: 16 residues processed: 199 average time/residue: 0.6787 time to fit residues: 146.0330 Evaluate side-chains 204 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 55 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN N 84 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.176815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133507 restraints weight = 17627.051| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 0.89 r_work: 0.3223 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16887 Z= 0.152 Angle : 0.629 7.368 24058 Z= 0.356 Chirality : 0.045 0.267 2746 Planarity : 0.005 0.042 2050 Dihedral : 28.644 165.079 4551 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.92 % Allowed : 15.04 % Favored : 82.04 % 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: 1.17 (0.24), residues: 1240 helix: 2.36 (0.20), residues: 681 sheet: -0.56 (0.78), residues: 54 loop : -1.39 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 101 TYR 0.011 0.002 TYR F 51 PHE 0.015 0.002 PHE N 106 TRP 0.004 0.001 TRP N 17 HIS 0.005 0.001 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (16871) covalent geometry : angle 0.62595 / 0.36 (24040) hydrogen bonds : bond 0.06313 / 4.19 ( 886) hydrogen bonds : angle 3.18005 / 2.27 ( 2246) metal coordination : bond 0.00833 / 0.60 ( 16) metal coordination : angle 2.48501 / 1.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.312 Fit side-chains REVERT: C 92 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: D 113 LYS cc_start: 0.8652 (tttm) cc_final: 0.8426 (ttmt) REVERT: E 123 ASP cc_start: 0.8970 (m-30) cc_final: 0.8608 (m-30) REVERT: G 35 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7988 (mtp85) REVERT: G 74 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7528 (mppt) REVERT: H 73 GLU cc_start: 0.8269 (tp30) cc_final: 0.8049 (tp30) REVERT: H 109 SER cc_start: 0.8811 (t) cc_final: 0.8423 (m) REVERT: N 66 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: P 55 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.5539 (m-70) REVERT: P 110 LEU cc_start: 0.4135 (mt) cc_final: 0.3928 (mt) outliers start: 32 outliers final: 13 residues processed: 196 average time/residue: 0.6552 time to fit residues: 138.9512 Evaluate side-chains 196 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 55 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 36 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 0.0980 chunk 132 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN N 84 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.176403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133650 restraints weight = 17619.820| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 0.87 r_work: 0.3217 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16887 Z= 0.156 Angle : 0.635 7.559 24058 Z= 0.358 Chirality : 0.046 0.273 2746 Planarity : 0.005 0.042 2050 Dihedral : 28.711 163.852 4551 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.28 % Allowed : 15.86 % Favored : 80.86 % 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: 1.17 (0.24), residues: 1240 helix: 2.37 (0.20), residues: 680 sheet: -0.63 (0.79), residues: 54 loop : -1.40 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 131 TYR 0.012 0.002 TYR F 88 PHE 0.018 0.002 PHE N 106 TRP 0.005 0.001 TRP P 141 HIS 0.005 0.001 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (16871) covalent geometry : angle 0.63105 / 0.36 (24040) hydrogen bonds : bond 0.06374 / 4.22 ( 886) hydrogen bonds : angle 3.13316 / 2.24 ( 2246) metal coordination : bond 0.00808 / 0.59 ( 16) metal coordination : angle 2.55180 / 1.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6497 (m-40) REVERT: C 92 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: D 68 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: D 90 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: E 56 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7962 (ttpp) REVERT: E 123 ASP cc_start: 0.8962 (m-30) cc_final: 0.8684 (m-30) REVERT: G 35 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7956 (mtp85) REVERT: G 74 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7521 (mppt) REVERT: H 73 GLU cc_start: 0.8181 (tp30) cc_final: 0.7875 (tp30) REVERT: H 109 SER cc_start: 0.8818 (t) cc_final: 0.8423 (m) REVERT: M 81 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7579 (mptm) REVERT: N 66 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: P 30 MET cc_start: 0.5914 (tpt) cc_final: 0.5522 (tpt) outliers start: 36 outliers final: 15 residues processed: 197 average time/residue: 0.6855 time to fit residues: 145.9844 Evaluate side-chains 204 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 93 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 84 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.177164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134795 restraints weight = 17566.788| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.11 r_work: 0.3185 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16887 Z= 0.137 Angle : 0.613 9.291 24058 Z= 0.347 Chirality : 0.045 0.381 2746 Planarity : 0.004 0.040 2050 Dihedral : 28.695 163.962 4551 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.83 % Allowed : 17.14 % Favored : 80.04 % 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: 1.29 (0.24), residues: 1240 helix: 2.50 (0.20), residues: 680 sheet: -0.58 (0.79), residues: 54 loop : -1.39 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 101 TYR 0.013 0.001 TYR H 80 PHE 0.013 0.002 PHE O 45 TRP 0.004 0.001 TRP N 17 HIS 0.004 0.001 HIS P 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (16871) covalent geometry : angle 0.60929 / 0.35 (24040) hydrogen bonds : bond 0.05874 / 3.91 ( 886) hydrogen bonds : angle 3.13162 / 2.24 ( 2246) metal coordination : bond 0.00819 / 0.60 ( 16) metal coordination : angle 2.57321 / 1.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.383 Fit side-chains REVERT: C 73 ASN cc_start: 0.6841 (OUTLIER) cc_final: 0.6481 (m-40) REVERT: C 92 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: D 68 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: D 90 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: E 56 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8034 (ttpp) REVERT: E 123 ASP cc_start: 0.8962 (m-30) cc_final: 0.8679 (m-30) REVERT: G 35 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7996 (mtp85) REVERT: G 74 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7539 (mppt) REVERT: H 73 GLU cc_start: 0.8224 (tp30) cc_final: 0.7998 (tp30) REVERT: H 109 SER cc_start: 0.8823 (t) cc_final: 0.8441 (m) REVERT: M 81 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7595 (mptm) REVERT: N 66 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: P 30 MET cc_start: 0.5998 (tpt) cc_final: 0.5639 (tpt) REVERT: O 48 LYS cc_start: 0.5602 (pmtt) cc_final: 0.5001 (pttp) outliers start: 31 outliers final: 19 residues processed: 191 average time/residue: 0.6995 time to fit residues: 144.2417 Evaluate side-chains 206 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain O residue 56 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 72 optimal weight: 50.0000 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 74 optimal weight: 40.0000 chunk 126 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 84 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.177248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136061 restraints weight = 17133.786| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 0.84 r_work: 0.3207 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16887 Z= 0.158 Angle : 0.640 8.175 24058 Z= 0.360 Chirality : 0.046 0.272 2746 Planarity : 0.005 0.042 2050 Dihedral : 28.762 163.543 4551 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.28 % Allowed : 17.41 % Favored : 79.31 % 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: 1.09 (0.24), residues: 1240 helix: 2.31 (0.20), residues: 687 sheet: -0.65 (0.78), residues: 54 loop : -1.50 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 81 TYR 0.012 0.002 TYR F 88 PHE 0.021 0.002 PHE N 106 TRP 0.004 0.001 TRP P 141 HIS 0.005 0.001 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (16871) covalent geometry : angle 0.63586 / 0.36 (24040) hydrogen bonds : bond 0.06482 / 4.29 ( 886) hydrogen bonds : angle 3.17074 / 2.27 ( 2246) metal coordination : bond 0.00738 / 0.53 ( 16) metal coordination : angle 2.61941 / 1.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.392 Fit side-chains REVERT: C 73 ASN cc_start: 0.6925 (OUTLIER) cc_final: 0.6509 (m-40) REVERT: C 92 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: D 32 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6742 (mt-10) REVERT: D 90 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: D 113 LYS cc_start: 0.8682 (tttm) cc_final: 0.8463 (ttmt) REVERT: E 56 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7940 (ttpp) REVERT: E 123 ASP cc_start: 0.8974 (m-30) cc_final: 0.8706 (m-30) REVERT: G 35 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7956 (mtp85) REVERT: G 74 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7594 (mppt) REVERT: H 73 GLU cc_start: 0.8198 (tp30) cc_final: 0.7887 (tp30) REVERT: H 109 SER cc_start: 0.8808 (t) cc_final: 0.8424 (m) REVERT: M 81 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7607 (mptm) REVERT: N 66 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: O 1 MET cc_start: 0.3210 (pmm) cc_final: 0.1026 (tpt) outliers start: 36 outliers final: 19 residues processed: 197 average time/residue: 0.7156 time to fit residues: 152.1932 Evaluate side-chains 205 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 56 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 139 optimal weight: 0.0060 chunk 105 optimal weight: 0.8980 chunk 84 optimal weight: 50.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 overall best weight: 3.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 84 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.176023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134366 restraints weight = 17201.451| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 0.87 r_work: 0.3202 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16887 Z= 0.180 Angle : 0.682 9.909 24058 Z= 0.379 Chirality : 0.048 0.270 2746 Planarity : 0.005 0.044 2050 Dihedral : 28.850 162.995 4551 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.19 % Allowed : 18.23 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.24), residues: 1240 helix: 2.16 (0.19), residues: 687 sheet: -0.78 (0.78), residues: 55 loop : -1.61 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 45 TYR 0.016 0.002 TYR D 80 PHE 0.027 0.002 PHE N 106 TRP 0.005 0.002 TRP N 17 HIS 0.005 0.001 HIS P 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (16871) covalent geometry : angle 0.67808 / 0.38 (24040) hydrogen bonds : bond 0.07046 / 4.65 ( 886) hydrogen bonds : angle 3.24381 / 2.31 ( 2246) metal coordination : bond 0.00941 / 0.70 ( 16) metal coordination : angle 2.78700 / 1.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.493 Fit side-chains REVERT: C 91 GLU cc_start: 0.7320 (tt0) cc_final: 0.7047 (mp0) REVERT: C 92 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: D 90 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: E 56 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7941 (ttpp) REVERT: E 59 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7258 (pp20) REVERT: E 123 ASP cc_start: 0.8963 (m-30) cc_final: 0.8701 (m-30) REVERT: G 35 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7910 (mtp85) REVERT: G 74 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7706 (mppt) REVERT: H 73 GLU cc_start: 0.8171 (tp30) cc_final: 0.7949 (tp30) REVERT: H 109 SER cc_start: 0.8815 (t) cc_final: 0.8423 (m) REVERT: M 81 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7640 (mptm) REVERT: M 89 ASN cc_start: 0.7448 (t0) cc_final: 0.7028 (m110) REVERT: O 1 MET cc_start: 0.3405 (pmm) cc_final: 0.1164 (tpt) REVERT: O 45 PHE cc_start: 0.4853 (t80) cc_final: 0.4549 (t80) REVERT: O 48 LYS cc_start: 0.5555 (pmtt) cc_final: 0.5049 (pttp) outliers start: 35 outliers final: 18 residues processed: 196 average time/residue: 0.7514 time to fit residues: 159.1603 Evaluate side-chains 202 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 56 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 124 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 30.0000 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 84 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.177299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135634 restraints weight = 17221.582| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 0.85 r_work: 0.3226 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16887 Z= 0.141 Angle : 0.635 12.462 24058 Z= 0.356 Chirality : 0.046 0.261 2746 Planarity : 0.004 0.044 2050 Dihedral : 28.808 163.236 4551 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.55 % Allowed : 19.23 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.24), residues: 1240 helix: 2.31 (0.20), residues: 690 sheet: -0.68 (0.79), residues: 55 loop : -1.54 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 99 TYR 0.018 0.002 TYR H 80 PHE 0.020 0.002 PHE N 106 TRP 0.004 0.001 TRP P 33 HIS 0.004 0.001 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (16871) covalent geometry : angle 0.63086 / 0.36 (24040) hydrogen bonds : bond 0.06185 / 4.11 ( 886) hydrogen bonds : angle 3.17291 / 2.26 ( 2246) metal coordination : bond 0.00812 / 0.59 ( 16) metal coordination : angle 2.58075 / 1.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.462 Fit side-chains REVERT: C 73 ASN cc_start: 0.6843 (OUTLIER) cc_final: 0.6392 (m-40) REVERT: C 91 GLU cc_start: 0.7246 (tt0) cc_final: 0.7001 (mp0) REVERT: C 92 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: D 90 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: D 113 LYS cc_start: 0.8635 (tttm) cc_final: 0.8433 (ttmt) REVERT: E 56 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7906 (ttpp) REVERT: E 123 ASP cc_start: 0.8946 (m-30) cc_final: 0.8683 (m-30) REVERT: G 35 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7871 (mtp85) REVERT: G 74 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7711 (mppt) REVERT: H 73 GLU cc_start: 0.8122 (tp30) cc_final: 0.7882 (tp30) REVERT: H 109 SER cc_start: 0.8780 (t) cc_final: 0.8404 (m) REVERT: M 81 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7574 (mptm) REVERT: O 1 MET cc_start: 0.3368 (pmm) cc_final: 0.1146 (tpt) REVERT: O 45 PHE cc_start: 0.4899 (t80) cc_final: 0.4611 (t80) REVERT: O 48 LYS cc_start: 0.5596 (pmtt) cc_final: 0.5091 (pttp) outliers start: 28 outliers final: 17 residues processed: 194 average time/residue: 0.6781 time to fit residues: 142.2544 Evaluate side-chains 202 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 75 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 84 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.178253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137005 restraints weight = 17182.561| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 0.92 r_work: 0.3252 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16887 Z= 0.138 Angle : 0.617 9.303 24058 Z= 0.348 Chirality : 0.044 0.256 2746 Planarity : 0.004 0.046 2050 Dihedral : 28.767 163.498 4551 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.55 % Allowed : 19.69 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.24), residues: 1240 helix: 2.40 (0.20), residues: 690 sheet: -0.65 (0.79), residues: 55 loop : -1.47 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 99 TYR 0.016 0.002 TYR H 80 PHE 0.019 0.002 PHE N 106 TRP 0.004 0.001 TRP P 141 HIS 0.004 0.001 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (16871) covalent geometry : angle 0.61333 / 0.35 (24040) hydrogen bonds : bond 0.05803 / 3.86 ( 886) hydrogen bonds : angle 3.09777 / 2.21 ( 2246) metal coordination : bond 0.00690 / 0.50 ( 16) metal coordination : angle 2.42880 / 1.55 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.458 Fit side-chains REVERT: C 73 ASN cc_start: 0.6790 (OUTLIER) cc_final: 0.6334 (m-40) REVERT: C 92 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: D 90 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: D 113 LYS cc_start: 0.8657 (tttm) cc_final: 0.8448 (ttmt) REVERT: E 56 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7915 (ttpp) REVERT: E 123 ASP cc_start: 0.8916 (m-30) cc_final: 0.8645 (m-30) REVERT: G 35 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7903 (mtp85) REVERT: G 74 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7690 (mppt) REVERT: H 73 GLU cc_start: 0.8124 (tp30) cc_final: 0.7897 (tp30) REVERT: H 109 SER cc_start: 0.8780 (t) cc_final: 0.8413 (m) REVERT: M 81 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7575 (mptm) REVERT: P 30 MET cc_start: 0.5407 (mmm) cc_final: 0.4991 (tpp) REVERT: O 1 MET cc_start: 0.3357 (pmm) cc_final: 0.1154 (tpt) REVERT: O 45 PHE cc_start: 0.4898 (t80) cc_final: 0.4616 (t80) REVERT: O 48 LYS cc_start: 0.5504 (pmtt) cc_final: 0.5027 (pttp) outliers start: 28 outliers final: 17 residues processed: 189 average time/residue: 0.6649 time to fit residues: 136.2614 Evaluate side-chains 197 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 3.9990 chunk 141 optimal weight: 0.0020 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 84 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.177929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138191 restraints weight = 17161.071| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 0.93 r_work: 0.3244 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16887 Z= 0.145 Angle : 0.623 10.765 24058 Z= 0.350 Chirality : 0.045 0.301 2746 Planarity : 0.005 0.046 2050 Dihedral : 28.772 163.130 4551 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.37 % Allowed : 20.05 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1240 helix: 2.36 (0.20), residues: 690 sheet: -0.62 (0.79), residues: 55 loop : -1.47 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 99 TYR 0.016 0.002 TYR F 88 PHE 0.020 0.002 PHE N 106 TRP 0.005 0.001 TRP P 33 HIS 0.004 0.001 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (16871) covalent geometry : angle 0.61932 / 0.35 (24040) hydrogen bonds : bond 0.05990 / 3.97 ( 886) hydrogen bonds : angle 3.10557 / 2.22 ( 2246) metal coordination : bond 0.00684 / 0.50 ( 16) metal coordination : angle 2.47646 / 1.58 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5185.65 seconds wall clock time: 88 minutes 31.46 seconds (5311.46 seconds total)