Starting phenix.real_space_refine on Thu Jul 2 23:43:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k7g_22698/07_2026/7k7g_22698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k7g_22698/07_2026/7k7g_22698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k7g_22698/07_2026/7k7g_22698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k7g_22698/07_2026/7k7g_22698.map" model { file = "/net/cci-nas-00/data/ceres_data/7k7g_22698/07_2026/7k7g_22698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k7g_22698/07_2026/7k7g_22698.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7k7g_22698/07_2026/7k7g_22698.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k7g_22698/07_2026/7k7g_22698.cif" } resolution = 4.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 246 5.49 5 S 10 5.16 5 C 6198 2.51 5 N 2071 2.21 5 O 2571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s 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: 11098 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 741 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 749 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 741 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 772 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2522 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2521 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "M" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 336 Classifications: {'peptide': 43} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 40} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10831 SG CYS M 14 63.870 26.104 96.501 1.00380.11 S ATOM 10850 SG CYS M 17 62.190 27.132 94.952 1.00375.25 S ATOM 10910 SG CYS M 24 63.976 25.849 92.055 1.00349.57 S ATOM 10958 SG CYS M 30 66.711 27.538 93.702 1.00397.98 S ATOM 10831 SG CYS M 14 63.870 26.104 96.501 1.00380.11 S ATOM 10976 SG CYS M 33 66.258 27.313 98.467 1.00424.58 S ATOM 11049 SG CYS M 42 67.639 24.000 98.551 1.00431.44 S Time building chain proxies: 2.23, per 1000 atoms: 0.20 Number of scatterers: 11098 At special positions: 0 Unit cell: (83.74, 126.14, 128.26, 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 2 29.99 S 10 16.00 P 246 15.00 O 2571 8.00 N 2071 7.00 C 6198 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: 0.72 Conformation dependent library (CDL) restraints added in 239.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 701 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 14 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 17 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 30 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 24 " pdb=" ZN M 702 " pdb="ZN ZN M 702 " - pdb=" SG CYS M 33 " pdb="ZN ZN M 702 " - pdb=" SG CYS M 14 " pdb="ZN ZN M 702 " - pdb=" SG CYS M 42 " Number of angles added : 6 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1436 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 67.6% alpha, 2.1% beta 109 base pairs and 208 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.643A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.818A pdb=" N ILE A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.569A pdb=" N ILE A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.561A pdb=" N GLN B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.651A pdb=" N GLU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.785A pdb=" N ARG B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 28 through 38 removed outlier: 3.905A pdb=" N ARG C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 75 removed outlier: 3.796A pdb=" N ALA C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.566A pdb=" N ALA C 88 " --> pdb=" O HIS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.699A pdb=" N LYS D 50 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 88 Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.572A pdb=" N ILE D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 127 removed outlier: 3.909A pdb=" N SER D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 122 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.642A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.818A pdb=" N ILE E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.569A pdb=" N ILE E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 removed outlier: 3.562A pdb=" N GLN F 28 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 30 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 43 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.652A pdb=" N GLU F 53 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.785A pdb=" N ARG F 93 " --> pdb=" O TYR F 89 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 28 through 38 removed outlier: 3.505A pdb=" N ARG G 37 " --> pdb=" O HIS G 33 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 74 removed outlier: 3.603A pdb=" N ALA G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 removed outlier: 3.664A pdb=" N LEU G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 53 removed outlier: 3.699A pdb=" N LYS H 50 " --> pdb=" O TYR H 46 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 88 Processing helix chain 'H' and resid 94 through 106 removed outlier: 3.572A pdb=" N ILE H 98 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 127 removed outlier: 3.908A pdb=" N SER H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU H 117 " --> pdb=" O HIS H 113 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL H 122 " --> pdb=" O GLY H 118 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 20 Processing helix chain 'M' and resid 38 through 43 removed outlier: 4.214A pdb=" N CYS M 42 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.182A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 removed outlier: 6.622A pdb=" N THR B 97 " --> pdb=" O THR G 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 44 through 45 removed outlier: 7.810A pdb=" N ARG C 44 " --> pdb=" O ILE D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA6, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.280A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA8, first strand: chain 'G' and resid 44 through 45 removed outlier: 7.616A pdb=" N ARG G 44 " --> pdb=" O ILE H 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 337 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 262 hydrogen bonds 502 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 208 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1658 1.33 - 1.45: 4068 1.45 - 1.57: 5550 1.57 - 1.69: 489 1.69 - 1.81: 14 Bond restraints: 11779 Sorted by residual: bond pdb=" C5' DT J 174 " pdb=" C4' DT J 174 " ideal model delta sigma weight residual 1.512 1.547 -0.035 7.00e-03 2.04e+04 2.52e+01 bond pdb=" C5' DA I 136 " pdb=" C4' DA I 136 " ideal model delta sigma weight residual 1.512 1.544 -0.032 7.00e-03 2.04e+04 2.14e+01 bond pdb=" C3' DT J 173 " pdb=" O3' DT J 173 " ideal model delta sigma weight residual 1.435 1.494 -0.059 1.30e-02 5.92e+03 2.05e+01 bond pdb=" C3' DG J 247 " pdb=" O3' DG J 247 " ideal model delta sigma weight residual 1.435 1.378 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" C3' DT J 157 " pdb=" C2' DT J 157 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.79e+01 ... (remaining 11774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 15740 2.14 - 4.28: 1094 4.28 - 6.42: 85 6.42 - 8.56: 14 8.56 - 10.70: 12 Bond angle restraints: 16945 Sorted by residual: angle pdb=" O4' DT J 173 " pdb=" C1' DT J 173 " pdb=" N1 DT J 173 " ideal model delta sigma weight residual 108.00 113.08 -5.08 7.00e-01 2.04e+00 5.27e+01 angle pdb=" O4' DC I 78 " pdb=" C4' DC I 78 " pdb=" C3' DC I 78 " ideal model delta sigma weight residual 106.00 101.79 4.21 6.00e-01 2.78e+00 4.93e+01 angle pdb=" O4' DC I 65 " pdb=" C4' DC I 65 " pdb=" C3' DC I 65 " ideal model delta sigma weight residual 106.00 102.37 3.63 6.00e-01 2.78e+00 3.66e+01 angle pdb=" O5' DT J 174 " pdb=" C5' DT J 174 " pdb=" C4' DT J 174 " ideal model delta sigma weight residual 109.40 114.13 -4.73 8.00e-01 1.56e+00 3.49e+01 angle pdb=" O4' DG I 62 " pdb=" C4' DG I 62 " pdb=" C3' DG I 62 " ideal model delta sigma weight residual 106.00 102.47 3.53 6.00e-01 2.78e+00 3.45e+01 ... (remaining 16940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.31: 4920 32.31 - 64.61: 1531 64.61 - 96.91: 79 96.91 - 129.22: 2 129.22 - 161.52: 2 Dihedral angle restraints: 6534 sinusoidal: 4315 harmonic: 2219 Sorted by residual: dihedral pdb=" CA ASP A 82 " pdb=" C ASP A 82 " pdb=" N LEU A 83 " pdb=" CA LEU A 83 " ideal model delta harmonic sigma weight residual 180.00 -155.29 -24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ASP E 82 " pdb=" C ASP E 82 " pdb=" N LEU E 83 " pdb=" CA LEU E 83 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ARG E 64 " pdb=" C ARG E 64 " pdb=" N LYS E 65 " pdb=" CA LYS E 65 " ideal model delta harmonic sigma weight residual -180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 6531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1421 0.061 - 0.121: 429 0.121 - 0.182: 71 0.182 - 0.242: 11 0.242 - 0.303: 6 Chirality restraints: 1938 Sorted by residual: chirality pdb=" C3' DA I 90 " pdb=" C4' DA I 90 " pdb=" O3' DA I 90 " pdb=" C2' DA I 90 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU E 127 " pdb=" CB LEU E 127 " pdb=" CD1 LEU E 127 " pdb=" CD2 LEU E 127 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU A 127 " pdb=" CB LEU A 127 " pdb=" CD1 LEU A 127 " pdb=" CD2 LEU A 127 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1935 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 38 " -0.048 2.00e-02 2.50e+03 2.06e-02 1.17e+01 pdb=" N9 DA I 38 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DA I 38 " 0.023 2.00e-02 2.50e+03 pdb=" N7 DA I 38 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DA I 38 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 38 " -0.007 2.00e-02 2.50e+03 pdb=" N6 DA I 38 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DA I 38 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 38 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 38 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DA I 38 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 67 " 0.043 2.00e-02 2.50e+03 1.96e-02 9.65e+00 pdb=" N1 DT I 67 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 67 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 67 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT I 67 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 67 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 67 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT I 67 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 67 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 67 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 227 " -0.040 2.00e-02 2.50e+03 2.05e-02 9.43e+00 pdb=" N1 DC J 227 " 0.033 2.00e-02 2.50e+03 pdb=" C2 DC J 227 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DC J 227 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DC J 227 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC J 227 " -0.025 2.00e-02 2.50e+03 pdb=" N4 DC J 227 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC J 227 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DC J 227 " 0.014 2.00e-02 2.50e+03 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2294 2.78 - 3.31: 9640 3.31 - 3.84: 22729 3.84 - 4.37: 24369 4.37 - 4.90: 34765 Nonbonded interactions: 93797 Sorted by model distance: nonbonded pdb=" O6 DG I 111 " pdb=" O4 DT J 181 " model vdw 2.251 2.432 nonbonded pdb=" OH TYR E 100 " pdb=" OE2 GLU E 134 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 100 " pdb=" OE2 GLU A 134 " model vdw 2.268 3.040 nonbonded pdb=" N2 DG I 98 " pdb=" O2 DC J 195 " model vdw 2.273 2.496 nonbonded pdb=" NH2 ARG E 70 " pdb=" OP1 DA I 90 " model vdw 2.283 3.120 ... (remaining 93792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 19 through 115) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 12.510 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.011 0.647 11786 Z= 0.769 Angle : 1.281 55.173 16951 Z= 0.906 Chirality : 0.059 0.303 1938 Planarity : 0.006 0.048 1293 Dihedral : 29.994 161.524 5098 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.83 (0.27), residues: 748 helix: -0.63 (0.21), residues: 499 sheet: None (None), residues: 0 loop : -2.27 (0.32), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 79 TYR 0.016 0.003 TYR B 52 PHE 0.027 0.004 PHE E 105 HIS 0.013 0.003 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.73 (11779) covalent geometry : angle 1.12934 / 0.90 (16945) hydrogen bonds : bond 0.15864 / 10.69 ( 599) hydrogen bonds : angle 5.58527 / 3.94 ( 1507) metal coordination : bond 0.29767 / 20.11 ( 7) metal coordination : angle 32.14460 / 17.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8375 (pm20) REVERT: A 53 ARG cc_start: 0.6995 (ttt180) cc_final: 0.6754 (mmm160) REVERT: A 103 SER cc_start: 0.9557 (t) cc_final: 0.9237 (p) REVERT: A 124 ASP cc_start: 0.8942 (m-30) cc_final: 0.8459 (m-30) REVERT: B 76 HIS cc_start: 0.8290 (t70) cc_final: 0.7844 (t70) REVERT: C 103 THR cc_start: 0.8727 (m) cc_final: 0.8235 (p) REVERT: E 74 GLU cc_start: 0.8302 (tp30) cc_final: 0.7957 (tt0) REVERT: F 52 TYR cc_start: 0.8710 (m-80) cc_final: 0.8504 (m-80) REVERT: G 40 ASN cc_start: 0.8805 (m-40) cc_final: 0.7725 (t0) REVERT: G 66 GLU cc_start: 0.8397 (tt0) cc_final: 0.8156 (tp30) REVERT: G 73 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7798 (tpt90) REVERT: G 90 ARG cc_start: 0.9243 (mmt-90) cc_final: 0.8898 (mmm-85) REVERT: G 94 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7763 (mm-30) REVERT: G 106 GLN cc_start: 0.8231 (mt0) cc_final: 0.7667 (mp10) REVERT: H 38 LYS cc_start: 0.6277 (mtpp) cc_final: 0.6031 (ttmm) REVERT: H 99 GLN cc_start: 0.8901 (tt0) cc_final: 0.8625 (tm-30) REVERT: H 103 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7831 (ptp90) REVERT: H 125 TYR cc_start: 0.8422 (t80) cc_final: 0.8220 (t80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1372 time to fit residues: 27.9169 Evaluate side-chains 73 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN E 109 ASN G 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.050211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.035673 restraints weight = 108795.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.036415 restraints weight = 63133.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.036910 restraints weight = 44170.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.037171 restraints weight = 34992.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.037337 restraints weight = 30646.911| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11786 Z= 0.180 Angle : 0.835 22.607 16951 Z= 0.456 Chirality : 0.051 0.282 1938 Planarity : 0.006 0.070 1293 Dihedral : 32.833 161.571 3592 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.46 % Allowed : 9.60 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.28), residues: 748 helix: 0.37 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -2.53 (0.32), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 34 TYR 0.022 0.002 TYR B 99 PHE 0.033 0.002 PHE E 105 HIS 0.006 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.18 (11779) covalent geometry : angle 0.77739 / 0.45 (16945) hydrogen bonds : bond 0.08910 / 6.20 ( 599) hydrogen bonds : angle 4.09315 / 2.90 ( 1507) metal coordination : bond 0.00944 / 0.64 ( 7) metal coordination : angle 16.16910 / 8.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8564 (pm20) REVERT: A 103 SER cc_start: 0.9628 (t) cc_final: 0.9335 (p) REVERT: A 124 ASP cc_start: 0.8895 (m-30) cc_final: 0.7643 (t0) REVERT: B 97 THR cc_start: 0.8513 (m) cc_final: 0.8286 (p) REVERT: C 40 ASN cc_start: 0.8451 (p0) cc_final: 0.7532 (p0) REVERT: D 63 MET cc_start: 0.9015 (mtp) cc_final: 0.8666 (mtm) REVERT: F 85 LEU cc_start: 0.9311 (tp) cc_final: 0.9105 (tp) REVERT: G 40 ASN cc_start: 0.8584 (m-40) cc_final: 0.7713 (t0) REVERT: G 66 GLU cc_start: 0.8552 (tt0) cc_final: 0.8316 (tp30) REVERT: G 73 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.7890 (tpt90) REVERT: G 90 ARG cc_start: 0.9314 (mmt-90) cc_final: 0.8906 (mmm-85) REVERT: G 94 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7235 (tp30) REVERT: G 106 GLN cc_start: 0.8180 (mt0) cc_final: 0.7656 (mp10) REVERT: H 99 GLN cc_start: 0.8828 (tt0) cc_final: 0.8459 (tm-30) REVERT: H 103 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7635 (ptt180) REVERT: H 110 LEU cc_start: 0.8739 (tp) cc_final: 0.8477 (tt) outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 0.1171 time to fit residues: 17.3140 Evaluate side-chains 68 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 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 = 0.3348 r_free = 0.3348 target = 0.048478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.034310 restraints weight = 113469.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.035052 restraints weight = 63782.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035562 restraints weight = 44538.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.035835 restraints weight = 35065.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.036102 restraints weight = 30461.051| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11786 Z= 0.249 Angle : 0.843 20.921 16951 Z= 0.466 Chirality : 0.051 0.317 1938 Planarity : 0.006 0.048 1293 Dihedral : 32.628 164.148 3592 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.15 % Allowed : 5.42 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.61 (0.29), residues: 748 helix: 0.47 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -2.26 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 117 TYR 0.033 0.002 TYR F 52 PHE 0.017 0.002 PHE E 105 HIS 0.014 0.003 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.25 (11779) covalent geometry : angle 0.80245 / 0.46 (16945) hydrogen bonds : bond 0.10518 / 7.07 ( 599) hydrogen bonds : angle 4.27464 / 3.05 ( 1507) metal coordination : bond 0.01121 / 0.82 ( 7) metal coordination : angle 13.78900 / 7.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8965 (m-30) cc_final: 0.8578 (m-30) REVERT: B 85 LEU cc_start: 0.9582 (mp) cc_final: 0.9306 (mp) REVERT: B 89 TYR cc_start: 0.9156 (m-80) cc_final: 0.8917 (m-80) REVERT: B 97 THR cc_start: 0.8689 (m) cc_final: 0.8348 (p) REVERT: D 63 MET cc_start: 0.9135 (mtp) cc_final: 0.8707 (mtt) REVERT: F 28 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8650 (mm-40) REVERT: G 66 GLU cc_start: 0.8632 (tt0) cc_final: 0.8372 (tp30) REVERT: G 73 ARG cc_start: 0.8271 (ttp-170) cc_final: 0.7870 (tpt90) REVERT: G 90 ARG cc_start: 0.9387 (mmt-90) cc_final: 0.9104 (mmm-85) REVERT: G 106 GLN cc_start: 0.8274 (mt0) cc_final: 0.7840 (mp10) REVERT: H 99 GLN cc_start: 0.8896 (tt0) cc_final: 0.8618 (tm-30) REVERT: H 103 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7856 (ttm170) REVERT: H 125 TYR cc_start: 0.8594 (t80) cc_final: 0.8373 (t80) outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.0864 time to fit residues: 11.0345 Evaluate side-chains 65 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 0.0070 chunk 85 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 40 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.048108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.033902 restraints weight = 114697.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.034574 restraints weight = 65119.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.035130 restraints weight = 46368.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035405 restraints weight = 36591.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035557 restraints weight = 31774.813| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11786 Z= 0.251 Angle : 0.822 20.891 16951 Z= 0.454 Chirality : 0.051 0.291 1938 Planarity : 0.006 0.065 1293 Dihedral : 32.694 166.010 3592 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.31 % Allowed : 6.35 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.56 (0.29), residues: 748 helix: 0.57 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -2.43 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 64 TYR 0.020 0.003 TYR F 52 PHE 0.013 0.002 PHE C 27 HIS 0.010 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.25 (11779) covalent geometry : angle 0.79184 / 0.45 (16945) hydrogen bonds : bond 0.09433 / 6.41 ( 599) hydrogen bonds : angle 4.34165 / 3.10 ( 1507) metal coordination : bond 0.01964 / 1.33 ( 7) metal coordination : angle 11.73794 / 6.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8992 (m-30) cc_final: 0.8614 (m-30) REVERT: B 97 THR cc_start: 0.8842 (m) cc_final: 0.8460 (p) REVERT: D 63 MET cc_start: 0.9133 (mtp) cc_final: 0.8750 (mtt) REVERT: D 72 ASP cc_start: 0.9218 (t0) cc_final: 0.8943 (t0) REVERT: E 126 LYS cc_start: 0.9636 (pttm) cc_final: 0.9400 (mtmm) REVERT: F 28 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8614 (mm-40) REVERT: G 38 ARG cc_start: 0.8756 (ptp-110) cc_final: 0.8389 (mtm110) REVERT: G 40 ASN cc_start: 0.9067 (m110) cc_final: 0.8216 (t0) REVERT: G 66 GLU cc_start: 0.8717 (tt0) cc_final: 0.8441 (tp30) REVERT: G 73 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.7936 (tpt90) REVERT: G 94 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7301 (tp30) REVERT: G 106 GLN cc_start: 0.8310 (mt0) cc_final: 0.7989 (mm-40) REVERT: H 125 TYR cc_start: 0.8596 (t80) cc_final: 0.8342 (t80) outliers start: 2 outliers final: 1 residues processed: 91 average time/residue: 0.1206 time to fit residues: 14.7956 Evaluate side-chains 63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 30.0000 chunk 96 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.047632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.033696 restraints weight = 113277.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.034436 restraints weight = 64432.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034874 restraints weight = 45028.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035122 restraints weight = 36022.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035326 restraints weight = 31576.661| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11786 Z= 0.270 Angle : 0.835 19.052 16951 Z= 0.463 Chirality : 0.051 0.275 1938 Planarity : 0.006 0.043 1293 Dihedral : 32.668 170.716 3592 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.54 (0.29), residues: 748 helix: 0.60 (0.22), residues: 509 sheet: None (None), residues: 0 loop : -2.48 (0.34), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 34 TYR 0.015 0.003 TYR F 99 PHE 0.031 0.002 PHE E 105 HIS 0.012 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.27 (11779) covalent geometry : angle 0.81025 / 0.46 (16945) hydrogen bonds : bond 0.10508 / 7.11 ( 599) hydrogen bonds : angle 4.43824 / 3.18 ( 1507) metal coordination : bond 0.00691 / 0.44 ( 7) metal coordination : angle 10.79843 / 6.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9040 (m-30) cc_final: 0.8644 (m-30) REVERT: B 89 TYR cc_start: 0.9245 (m-80) cc_final: 0.8878 (m-80) REVERT: B 97 THR cc_start: 0.8835 (m) cc_final: 0.8502 (p) REVERT: C 40 ASN cc_start: 0.8715 (p0) cc_final: 0.8015 (p0) REVERT: D 63 MET cc_start: 0.9161 (mtp) cc_final: 0.8730 (mtt) REVERT: G 38 ARG cc_start: 0.8878 (ptp-110) cc_final: 0.8493 (mtm110) REVERT: G 40 ASN cc_start: 0.9153 (m110) cc_final: 0.8256 (t0) REVERT: G 66 GLU cc_start: 0.8758 (tt0) cc_final: 0.8402 (tp30) REVERT: G 73 ARG cc_start: 0.8334 (ttp-170) cc_final: 0.7870 (tpt90) REVERT: G 90 ARG cc_start: 0.9406 (mmt90) cc_final: 0.9061 (mmm-85) REVERT: G 94 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7409 (tp30) REVERT: G 106 GLN cc_start: 0.8282 (mt0) cc_final: 0.7926 (mp10) REVERT: H 125 TYR cc_start: 0.8637 (t80) cc_final: 0.8346 (t80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1248 time to fit residues: 13.6923 Evaluate side-chains 58 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 42 optimal weight: 0.0030 chunk 74 optimal weight: 30.0000 chunk 82 optimal weight: 40.0000 chunk 90 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.047967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.034079 restraints weight = 116894.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.034624 restraints weight = 65792.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.035019 restraints weight = 45520.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.035386 restraints weight = 36450.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.035534 restraints weight = 31650.991| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11786 Z= 0.236 Angle : 0.793 15.307 16951 Z= 0.444 Chirality : 0.050 0.273 1938 Planarity : 0.006 0.064 1293 Dihedral : 32.679 174.167 3592 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.58 (0.30), residues: 748 helix: 0.52 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -2.48 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 96 TYR 0.018 0.002 TYR F 89 PHE 0.014 0.002 PHE E 105 HIS 0.011 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.24 (11779) covalent geometry : angle 0.77199 / 0.44 (16945) hydrogen bonds : bond 0.09240 / 6.30 ( 599) hydrogen bonds : angle 4.39221 / 3.15 ( 1507) metal coordination : bond 0.00498 / 0.31 ( 7) metal coordination : angle 9.70259 / 5.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9010 (m-30) cc_final: 0.8601 (m-30) REVERT: D 63 MET cc_start: 0.9072 (mtp) cc_final: 0.8659 (mtt) REVERT: D 72 ASP cc_start: 0.9059 (t0) cc_final: 0.8816 (t0) REVERT: F 89 TYR cc_start: 0.8573 (m-80) cc_final: 0.8200 (m-80) REVERT: G 66 GLU cc_start: 0.8761 (tt0) cc_final: 0.8414 (tp30) REVERT: G 73 ARG cc_start: 0.8362 (ttp-170) cc_final: 0.7955 (tpt90) REVERT: G 74 ASP cc_start: 0.8571 (p0) cc_final: 0.8293 (p0) REVERT: G 90 ARG cc_start: 0.9386 (mmt90) cc_final: 0.9068 (mmm-85) REVERT: G 106 GLN cc_start: 0.8272 (mt0) cc_final: 0.8004 (mp10) REVERT: H 125 TYR cc_start: 0.8661 (t80) cc_final: 0.8347 (t80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1132 time to fit residues: 12.8577 Evaluate side-chains 58 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 69 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 ASN H 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.048528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034727 restraints weight = 115271.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035271 restraints weight = 65421.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.035697 restraints weight = 44847.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.036080 restraints weight = 36268.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.036231 restraints weight = 31473.672| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11786 Z= 0.175 Angle : 0.735 14.600 16951 Z= 0.415 Chirality : 0.047 0.280 1938 Planarity : 0.005 0.086 1293 Dihedral : 32.538 173.633 3592 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.30), residues: 748 helix: 0.81 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -2.54 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 38 TYR 0.012 0.002 TYR F 52 PHE 0.015 0.001 PHE E 105 HIS 0.009 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (11779) covalent geometry : angle 0.71643 / 0.41 (16945) hydrogen bonds : bond 0.07963 / 5.48 ( 599) hydrogen bonds : angle 4.04949 / 2.91 ( 1507) metal coordination : bond 0.01044 / 0.72 ( 7) metal coordination : angle 8.66302 / 4.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9057 (m-30) cc_final: 0.8638 (m-30) REVERT: B 97 THR cc_start: 0.8896 (m) cc_final: 0.8512 (p) REVERT: D 72 ASP cc_start: 0.9067 (t0) cc_final: 0.8848 (t0) REVERT: G 38 ARG cc_start: 0.8391 (mtm110) cc_final: 0.7937 (mtm110) REVERT: G 40 ASN cc_start: 0.9057 (m110) cc_final: 0.8347 (t0) REVERT: G 66 GLU cc_start: 0.8748 (tt0) cc_final: 0.8484 (tp30) REVERT: G 73 ARG cc_start: 0.8358 (ttp-170) cc_final: 0.7936 (tpt90) REVERT: G 74 ASP cc_start: 0.8529 (p0) cc_final: 0.8250 (p0) REVERT: G 90 ARG cc_start: 0.9368 (mmt90) cc_final: 0.9077 (mmm-85) REVERT: G 106 GLN cc_start: 0.8271 (mt0) cc_final: 0.8000 (mp10) REVERT: H 125 TYR cc_start: 0.8646 (t80) cc_final: 0.8338 (t80) REVERT: M 41 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8393 (pp20) outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 0.1262 time to fit residues: 15.0212 Evaluate side-chains 62 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 overall best weight: 3.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 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 = 0.3326 r_free = 0.3326 target = 0.048084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.034249 restraints weight = 113178.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.035059 restraints weight = 62905.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035492 restraints weight = 43590.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035837 restraints weight = 35150.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.036026 restraints weight = 30200.390| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11786 Z= 0.196 Angle : 0.739 12.667 16951 Z= 0.419 Chirality : 0.047 0.267 1938 Planarity : 0.005 0.059 1293 Dihedral : 32.475 175.439 3592 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.30), residues: 748 helix: 0.80 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -2.55 (0.35), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG G 19 TYR 0.012 0.002 TYR C 41 PHE 0.009 0.001 PHE B 62 HIS 0.009 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.20 (11779) covalent geometry : angle 0.72376 / 0.42 (16945) hydrogen bonds : bond 0.08501 / 5.83 ( 599) hydrogen bonds : angle 4.09492 / 2.93 ( 1507) metal coordination : bond 0.00531 / 0.39 ( 7) metal coordination : angle 8.03145 / 4.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9084 (m-30) cc_final: 0.8645 (m-30) REVERT: B 85 LEU cc_start: 0.9708 (mp) cc_final: 0.9392 (mt) REVERT: B 89 TYR cc_start: 0.9176 (m-80) cc_final: 0.8905 (m-80) REVERT: B 97 THR cc_start: 0.8927 (m) cc_final: 0.8479 (p) REVERT: D 63 MET cc_start: 0.9033 (mtp) cc_final: 0.8684 (mtt) REVERT: G 66 GLU cc_start: 0.8771 (tt0) cc_final: 0.8509 (tp30) REVERT: G 73 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.7942 (tpt90) REVERT: G 74 ASP cc_start: 0.8519 (p0) cc_final: 0.8264 (p0) REVERT: G 90 ARG cc_start: 0.9361 (mmt90) cc_final: 0.9064 (mmm-85) REVERT: G 106 GLN cc_start: 0.8254 (mt0) cc_final: 0.8011 (mp10) REVERT: H 109 GLU cc_start: 0.9020 (mp0) cc_final: 0.8795 (mp0) REVERT: H 125 TYR cc_start: 0.8764 (t80) cc_final: 0.8547 (t80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1204 time to fit residues: 13.7725 Evaluate side-chains 56 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.0060 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.049354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.035338 restraints weight = 106026.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036149 restraints weight = 59239.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.036653 restraints weight = 41124.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.036988 restraints weight = 32702.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.037104 restraints weight = 28530.540| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11786 Z= 0.147 Angle : 0.719 16.921 16951 Z= 0.401 Chirality : 0.046 0.276 1938 Planarity : 0.005 0.050 1293 Dihedral : 32.339 172.861 3592 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.41 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.04 (0.30), residues: 748 helix: 1.01 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -2.51 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 38 TYR 0.019 0.002 TYR F 89 PHE 0.008 0.001 PHE G 27 HIS 0.010 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (11779) covalent geometry : angle 0.70203 / 0.40 (16945) hydrogen bonds : bond 0.07113 / 4.96 ( 599) hydrogen bonds : angle 3.77233 / 2.72 ( 1507) metal coordination : bond 0.01387 / 1.02 ( 7) metal coordination : angle 8.28776 / 4.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9069 (m-30) cc_final: 0.8606 (m-30) REVERT: B 89 TYR cc_start: 0.9073 (m-80) cc_final: 0.8821 (m-80) REVERT: B 97 THR cc_start: 0.8856 (m) cc_final: 0.8465 (p) REVERT: D 72 ASP cc_start: 0.9313 (t0) cc_final: 0.9005 (t0) REVERT: F 25 ASP cc_start: 0.9045 (p0) cc_final: 0.8805 (t70) REVERT: G 40 ASN cc_start: 0.8961 (m-40) cc_final: 0.8437 (t0) REVERT: G 58 GLU cc_start: 0.9036 (tt0) cc_final: 0.8747 (mt-10) REVERT: G 66 GLU cc_start: 0.8717 (tt0) cc_final: 0.8471 (tp30) REVERT: G 73 ARG cc_start: 0.8378 (ttp-170) cc_final: 0.7963 (tpt90) REVERT: G 74 ASP cc_start: 0.8571 (p0) cc_final: 0.8285 (p0) REVERT: G 90 ARG cc_start: 0.9369 (mmt90) cc_final: 0.9058 (mmm-85) REVERT: G 106 GLN cc_start: 0.8132 (mt0) cc_final: 0.7792 (mp10) REVERT: H 39 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8500 (tm-30) REVERT: H 109 GLU cc_start: 0.8980 (mp0) cc_final: 0.8736 (mp0) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1134 time to fit residues: 14.0872 Evaluate side-chains 64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.048798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.034871 restraints weight = 109444.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035674 restraints weight = 60866.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036196 restraints weight = 41725.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.036521 restraints weight = 33162.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036656 restraints weight = 28732.085| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11786 Z= 0.177 Angle : 0.724 17.979 16951 Z= 0.408 Chirality : 0.045 0.255 1938 Planarity : 0.005 0.052 1293 Dihedral : 32.299 175.113 3592 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.15 % Allowed : 0.31 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.07 (0.30), residues: 748 helix: 0.99 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -2.50 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 38 TYR 0.011 0.002 TYR G 52 PHE 0.016 0.001 PHE E 105 HIS 0.009 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (11779) covalent geometry : angle 0.70536 / 0.41 (16945) hydrogen bonds : bond 0.07932 / 5.49 ( 599) hydrogen bonds : angle 3.93004 / 2.82 ( 1507) metal coordination : bond 0.00846 / 0.55 ( 7) metal coordination : angle 8.70752 / 4.61 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9035 (m-30) cc_final: 0.8579 (m-30) REVERT: B 97 THR cc_start: 0.8949 (m) cc_final: 0.8451 (p) REVERT: D 63 MET cc_start: 0.9086 (ttt) cc_final: 0.8874 (mtp) REVERT: D 72 ASP cc_start: 0.9305 (t0) cc_final: 0.9017 (t0) REVERT: F 25 ASP cc_start: 0.9082 (p0) cc_final: 0.8836 (t70) REVERT: F 85 LEU cc_start: 0.9038 (tp) cc_final: 0.8745 (tt) REVERT: G 40 ASN cc_start: 0.9043 (m-40) cc_final: 0.8459 (t0) REVERT: G 66 GLU cc_start: 0.8733 (tt0) cc_final: 0.8489 (tp30) REVERT: G 73 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.7922 (tpt90) REVERT: G 74 ASP cc_start: 0.8479 (p0) cc_final: 0.8201 (p0) REVERT: G 90 ARG cc_start: 0.9370 (mmt90) cc_final: 0.9065 (mmm-85) REVERT: G 106 GLN cc_start: 0.8147 (mt0) cc_final: 0.7799 (mp10) outliers start: 1 outliers final: 1 residues processed: 86 average time/residue: 0.1112 time to fit residues: 12.9567 Evaluate side-chains 61 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 30.0000 chunk 98 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 83 optimal weight: 40.0000 chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.049615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035269 restraints weight = 108129.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.036063 restraints weight = 60156.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.036600 restraints weight = 41637.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.036856 restraints weight = 32964.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.037090 restraints weight = 29122.517| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11786 Z= 0.143 Angle : 0.705 15.369 16951 Z= 0.395 Chirality : 0.045 0.268 1938 Planarity : 0.004 0.047 1293 Dihedral : 32.254 173.036 3592 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.01 (0.30), residues: 748 helix: 1.06 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.47 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 19 TYR 0.014 0.001 TYR C 41 PHE 0.007 0.001 PHE A 105 HIS 0.010 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (11779) covalent geometry : angle 0.68968 / 0.39 (16945) hydrogen bonds : bond 0.06992 / 4.91 ( 599) hydrogen bonds : angle 3.76484 / 2.70 ( 1507) metal coordination : bond 0.00677 / 0.44 ( 7) metal coordination : angle 7.67441 / 4.12 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.57 seconds wall clock time: 30 minutes 13.67 seconds (1813.67 seconds total)