Starting phenix.real_space_refine on Fri Sep 11 18:37:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k7g_22698/09_2026/7k7g_22698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k7g_22698/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7k7g_22698/09_2026/7k7g_22698.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k7g_22698/09_2026/7k7g_22698.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k7g_22698/09_2026/7k7g_22698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k7g_22698/09_2026/7k7g_22698.map" model { file = "/net/cci-nas-00/data/ceres_data/7k7g_22698/09_2026/7k7g_22698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k7g_22698/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 2.48, per 1000 atoms: 0.22 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: 0.79 Conformation dependent library (CDL) restraints added in 228.5 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: 1.48 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: 1.84 Time building geometry restraints manager: 1.10 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: 15724 2.14 - 4.28: 1109 4.28 - 6.42: 86 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.180 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.490 ------------------------------------------------------------------------------- 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= 0.770 Angle : 1.285 55.173 16951 Z= 0.912 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 1.13435 / 0.91 (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 : 0.306 Fit side-chains revert: symmetry clash 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: 0.8234 (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: 0.7764 (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: 0.7832 (ptp90) REVERT: H 125 TYR cc_start: 0.8422 (t80) cc_final: 0.8205 (t80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1309 time to fit residues: 26.6897 Evaluate side-chains 75 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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: 0.7980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 109 ASN G 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.049882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035418 restraints weight = 109626.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036215 restraints weight = 62596.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.036698 restraints weight = 43765.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 73)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.036950 restraints weight = 34590.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.037138 restraints weight = 29918.347| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11786 Z= 0.196 Angle : 0.859 23.278 16951 Z= 0.467 Chirality : 0.052 0.324 1938 Planarity : 0.006 0.057 1293 Dihedral : 32.809 161.032 3592 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.31 % Allowed : 8.98 % Favored : 90.71 % 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: -0.86 (0.28), residues: 748 helix: 0.38 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -2.52 (0.32), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 34 TYR 0.021 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 0.00328 / 0.20 (11779) covalent geometry : angle 0.79773 / 0.46 (16945) hydrogen bonds : bond 0.09111 / 6.28 ( 599) hydrogen bonds : angle 4.15555 / 2.95 ( 1507) metal coordination : bond 0.01089 / 0.77 ( 7) metal coordination : angle 16.93232 / 8.80 ( 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 104 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 SER cc_start: 0.9641 (t) cc_final: 0.9350 (p) REVERT: A 124 ASP cc_start: 0.8975 (m-30) cc_final: 0.8543 (m-30) REVERT: B 97 THR cc_start: 0.8535 (m) cc_final: 0.8321 (p) REVERT: C 40 ASN cc_start: 0.8396 (p0) cc_final: 0.7480 (p0) REVERT: D 63 MET cc_start: 0.9068 (mtp) cc_final: 0.8695 (mtt) REVERT: G 40 ASN cc_start: 0.8616 (m-40) cc_final: 0.7745 (t0) REVERT: G 66 GLU cc_start: 0.8560 (tt0) cc_final: 0.8320 (tp30) REVERT: G 73 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7815 (tpt90) REVERT: G 90 ARG cc_start: 0.9326 (mmt-90) cc_final: 0.8921 (mmm-85) REVERT: G 94 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7206 (tp30) REVERT: G 106 GLN cc_start: 0.8206 (mt0) cc_final: 0.7657 (mp10) REVERT: H 38 LYS cc_start: 0.6076 (mtpp) cc_final: 0.5859 (mtmm) REVERT: H 99 GLN cc_start: 0.8817 (tt0) cc_final: 0.8452 (tm-30) REVERT: H 103 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7643 (ptt180) REVERT: H 110 LEU cc_start: 0.8740 (tp) cc_final: 0.8484 (tt) REVERT: H 125 TYR cc_start: 0.8468 (t80) cc_final: 0.8267 (t80) outliers start: 2 outliers final: 1 residues processed: 104 average time/residue: 0.1135 time to fit residues: 16.7405 Evaluate side-chains 69 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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: 10.0000 chunk 88 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 overall best weight: 6.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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 = 0.3325 r_free = 0.3325 target = 0.047799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.033786 restraints weight = 116251.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.034401 restraints weight = 67402.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.034828 restraints weight = 46006.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035174 restraints weight = 36714.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035401 restraints weight = 31638.442| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11786 Z= 0.299 Angle : 0.923 19.456 16951 Z= 0.502 Chirality : 0.054 0.309 1938 Planarity : 0.007 0.073 1293 Dihedral : 32.674 164.517 3592 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.15 % Allowed : 6.50 % 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: -0.83 (0.29), residues: 748 helix: 0.30 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -2.36 (0.34), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 34 TYR 0.037 0.003 TYR F 52 PHE 0.020 0.002 PHE E 105 HIS 0.014 0.003 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.30 (11779) covalent geometry : angle 0.88337 / 0.50 (16945) hydrogen bonds : bond 0.11576 / 7.77 ( 599) hydrogen bonds : angle 4.58465 / 3.27 ( 1507) metal coordination : bond 0.01191 / 0.83 ( 7) metal coordination : angle 14.24885 / 7.25 ( 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 88 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8942 (m-30) cc_final: 0.8593 (m-30) REVERT: B 89 TYR cc_start: 0.9140 (m-80) cc_final: 0.8909 (m-80) REVERT: B 97 THR cc_start: 0.8762 (m) cc_final: 0.8411 (p) REVERT: D 63 MET cc_start: 0.9157 (mtp) cc_final: 0.8891 (mtp) REVERT: F 28 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8613 (mm-40) REVERT: G 66 GLU cc_start: 0.8658 (tt0) cc_final: 0.8388 (tp30) REVERT: G 73 ARG cc_start: 0.8298 (ttp-170) cc_final: 0.7909 (tpt90) REVERT: G 90 ARG cc_start: 0.9395 (mmt-90) cc_final: 0.9133 (mmm-85) REVERT: H 99 GLN cc_start: 0.8886 (tt0) cc_final: 0.8595 (tm-30) REVERT: H 103 ARG cc_start: 0.8241 (mtt180) cc_final: 0.7856 (ttm-80) outliers start: 1 outliers final: 1 residues processed: 88 average time/residue: 0.1133 time to fit residues: 14.0808 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 : 0.228 ------------------------------------------------------------------------------- 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: 8.9990 chunk 85 optimal weight: 40.0000 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN 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 ** 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 = 0.3325 r_free = 0.3325 target = 0.048257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.034172 restraints weight = 114125.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034908 restraints weight = 64726.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035335 restraints weight = 45302.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.035662 restraints weight = 36049.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035824 restraints weight = 31390.952| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11786 Z= 0.232 Angle : 0.822 21.882 16951 Z= 0.453 Chirality : 0.051 0.346 1938 Planarity : 0.006 0.063 1293 Dihedral : 32.660 161.635 3592 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.15 % Allowed : 5.26 % Favored : 94.58 % 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: -0.53 (0.29), residues: 748 helix: 0.61 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -2.45 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 37 TYR 0.024 0.003 TYR F 52 PHE 0.012 0.002 PHE B 62 HIS 0.010 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.23 (11779) covalent geometry : angle 0.78584 / 0.45 (16945) hydrogen bonds : bond 0.09019 / 6.13 ( 599) hydrogen bonds : angle 4.35653 / 3.11 ( 1507) metal coordination : bond 0.00541 / 0.38 ( 7) metal coordination : angle 12.86517 / 6.95 ( 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 85 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8982 (m-30) cc_final: 0.8594 (m-30) REVERT: B 85 LEU cc_start: 0.9642 (mp) cc_final: 0.9267 (mp) REVERT: B 89 TYR cc_start: 0.9136 (m-80) cc_final: 0.8866 (m-80) REVERT: B 97 THR cc_start: 0.8767 (m) cc_final: 0.8483 (p) REVERT: D 63 MET cc_start: 0.9115 (mtp) cc_final: 0.8751 (mtt) REVERT: F 94 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8562 (tm-30) REVERT: G 66 GLU cc_start: 0.8692 (tt0) cc_final: 0.8417 (tp30) REVERT: G 73 ARG cc_start: 0.8313 (ttp-170) cc_final: 0.7890 (tpt90) REVERT: G 106 GLN cc_start: 0.8264 (mt0) cc_final: 0.7997 (mm-40) REVERT: H 125 TYR cc_start: 0.8462 (t80) cc_final: 0.8152 (t80) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.1451 time to fit residues: 16.3815 Evaluate side-chains 59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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: 20.0000 chunk 96 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 81 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 63 optimal weight: 0.0770 chunk 80 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 overall best weight: 2.3942 ------------------------------------------------------------------------------- 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** ** E 69 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.049019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.034819 restraints weight = 114987.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.035504 restraints weight = 67108.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036009 restraints weight = 48385.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.036325 restraints weight = 38871.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.036443 restraints weight = 33876.163| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11786 Z= 0.170 Angle : 0.747 16.681 16951 Z= 0.418 Chirality : 0.049 0.331 1938 Planarity : 0.005 0.072 1293 Dihedral : 32.493 161.760 3592 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -0.11 (0.30), residues: 748 helix: 0.97 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -2.39 (0.34), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 96 TYR 0.022 0.002 TYR F 52 PHE 0.012 0.001 PHE E 105 HIS 0.011 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (11779) covalent geometry : angle 0.72221 / 0.42 (16945) hydrogen bonds : bond 0.07958 / 5.46 ( 599) hydrogen bonds : angle 3.96414 / 2.83 ( 1507) metal coordination : bond 0.00499 / 0.35 ( 7) metal coordination : angle 10.08304 / 5.49 ( 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 91 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.315 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: 0.8926 (m-30) cc_final: 0.8472 (m-30) REVERT: B 89 TYR cc_start: 0.9015 (m-80) cc_final: 0.8806 (m-80) REVERT: B 97 THR cc_start: 0.8899 (m) cc_final: 0.8526 (p) REVERT: D 63 MET cc_start: 0.9006 (mtp) cc_final: 0.8583 (mtt) REVERT: D 72 ASP cc_start: 0.8957 (t0) cc_final: 0.8639 (t0) REVERT: G 66 GLU cc_start: 0.8709 (tt0) cc_final: 0.8441 (tp30) REVERT: G 73 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.7954 (tpt90) REVERT: G 74 ASP cc_start: 0.8595 (p0) cc_final: 0.8293 (p0) REVERT: G 90 ARG cc_start: 0.9282 (mmt90) cc_final: 0.8912 (mmm-85) REVERT: G 106 GLN cc_start: 0.8331 (mt0) cc_final: 0.8019 (mp10) REVERT: H 125 TYR cc_start: 0.8448 (t80) cc_final: 0.8195 (t80) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1314 time to fit residues: 16.3471 Evaluate side-chains 63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 10.0000 chunk 86 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 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: 0.9980 chunk 24 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.047181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.033067 restraints weight = 114839.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.033640 restraints weight = 66464.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.034073 restraints weight = 45899.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.034419 restraints weight = 37293.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.034615 restraints weight = 32283.494| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 11786 Z= 0.312 Angle : 0.874 17.876 16951 Z= 0.479 Chirality : 0.052 0.309 1938 Planarity : 0.006 0.052 1293 Dihedral : 32.556 164.574 3592 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.15 % Allowed : 3.56 % Favored : 96.28 % 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: -0.53 (0.29), residues: 748 helix: 0.61 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -2.45 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG M 34 TYR 0.016 0.003 TYR F 99 PHE 0.031 0.002 PHE E 105 HIS 0.009 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.31 (11779) covalent geometry : angle 0.85084 / 0.48 (16945) hydrogen bonds : bond 0.11250 / 7.61 ( 599) hydrogen bonds : angle 4.58050 / 3.28 ( 1507) metal coordination : bond 0.00714 / 0.46 ( 7) metal coordination : angle 10.76484 / 5.83 ( 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 77 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9262 (t0) cc_final: 0.9060 (t0) REVERT: A 124 ASP cc_start: 0.9017 (m-30) cc_final: 0.8642 (m-30) REVERT: B 89 TYR cc_start: 0.9159 (m-80) cc_final: 0.8945 (m-80) REVERT: B 97 THR cc_start: 0.8884 (m) cc_final: 0.8546 (p) REVERT: D 63 MET cc_start: 0.9127 (mtp) cc_final: 0.8721 (mtt) REVERT: D 72 ASP cc_start: 0.9085 (t0) cc_final: 0.8854 (t0) REVERT: F 94 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8565 (tm-30) REVERT: G 38 ARG cc_start: 0.8180 (mtm110) cc_final: 0.7595 (mtm110) REVERT: G 40 ASN cc_start: 0.9130 (m110) cc_final: 0.8367 (t0) REVERT: G 66 GLU cc_start: 0.8753 (tt0) cc_final: 0.8409 (tp30) REVERT: G 73 ARG cc_start: 0.8384 (ttp-170) cc_final: 0.7946 (tpt90) REVERT: G 74 ASP cc_start: 0.8566 (p0) cc_final: 0.8267 (p0) REVERT: G 90 ARG cc_start: 0.9307 (mmt90) cc_final: 0.9002 (mmm-85) REVERT: G 106 GLN cc_start: 0.8298 (mt0) cc_final: 0.7955 (mp10) REVERT: H 109 GLU cc_start: 0.9045 (mp0) cc_final: 0.8813 (mp0) REVERT: H 125 TYR cc_start: 0.8440 (t80) cc_final: 0.8151 (t80) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.1283 time to fit residues: 13.6693 Evaluate side-chains 60 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 7.9990 chunk 71 optimal weight: 50.0000 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.049194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.034929 restraints weight = 108160.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035610 restraints weight = 62729.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.036044 restraints weight = 42623.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.036406 restraints weight = 34112.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.036607 restraints weight = 29505.794| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11786 Z= 0.154 Angle : 0.741 14.138 16951 Z= 0.413 Chirality : 0.048 0.331 1938 Planarity : 0.005 0.050 1293 Dihedral : 32.421 162.871 3592 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: -0.02 (0.30), residues: 748 helix: 1.06 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -2.42 (0.33), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 38 TYR 0.019 0.002 TYR C 41 PHE 0.009 0.002 PHE G 27 HIS 0.009 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (11779) covalent geometry : angle 0.72527 / 0.41 (16945) hydrogen bonds : bond 0.07446 / 5.17 ( 599) hydrogen bonds : angle 3.89760 / 2.79 ( 1507) metal coordination : bond 0.00387 / 0.26 ( 7) metal coordination : angle 8.14706 / 4.47 ( 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 85 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.9160 (pp20) cc_final: 0.8942 (pp20) REVERT: A 124 ASP cc_start: 0.9071 (m-30) cc_final: 0.8641 (m-30) REVERT: D 63 MET cc_start: 0.9010 (mtp) cc_final: 0.8606 (mtt) REVERT: D 72 ASP cc_start: 0.9030 (t0) cc_final: 0.8764 (t0) REVERT: F 85 LEU cc_start: 0.8968 (tt) cc_final: 0.8743 (tp) REVERT: G 66 GLU cc_start: 0.8679 (tt0) cc_final: 0.8426 (tp30) REVERT: G 73 ARG cc_start: 0.8307 (ttp-170) cc_final: 0.7907 (tpt90) REVERT: G 74 ASP cc_start: 0.8595 (p0) cc_final: 0.8300 (p0) REVERT: G 90 ARG cc_start: 0.9312 (mmt90) cc_final: 0.8981 (mmm-85) REVERT: G 106 GLN cc_start: 0.8210 (mt0) cc_final: 0.7836 (mp10) REVERT: H 109 GLU cc_start: 0.8972 (mp0) cc_final: 0.8711 (mp0) REVERT: H 125 TYR cc_start: 0.8485 (t80) cc_final: 0.8217 (t80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1281 time to fit residues: 15.1191 Evaluate side-chains 59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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: 1.9990 chunk 92 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035027 restraints weight = 105998.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035730 restraints weight = 61681.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.036204 restraints weight = 42051.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036525 restraints weight = 33612.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.036604 restraints weight = 29291.103| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11786 Z= 0.149 Angle : 0.728 18.431 16951 Z= 0.406 Chirality : 0.046 0.311 1938 Planarity : 0.005 0.048 1293 Dihedral : 32.280 163.824 3592 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.15 % Allowed : 2.17 % Favored : 97.68 % 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: -0.03 (0.30), residues: 748 helix: 1.00 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -2.45 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 38 TYR 0.012 0.001 TYR C 41 PHE 0.040 0.002 PHE A 105 HIS 0.010 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (11779) covalent geometry : angle 0.70515 / 0.40 (16945) hydrogen bonds : bond 0.07458 / 5.18 ( 599) hydrogen bonds : angle 3.90925 / 2.81 ( 1507) metal coordination : bond 0.00661 / 0.44 ( 7) metal coordination : angle 9.69217 / 5.47 ( 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 86 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9079 (m-30) cc_final: 0.8611 (m-30) REVERT: B 89 TYR cc_start: 0.9160 (m-80) cc_final: 0.8886 (m-80) REVERT: B 97 THR cc_start: 0.8917 (m) cc_final: 0.8475 (p) REVERT: C 40 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7261 (p0) REVERT: D 63 MET cc_start: 0.9035 (mtp) cc_final: 0.8621 (mtt) REVERT: G 40 ASN cc_start: 0.9067 (m110) cc_final: 0.8349 (t0) REVERT: G 66 GLU cc_start: 0.8640 (tt0) cc_final: 0.8412 (tp30) REVERT: G 73 ARG cc_start: 0.8304 (ttp-170) cc_final: 0.7904 (tpt90) REVERT: G 74 ASP cc_start: 0.8622 (p0) cc_final: 0.8320 (p0) REVERT: G 90 ARG cc_start: 0.9323 (mmt90) cc_final: 0.8990 (mmm-85) REVERT: G 106 GLN cc_start: 0.8170 (mt0) cc_final: 0.7775 (mp10) REVERT: H 125 TYR cc_start: 0.8476 (t80) cc_final: 0.8225 (t80) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1141 time to fit residues: 14.1177 Evaluate side-chains 60 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** E 121 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 = 0.3368 r_free = 0.3368 target = 0.049468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.035257 restraints weight = 104494.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.035976 restraints weight = 60867.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.036501 restraints weight = 41762.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.036743 restraints weight = 33062.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.036973 restraints weight = 29207.471| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4316 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= 0.151 Angle : 0.716 16.393 16951 Z= 0.399 Chirality : 0.046 0.304 1938 Planarity : 0.004 0.049 1293 Dihedral : 32.212 163.786 3592 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.15 % Allowed : 0.93 % Favored : 98.92 % 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: 1.09 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -2.43 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 38 TYR 0.015 0.001 TYR F 89 PHE 0.012 0.001 PHE E 105 HIS 0.009 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (11779) covalent geometry : angle 0.69707 / 0.40 (16945) hydrogen bonds : bond 0.07338 / 5.11 ( 599) hydrogen bonds : angle 3.90397 / 2.79 ( 1507) metal coordination : bond 0.02253 / 1.57 ( 7) metal coordination : angle 8.73613 / 4.98 ( 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 86 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9078 (m-30) cc_final: 0.8628 (m-30) REVERT: B 89 TYR cc_start: 0.9170 (m-80) cc_final: 0.8838 (m-80) REVERT: B 97 THR cc_start: 0.8842 (m) cc_final: 0.8465 (p) REVERT: D 63 MET cc_start: 0.9055 (mtp) cc_final: 0.8644 (mtt) REVERT: D 72 ASP cc_start: 0.9328 (t0) cc_final: 0.9061 (t0) REVERT: F 89 TYR cc_start: 0.8626 (m-80) cc_final: 0.8351 (m-80) REVERT: G 58 GLU cc_start: 0.9017 (tt0) cc_final: 0.8728 (mt-10) REVERT: G 66 GLU cc_start: 0.8651 (tt0) cc_final: 0.8419 (tp30) REVERT: G 73 ARG cc_start: 0.8262 (ttp-170) cc_final: 0.7873 (tpt90) REVERT: G 74 ASP cc_start: 0.8602 (p0) cc_final: 0.8269 (p0) REVERT: G 90 ARG cc_start: 0.9344 (mmt90) cc_final: 0.9017 (mmm-85) REVERT: G 106 GLN cc_start: 0.8166 (mt0) cc_final: 0.7776 (mp10) REVERT: H 125 TYR cc_start: 0.8500 (t80) cc_final: 0.8244 (t80) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1223 time to fit residues: 14.7339 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 : 0.319 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.048195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.034131 restraints weight = 110252.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.034813 restraints weight = 62801.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.035357 restraints weight = 44637.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.035680 restraints weight = 34967.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.035838 restraints weight = 30503.223| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11786 Z= 0.218 Angle : 0.771 18.777 16951 Z= 0.426 Chirality : 0.047 0.292 1938 Planarity : 0.005 0.056 1293 Dihedral : 32.254 164.837 3592 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.15 % Allowed : 0.62 % Favored : 99.23 % 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: 0.96 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -2.36 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 44 TYR 0.013 0.002 TYR F 99 PHE 0.015 0.002 PHE A 105 HIS 0.009 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.22 (11779) covalent geometry : angle 0.75070 / 0.42 (16945) hydrogen bonds : bond 0.09261 / 6.35 ( 599) hydrogen bonds : angle 4.20690 / 3.00 ( 1507) metal coordination : bond 0.00796 / 0.50 ( 7) metal coordination : angle 9.44380 / 4.86 ( 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 84 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9099 (m-30) cc_final: 0.8684 (m-30) REVERT: B 89 TYR cc_start: 0.9200 (m-80) cc_final: 0.8847 (m-80) REVERT: B 97 THR cc_start: 0.8932 (m) cc_final: 0.8504 (p) REVERT: C 40 ASN cc_start: 0.8702 (p0) cc_final: 0.8157 (p0) REVERT: D 63 MET cc_start: 0.9097 (mtp) cc_final: 0.8692 (mtt) REVERT: D 72 ASP cc_start: 0.9319 (t0) cc_final: 0.9080 (t0) REVERT: G 38 ARG cc_start: 0.8238 (mtm110) cc_final: 0.7670 (mtm110) REVERT: G 40 ASN cc_start: 0.9228 (m110) cc_final: 0.8316 (t0) REVERT: G 66 GLU cc_start: 0.8702 (tt0) cc_final: 0.8466 (tp30) REVERT: G 73 ARG cc_start: 0.8356 (ttp-170) cc_final: 0.7948 (tpt90) REVERT: G 74 ASP cc_start: 0.8499 (p0) cc_final: 0.8239 (p0) REVERT: G 90 ARG cc_start: 0.9364 (mmt90) cc_final: 0.9054 (mmm-85) REVERT: G 106 GLN cc_start: 0.8192 (mt0) cc_final: 0.7798 (mp10) REVERT: H 125 TYR cc_start: 0.8503 (t80) cc_final: 0.8240 (t80) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1282 time to fit residues: 14.7597 Evaluate side-chains 60 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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: 4.9990 chunk 73 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 50.0000 chunk 60 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.048492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.034391 restraints weight = 109652.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.035067 restraints weight = 63540.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035582 restraints weight = 43731.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.035893 restraints weight = 34713.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.036088 restraints weight = 30046.552| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11786 Z= 0.177 Angle : 0.734 16.737 16951 Z= 0.409 Chirality : 0.046 0.300 1938 Planarity : 0.006 0.098 1293 Dihedral : 32.258 163.899 3592 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % 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: 0.05 (0.30), residues: 748 helix: 1.05 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -2.36 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 83 TYR 0.013 0.002 TYR C 41 PHE 0.011 0.001 PHE A 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 0.71580 / 0.41 (16945) hydrogen bonds : bond 0.07914 / 5.49 ( 599) hydrogen bonds : angle 4.07857 / 2.92 ( 1507) metal coordination : bond 0.01070 / 0.71 ( 7) metal coordination : angle 8.60808 / 4.74 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1829.47 seconds wall clock time: 32 minutes 23.55 seconds (1943.55 seconds total)