Starting phenix.real_space_refine on Sat Jul 4 07:46:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v6s_64806/07_2026/9v6s_64806.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v6s_64806/07_2026/9v6s_64806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v6s_64806/07_2026/9v6s_64806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v6s_64806/07_2026/9v6s_64806.map" model { file = "/net/cci-nas-00/data/ceres_data/9v6s_64806/07_2026/9v6s_64806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v6s_64806/07_2026/9v6s_64806.cif" } resolution = 3.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7390 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 289 5.49 5 S 33 5.16 5 C 7563 2.51 5 N 2501 2.21 5 O 3064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13454 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 806 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "G" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "F" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "N" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11972 SG CYS M 18 62.778 88.196 53.431 1.00 39.49 S ATOM 11993 SG CYS M 21 63.792 91.573 52.034 1.00 41.71 S ATOM 12131 SG CYS M 39 62.651 88.771 49.767 1.00 36.68 S ATOM 12153 SG CYS M 42 66.085 88.531 51.505 1.00 34.84 S ATOM 12090 SG CYS M 34 58.923 76.330 58.406 1.00 31.63 S ATOM 12248 SG CYS M 53 61.304 79.167 59.566 1.00 30.50 S ATOM 12269 SG CYS M 56 59.019 77.302 62.052 1.00 36.45 S ATOM 12946 SG CYS N 51 40.906 71.543 44.389 1.00 45.61 S ATOM 12967 SG CYS N 54 37.282 72.123 44.486 1.00 48.97 S ATOM 13115 SG CYS N 72 39.558 72.811 47.531 1.00 38.59 S ATOM 13134 SG CYS N 75 38.669 69.199 46.586 1.00 33.26 S ATOM 13069 SG CYS N 67 53.783 68.957 43.797 1.00 28.05 S ATOM 13223 SG CYS N 87 50.918 66.883 42.306 1.00 34.35 S ATOM 13243 SG CYS N 90 54.251 67.182 40.416 1.00 32.90 S Time building chain proxies: 2.51, per 1000 atoms: 0.19 Number of scatterers: 13454 At special positions: 0 Unit cell: (125.4, 114.4, 119.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 33 16.00 P 289 15.00 O 3064 8.00 N 2501 7.00 C 7563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 447.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 21 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 42 " pdb=" ZN M 402 " pdb="ZN ZN M 402 " - pdb=" ND1 HIS M 36 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 56 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 53 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 72 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " Number of angles added : 18 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 65.3% alpha, 3.8% beta 137 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.508A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.782A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.539A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.578A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.676A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.544A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.534A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.885A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.758A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.387A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.509A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.706A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.028A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.503A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.699A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.939A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.502A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 13 removed outlier: 3.643A pdb=" N LEU M 12 " --> pdb=" O LYS M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 48 removed outlier: 3.833A pdb=" N GLU M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 72 through 83 removed outlier: 3.660A pdb=" N VAL M 83 " --> pdb=" O VAL M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 98 removed outlier: 3.610A pdb=" N ASN M 89 " --> pdb=" O GLY M 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 25 Processing helix chain 'N' and resid 73 through 83 Processing helix chain 'N' and resid 96 through 98 No H-bonds generated for 'chain 'N' and resid 96 through 98' Processing helix chain 'N' and resid 103 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.019A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.260A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.043A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.399A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.925A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 17 through 18 removed outlier: 3.688A pdb=" N GLY M 23 " --> pdb=" O CYS M 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AB3, first strand: chain 'N' and resid 70 through 72 432 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.56 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: 2466 1.33 - 1.45: 4574 1.45 - 1.57: 6616 1.57 - 1.69: 576 1.69 - 1.81: 48 Bond restraints: 14280 Sorted by residual: bond pdb=" C3' DT J 35 " pdb=" C2' DT J 35 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.44e+01 bond pdb=" C3' DA I 135 " pdb=" C2' DA I 135 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DT J 79 " pdb=" C2' DT J 79 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DG J 64 " pdb=" C2' DG J 64 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 14275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 19555 1.67 - 3.35: 940 3.35 - 5.02: 28 5.02 - 6.69: 3 6.69 - 8.37: 3 Bond angle restraints: 20529 Sorted by residual: angle pdb=" O4' DA I 91 " pdb=" C4' DA I 91 " pdb=" C3' DA I 91 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.63e+01 angle pdb=" N3 DT J 105 " pdb=" C4 DT J 105 " pdb=" O4 DT J 105 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I 134 " pdb=" C4 DT I 134 " pdb=" O4 DT I 134 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 112 " pdb=" C4 DT I 112 " pdb=" O4 DT I 112 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 20524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.27: 6463 34.27 - 68.54: 1382 68.54 - 102.81: 23 102.81 - 137.08: 1 137.08 - 171.35: 2 Dihedral angle restraints: 7871 sinusoidal: 5114 harmonic: 2757 Sorted by residual: dihedral pdb=" CA ILE M 32 " pdb=" C ILE M 32 " pdb=" N GLU M 33 " pdb=" CA GLU M 33 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C4' DT J 140 " pdb=" C3' DT J 140 " pdb=" O3' DT J 140 " pdb=" P DT J 141 " ideal model delta sinusoidal sigma weight residual 220.00 48.65 171.35 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 57 " pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " pdb=" P DT J 58 " ideal model delta sinusoidal sigma weight residual 220.00 72.53 147.47 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 7868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1626 0.040 - 0.080: 567 0.080 - 0.120: 147 0.120 - 0.161: 6 0.161 - 0.201: 2 Chirality restraints: 2348 Sorted by residual: chirality pdb=" C3' DT J 57 " pdb=" C4' DT J 57 " pdb=" O3' DT J 57 " pdb=" C2' DT J 57 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CG LEU H 101 " pdb=" CB LEU H 101 " pdb=" CD1 LEU H 101 " pdb=" CD2 LEU H 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE M 31 " pdb=" N ILE M 31 " pdb=" C ILE M 31 " pdb=" CB ILE M 31 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2345 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO D 103 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO H 103 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO C 80 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.023 5.00e-02 4.00e+02 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3123 2.82 - 3.34: 11500 3.34 - 3.86: 24706 3.86 - 4.38: 29202 4.38 - 4.90: 42295 Nonbonded interactions: 110826 Sorted by model distance: nonbonded pdb=" OE2 GLU M 90 " pdb=" NE2 GLN N 29 " model vdw 2.302 3.120 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.303 3.120 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.311 3.040 nonbonded pdb=" O GLN A 125 " pdb=" NH2 ARG A 134 " model vdw 2.313 3.120 nonbonded pdb=" N SER N 20 " pdb=" OE2 GLU N 23 " model vdw 2.340 3.120 ... (remaining 110821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.430 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14296 Z= 0.482 Angle : 0.699 8.367 20547 Z= 0.619 Chirality : 0.042 0.201 2348 Planarity : 0.004 0.066 1591 Dihedral : 26.634 171.346 6089 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.28), residues: 928 helix: 2.28 (0.22), residues: 591 sheet: -0.09 (3.36), residues: 5 loop : -1.09 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.010 0.001 TYR M 24 PHE 0.018 0.001 PHE C 25 TRP 0.002 0.001 TRP N 17 HIS 0.004 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.48 (14280) covalent geometry : angle 0.69417 / 0.62 (20529) hydrogen bonds : bond 0.10951 / 7.34 ( 783) hydrogen bonds : angle 3.58831 / 2.66 ( 1968) metal coordination : bond 0.00573 / 0.44 ( 16) metal coordination : angle 2.77426 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.286 Fit side-chains REVERT: A 53 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7889 (ttm170) REVERT: E 68 GLN cc_start: 0.8027 (tt0) cc_final: 0.7824 (tt0) outliers start: 0 outliers final: 1 residues processed: 180 average time/residue: 0.7538 time to fit residues: 144.3151 Evaluate side-chains 155 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 22 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.0570 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 HIS D 109 HIS M 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.188944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138171 restraints weight = 16113.421| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.69 r_work: 0.3079 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14296 Z= 0.140 Angle : 0.595 8.412 20547 Z= 0.352 Chirality : 0.045 0.351 2348 Planarity : 0.005 0.047 1591 Dihedral : 30.024 172.170 4209 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.98 % Allowed : 10.78 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.28), residues: 928 helix: 2.33 (0.22), residues: 599 sheet: None (None), residues: 0 loop : -1.06 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 95 TYR 0.010 0.001 TYR N 114 PHE 0.009 0.001 PHE M 87 TRP 0.002 0.001 TRP N 17 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.14 (14280) covalent geometry : angle 0.59186 / 0.35 (20529) hydrogen bonds : bond 0.05547 / 3.82 ( 783) hydrogen bonds : angle 2.72097 / 2.03 ( 1968) metal coordination : bond 0.00458 / 0.33 ( 16) metal coordination : angle 2.09254 / 1.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.428 Fit side-chains REVERT: A 53 ARG cc_start: 0.8717 (ttp-110) cc_final: 0.8492 (ttm170) REVERT: E 68 GLN cc_start: 0.8417 (tt0) cc_final: 0.8214 (tt0) REVERT: E 105 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: E 133 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: H 85 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8070 (mttp) REVERT: H 93 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: M 77 ASP cc_start: 0.7665 (m-30) cc_final: 0.7392 (m-30) REVERT: M 82 LEU cc_start: 0.8167 (tm) cc_final: 0.7950 (tp) outliers start: 16 outliers final: 6 residues processed: 160 average time/residue: 0.6924 time to fit residues: 118.1259 Evaluate side-chains 158 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 61 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 98 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.189128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140769 restraints weight = 16337.722| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.82 r_work: 0.3053 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14296 Z= 0.131 Angle : 0.549 7.695 20547 Z= 0.329 Chirality : 0.042 0.330 2348 Planarity : 0.004 0.046 1591 Dihedral : 30.222 172.481 4207 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.10 % Allowed : 11.40 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.28), residues: 928 helix: 2.56 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -1.03 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 95 TYR 0.016 0.001 TYR N 22 PHE 0.018 0.001 PHE M 87 TRP 0.002 0.001 TRP N 17 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.13 (14280) covalent geometry : angle 0.54701 / 0.33 (20529) hydrogen bonds : bond 0.05014 / 3.42 ( 783) hydrogen bonds : angle 2.56163 / 1.91 ( 1968) metal coordination : bond 0.00496 / 0.38 ( 16) metal coordination : angle 1.79479 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.287 Fit side-chains REVERT: A 125 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: E 133 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: H 93 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: M 77 ASP cc_start: 0.7716 (m-30) cc_final: 0.7417 (m-30) REVERT: M 91 MET cc_start: 0.6897 (mpm) cc_final: 0.6484 (mpm) outliers start: 25 outliers final: 11 residues processed: 168 average time/residue: 0.6881 time to fit residues: 123.3681 Evaluate side-chains 163 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 82 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 94 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 40.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN M 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.186865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137440 restraints weight = 16185.003| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.83 r_work: 0.2994 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14296 Z= 0.164 Angle : 0.596 7.864 20547 Z= 0.346 Chirality : 0.044 0.333 2348 Planarity : 0.005 0.046 1591 Dihedral : 30.389 173.563 4207 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.59 % Allowed : 12.52 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.28), residues: 928 helix: 2.35 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -1.11 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 95 TYR 0.010 0.002 TYR B 51 PHE 0.010 0.002 PHE D 65 TRP 0.003 0.001 TRP N 17 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (14280) covalent geometry : angle 0.59372 / 0.35 (20529) hydrogen bonds : bond 0.06052 / 4.09 ( 783) hydrogen bonds : angle 2.64623 / 1.97 ( 1968) metal coordination : bond 0.00775 / 0.60 ( 16) metal coordination : angle 1.88765 / 1.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.364 Fit side-chains REVERT: A 125 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8332 (mt0) REVERT: G 91 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: E 133 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: H 85 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8128 (mptt) REVERT: H 93 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: M 77 ASP cc_start: 0.7561 (m-30) cc_final: 0.7332 (m-30) REVERT: M 82 LEU cc_start: 0.8450 (tp) cc_final: 0.8133 (tm) REVERT: N 23 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6450 (pm20) outliers start: 29 outliers final: 11 residues processed: 168 average time/residue: 0.7348 time to fit residues: 131.6440 Evaluate side-chains 170 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 86 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 50.0000 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 104 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN M 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.184628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134756 restraints weight = 16068.816| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.84 r_work: 0.2961 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14296 Z= 0.203 Angle : 0.663 8.567 20547 Z= 0.374 Chirality : 0.048 0.332 2348 Planarity : 0.006 0.049 1591 Dihedral : 30.638 174.205 4207 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.34 % Allowed : 12.64 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.27), residues: 928 helix: 1.95 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -1.29 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 131 TYR 0.016 0.002 TYR N 22 PHE 0.011 0.002 PHE D 65 TRP 0.005 0.002 TRP N 17 HIS 0.005 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (14280) covalent geometry : angle 0.65939 / 0.37 (20529) hydrogen bonds : bond 0.07125 / 4.79 ( 783) hydrogen bonds : angle 2.78869 / 2.07 ( 1968) metal coordination : bond 0.01005 / 0.80 ( 16) metal coordination : angle 2.41356 / 1.39 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.231 Fit side-chains REVERT: A 125 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8375 (mt0) REVERT: G 91 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: G 104 GLN cc_start: 0.8197 (mm110) cc_final: 0.7887 (mm110) REVERT: E 133 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: H 85 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8143 (mptt) REVERT: H 93 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: M 77 ASP cc_start: 0.7688 (m-30) cc_final: 0.7382 (m-30) REVERT: M 82 LEU cc_start: 0.8424 (tp) cc_final: 0.8085 (tm) REVERT: N 23 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6573 (pm20) outliers start: 35 outliers final: 17 residues processed: 170 average time/residue: 0.7196 time to fit residues: 130.2808 Evaluate side-chains 176 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 82 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 112 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 88 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 50.0000 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN M 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.183859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134113 restraints weight = 16119.984| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.82 r_work: 0.2944 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14296 Z= 0.228 Angle : 0.695 9.262 20547 Z= 0.388 Chirality : 0.050 0.329 2348 Planarity : 0.006 0.064 1591 Dihedral : 30.796 174.928 4207 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.09 % Allowed : 14.99 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 928 helix: 1.67 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.40 (0.29), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 45 TYR 0.017 0.002 TYR N 22 PHE 0.010 0.002 PHE B 61 TRP 0.005 0.002 TRP N 17 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.23 (14280) covalent geometry : angle 0.69035 / 0.39 (20529) hydrogen bonds : bond 0.07400 / 4.96 ( 783) hydrogen bonds : angle 2.83461 / 2.10 ( 1968) metal coordination : bond 0.01158 / 0.89 ( 16) metal coordination : angle 2.77184 / 1.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.263 Fit side-chains REVERT: A 56 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8339 (tttt) REVERT: A 125 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: G 91 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6994 (tp30) REVERT: G 104 GLN cc_start: 0.8248 (mm110) cc_final: 0.7942 (mm110) REVERT: E 133 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: H 85 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8127 (mptt) REVERT: H 93 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: H 116 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8437 (ttmt) REVERT: M 77 ASP cc_start: 0.7678 (m-30) cc_final: 0.7407 (m-30) REVERT: M 80 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: M 82 LEU cc_start: 0.8417 (tp) cc_final: 0.8070 (tm) REVERT: N 85 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7444 (mmtm) outliers start: 33 outliers final: 14 residues processed: 168 average time/residue: 0.7039 time to fit residues: 125.9765 Evaluate side-chains 171 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain M residue 80 TYR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 52 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.186281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134841 restraints weight = 16024.532| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.68 r_work: 0.3021 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14296 Z= 0.139 Angle : 0.620 9.451 20547 Z= 0.351 Chirality : 0.045 0.332 2348 Planarity : 0.004 0.045 1591 Dihedral : 30.741 174.159 4207 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.47 % Allowed : 16.85 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.28), residues: 928 helix: 2.15 (0.21), residues: 603 sheet: None (None), residues: 0 loop : -1.27 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 45 TYR 0.016 0.001 TYR F 51 PHE 0.006 0.001 PHE B 61 TRP 0.002 0.001 TRP N 17 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (14280) covalent geometry : angle 0.61651 / 0.35 (20529) hydrogen bonds : bond 0.05790 / 3.89 ( 783) hydrogen bonds : angle 2.67841 / 1.99 ( 1968) metal coordination : bond 0.00685 / 0.54 ( 16) metal coordination : angle 2.26555 / 1.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.293 Fit side-chains REVERT: A 125 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8340 (mt0) REVERT: G 91 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: E 105 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: H 85 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8123 (mptt) REVERT: H 93 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: H 116 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8377 (ttmt) REVERT: M 77 ASP cc_start: 0.7635 (m-30) cc_final: 0.7407 (m-30) REVERT: M 80 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.7227 (m-10) REVERT: M 82 LEU cc_start: 0.8398 (tp) cc_final: 0.8032 (tm) REVERT: M 91 MET cc_start: 0.7204 (mmp) cc_final: 0.6696 (mmm) REVERT: N 85 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7189 (mmtm) REVERT: N 93 LYS cc_start: 0.8261 (tttm) cc_final: 0.8005 (ttmm) REVERT: N 106 PHE cc_start: 0.7693 (m-80) cc_final: 0.7432 (m-80) outliers start: 28 outliers final: 13 residues processed: 171 average time/residue: 0.6816 time to fit residues: 124.5115 Evaluate side-chains 171 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 80 TYR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 88 optimal weight: 50.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN M 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.184707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135104 restraints weight = 15918.447| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.76 r_work: 0.2975 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14296 Z= 0.198 Angle : 0.657 9.023 20547 Z= 0.370 Chirality : 0.048 0.331 2348 Planarity : 0.005 0.054 1591 Dihedral : 30.762 174.355 4207 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.47 % Allowed : 17.97 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.27), residues: 928 helix: 1.93 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.31 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 45 TYR 0.015 0.002 TYR D 83 PHE 0.009 0.002 PHE B 61 TRP 0.004 0.001 TRP N 17 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (14280) covalent geometry : angle 0.65362 / 0.37 (20529) hydrogen bonds : bond 0.06779 / 4.55 ( 783) hydrogen bonds : angle 2.74501 / 2.04 ( 1968) metal coordination : bond 0.00999 / 0.78 ( 16) metal coordination : angle 2.41355 / 1.40 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.393 Fit side-chains REVERT: A 125 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8388 (mt0) REVERT: G 91 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6934 (tp30) REVERT: G 104 GLN cc_start: 0.8150 (mm110) cc_final: 0.7917 (mm110) REVERT: E 105 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: E 133 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: H 85 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8125 (mptt) REVERT: H 93 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: H 116 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8403 (ttmt) REVERT: F 92 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8238 (ttm-80) REVERT: M 77 ASP cc_start: 0.7651 (m-30) cc_final: 0.7413 (m-30) REVERT: M 80 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.7266 (m-10) REVERT: M 82 LEU cc_start: 0.8402 (tp) cc_final: 0.8027 (tm) REVERT: N 85 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7325 (mmtm) REVERT: N 93 LYS cc_start: 0.8287 (tttm) cc_final: 0.8039 (ttmm) REVERT: N 106 PHE cc_start: 0.7772 (m-80) cc_final: 0.7501 (m-80) outliers start: 28 outliers final: 13 residues processed: 167 average time/residue: 0.6921 time to fit residues: 123.1374 Evaluate side-chains 173 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 80 TYR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 75 optimal weight: 30.0000 chunk 72 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 chunk 35 optimal weight: 0.4980 chunk 79 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN M 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.182281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132157 restraints weight = 16040.207| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.83 r_work: 0.2928 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 14296 Z= 0.297 Angle : 0.790 9.181 20547 Z= 0.432 Chirality : 0.055 0.332 2348 Planarity : 0.007 0.060 1591 Dihedral : 30.944 175.802 4207 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.97 % Allowed : 18.59 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.26), residues: 928 helix: 1.30 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.58 (0.29), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 45 TYR 0.026 0.003 TYR F 88 PHE 0.012 0.003 PHE B 61 TRP 0.007 0.002 TRP N 17 HIS 0.006 0.002 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.30 (14280) covalent geometry : angle 0.78546 / 0.43 (20529) hydrogen bonds : bond 0.08708 / 5.82 ( 783) hydrogen bonds : angle 2.99885 / 2.22 ( 1968) metal coordination : bond 0.01561 / 1.24 ( 16) metal coordination : angle 3.05532 / 1.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.222 Fit side-chains REVERT: A 125 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8437 (mt0) REVERT: G 74 LYS cc_start: 0.8220 (tppt) cc_final: 0.7994 (tppp) REVERT: G 91 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: G 104 GLN cc_start: 0.8225 (mm110) cc_final: 0.7970 (mm-40) REVERT: E 133 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: H 85 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8278 (mptt) REVERT: H 93 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: F 92 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7734 (ttm-80) REVERT: M 82 LEU cc_start: 0.8385 (tp) cc_final: 0.7996 (tm) REVERT: N 85 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7440 (mmtm) REVERT: N 106 PHE cc_start: 0.7786 (m-80) cc_final: 0.7510 (m-80) REVERT: N 114 TYR cc_start: 0.6430 (m-10) cc_final: 0.6149 (m-10) outliers start: 24 outliers final: 10 residues processed: 167 average time/residue: 0.7032 time to fit residues: 125.0561 Evaluate side-chains 167 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 85 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 72 optimal weight: 50.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN M 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.186063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136037 restraints weight = 15986.589| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.66 r_work: 0.3027 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14296 Z= 0.137 Angle : 0.621 9.228 20547 Z= 0.353 Chirality : 0.045 0.314 2348 Planarity : 0.005 0.056 1591 Dihedral : 30.828 173.767 4207 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.98 % Allowed : 20.20 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.27), residues: 928 helix: 2.04 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.35 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 45 TYR 0.012 0.001 TYR D 83 PHE 0.007 0.001 PHE F 61 TRP 0.003 0.001 TRP N 17 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (14280) covalent geometry : angle 0.61808 / 0.35 (20529) hydrogen bonds : bond 0.05648 / 3.79 ( 783) hydrogen bonds : angle 2.66375 / 1.99 ( 1968) metal coordination : bond 0.00639 / 0.47 ( 16) metal coordination : angle 2.24863 / 1.32 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: G 71 ARG cc_start: 0.7723 (tmm160) cc_final: 0.7490 (tmm160) REVERT: G 91 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6879 (tp30) REVERT: H 85 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8147 (mptt) REVERT: M 77 ASP cc_start: 0.7633 (m-30) cc_final: 0.7367 (m-30) REVERT: M 82 LEU cc_start: 0.8418 (tp) cc_final: 0.8007 (tm) REVERT: M 91 MET cc_start: 0.7127 (mmp) cc_final: 0.6686 (mmm) REVERT: N 93 LYS cc_start: 0.8240 (tttm) cc_final: 0.8019 (ttmm) REVERT: N 106 PHE cc_start: 0.7803 (m-80) cc_final: 0.7525 (m-80) outliers start: 16 outliers final: 8 residues processed: 162 average time/residue: 0.6997 time to fit residues: 120.9775 Evaluate side-chains 161 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 82 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 88 optimal weight: 50.0000 chunk 42 optimal weight: 0.0770 chunk 105 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 95 GLN M 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.187046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136721 restraints weight = 16073.659| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.63 r_work: 0.3055 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14296 Z= 0.133 Angle : 0.592 8.963 20547 Z= 0.339 Chirality : 0.043 0.332 2348 Planarity : 0.005 0.049 1591 Dihedral : 30.673 174.023 4207 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.49 % Allowed : 20.69 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.28), residues: 928 helix: 2.27 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.19 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 45 TYR 0.010 0.001 TYR H 83 PHE 0.006 0.001 PHE B 61 TRP 0.002 0.001 TRP N 17 HIS 0.003 0.001 HIS M 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (14280) covalent geometry : angle 0.58831 / 0.34 (20529) hydrogen bonds : bond 0.05273 / 3.55 ( 783) hydrogen bonds : angle 2.58131 / 1.93 ( 1968) metal coordination : bond 0.00686 / 0.53 ( 16) metal coordination : angle 2.24365 / 1.31 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3779.18 seconds wall clock time: 64 minutes 50.97 seconds (3890.97 seconds total)