Starting phenix.real_space_refine on Thu Mar 5 03:55:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lyb_23591/03_2026/7lyb_23591.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyb_23591/03_2026/7lyb_23591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lyb_23591/03_2026/7lyb_23591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyb_23591/03_2026/7lyb_23591.map" model { file = "/net/cci-nas-00/data/ceres_data/7lyb_23591/03_2026/7lyb_23591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyb_23591/03_2026/7lyb_23591.cif" } resolution = 3.28 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= 0.023 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 5925 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 293 5.49 5 S 42 5.16 5 C 8325 2.51 5 N 2730 2.21 5 O 3305 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14699 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "M" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "P" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1172 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "N" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "C" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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 10581 SG CYS M 24 43.868 68.900 51.864 1.00119.93 S ATOM 10602 SG CYS M 27 44.034 71.422 49.323 1.00122.99 S ATOM 10738 SG CYS M 44 44.128 67.724 48.466 1.00120.03 S ATOM 10764 SG CYS M 47 47.166 69.234 50.677 1.00121.01 S ATOM 10695 SG CYS M 39 49.322 59.427 59.192 1.00105.98 S ATOM 10872 SG CYS M 61 49.091 63.127 60.251 1.00109.94 S ATOM 10893 SG CYS M 64 48.032 60.263 62.662 1.00113.55 S ATOM 12486 SG CYS N 50 39.500 41.325 49.940 1.00121.58 S ATOM 12509 SG CYS N 53 37.412 38.399 51.757 1.00124.96 S ATOM 12646 SG CYS N 71 37.226 41.341 52.330 1.00123.85 S ATOM 12666 SG CYS N 74 40.950 38.797 52.718 1.00122.85 S ATOM 12602 SG CYS N 66 50.300 46.406 49.328 1.00 97.99 S ATOM 12722 SG CYS N 83 49.746 42.722 48.383 1.00 96.27 S ATOM 12742 SG CYS N 86 51.078 45.165 45.752 1.00 92.11 S Time building chain proxies: 3.48, per 1000 atoms: 0.24 Number of scatterers: 14699 At special positions: 0 Unit cell: (127.844, 124.751, 119.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 42 16.00 P 293 15.00 O 3305 8.00 N 2730 7.00 C 8325 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 406.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 44 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 47 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 41 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 61 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 64 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 50 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 53 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 71 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 74 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" ND1 HIS N 68 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 86 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 83 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 66 " Number of angles added : 18 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 63.3% alpha, 4.0% beta 139 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.554A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.803A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.636A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.820A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.829A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.555A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.803A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.580A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.640A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.585A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 22 removed outlier: 3.699A pdb=" N VAL M 11 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN M 19 " --> pdb=" O ILE M 15 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS M 20 " --> pdb=" O ASN M 16 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 Processing helix chain 'M' and resid 79 through 97 removed outlier: 3.686A pdb=" N PHE M 93 " --> pdb=" O ILE M 89 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN M 94 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'P' and resid 86 through 91 Processing helix chain 'P' and resid 98 through 112 Processing helix chain 'P' and resid 120 through 130 removed outlier: 3.707A pdb=" N ALA P 124 " --> pdb=" O VAL P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 147 Processing helix chain 'N' and resid 34 through 46 removed outlier: 3.625A pdb=" N LEU N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 76 Processing helix chain 'N' and resid 98 through 116 removed outlier: 3.695A pdb=" N ILE N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.554A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.548A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.507A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.528A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.936A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.333A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.101A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.375A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'M' and resid 35 through 36 removed outlier: 3.683A pdb=" N GLN M 74 " --> pdb=" O SER M 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'P' and resid 21 through 25 Processing sheet with id=AB5, first strand: chain 'N' and resid 60 through 61 507 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 710 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2054 1.32 - 1.45: 5338 1.45 - 1.57: 7525 1.57 - 1.69: 584 1.69 - 1.81: 58 Bond restraints: 15559 Sorted by residual: bond pdb=" C MET E 90 " pdb=" O MET E 90 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.19e-02 7.06e+03 5.01e+00 bond pdb=" CG ARG H 33 " pdb=" CD ARG H 33 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C MET A 90 " pdb=" O MET A 90 " ideal model delta sigma weight residual 1.237 1.214 0.023 1.19e-02 7.06e+03 3.74e+00 bond pdb=" C6 DG J -36 " pdb=" O6 DG J -36 " ideal model delta sigma weight residual 1.239 1.203 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " ideal model delta sigma weight residual 1.326 1.308 0.018 1.10e-02 8.26e+03 2.63e+00 ... (remaining 15554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 21291 1.62 - 3.24: 885 3.24 - 4.85: 68 4.85 - 6.47: 14 6.47 - 8.09: 13 Bond angle restraints: 22271 Sorted by residual: angle pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " pdb=" NH1 ARG H 33 " ideal model delta sigma weight residual 121.50 118.14 3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" CA ARG A 134 " pdb=" CB ARG A 134 " pdb=" CG ARG A 134 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA ARG E 134 " pdb=" CB ARG E 134 " pdb=" CG ARG E 134 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA ARG H 33 " pdb=" CB ARG H 33 " pdb=" CG ARG H 33 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CB ARG H 33 " pdb=" CG ARG H 33 " pdb=" CD ARG H 33 " ideal model delta sigma weight residual 111.30 103.78 7.52 2.30e+00 1.89e-01 1.07e+01 ... (remaining 22266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.21: 6988 31.21 - 62.42: 1640 62.42 - 93.63: 40 93.63 - 124.84: 0 124.84 - 156.05: 2 Dihedral angle restraints: 8670 sinusoidal: 5482 harmonic: 3188 Sorted by residual: dihedral pdb=" CA CYS M 64 " pdb=" C CYS M 64 " pdb=" N LYS M 65 " pdb=" CA LYS M 65 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 63.95 156.05 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 68.67 151.33 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 8667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1866 0.044 - 0.087: 515 0.087 - 0.131: 129 0.131 - 0.175: 17 0.175 - 0.218: 3 Chirality restraints: 2530 Sorted by residual: chirality pdb=" CG LEU F 62 " pdb=" CB LEU F 62 " pdb=" CD1 LEU F 62 " pdb=" CD2 LEU F 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB THR G 101 " pdb=" CA THR G 101 " pdb=" OG1 THR G 101 " pdb=" CG2 THR G 101 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LYS G 118 " pdb=" N LYS G 118 " pdb=" C LYS G 118 " pdb=" CB LYS G 118 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 2527 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 35 " -0.037 2.00e-02 2.50e+03 3.29e-02 2.44e+01 pdb=" N1 DC I 35 " 0.058 2.00e-02 2.50e+03 pdb=" C2 DC I 35 " 0.020 2.00e-02 2.50e+03 pdb=" O2 DC I 35 " -0.026 2.00e-02 2.50e+03 pdb=" N3 DC I 35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 35 " 0.045 2.00e-02 2.50e+03 pdb=" N4 DC I 35 " -0.040 2.00e-02 2.50e+03 pdb=" C5 DC I 35 " -0.013 2.00e-02 2.50e+03 pdb=" C6 DC I 35 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J -9 " -0.038 2.00e-02 2.50e+03 3.17e-02 2.27e+01 pdb=" N1 DC J -9 " 0.078 2.00e-02 2.50e+03 pdb=" C2 DC J -9 " -0.037 2.00e-02 2.50e+03 pdb=" O2 DC J -9 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DC J -9 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC J -9 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC J -9 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC J -9 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC J -9 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -36 " 0.017 2.00e-02 2.50e+03 2.46e-02 1.82e+01 pdb=" N9 DG J -36 " -0.030 2.00e-02 2.50e+03 pdb=" C8 DG J -36 " 0.022 2.00e-02 2.50e+03 pdb=" N7 DG J -36 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG J -36 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -36 " -0.048 2.00e-02 2.50e+03 pdb=" O6 DG J -36 " 0.039 2.00e-02 2.50e+03 pdb=" N1 DG J -36 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG J -36 " -0.027 2.00e-02 2.50e+03 pdb=" N2 DG J -36 " 0.031 2.00e-02 2.50e+03 pdb=" N3 DG J -36 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG J -36 " -0.000 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 305 2.66 - 3.22: 12744 3.22 - 3.78: 25249 3.78 - 4.34: 34203 4.34 - 4.90: 48971 Nonbonded interactions: 121472 Sorted by model distance: nonbonded pdb=" NH2 ARG H 33 " pdb=" OP1 DA I 50 " model vdw 2.096 3.120 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.122 2.496 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.126 3.040 nonbonded pdb=" O GLU N 59 " pdb=" OG SER N 72 " model vdw 2.134 3.040 nonbonded pdb=" NH1 ARG H 33 " pdb=" O3' DC I 49 " model vdw 2.146 3.120 ... (remaining 121467 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' and resid 23 through 102) selection = (chain 'F' and (resid 23 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 119) } ncs_group { reference = (chain 'D' and resid 31 through 123) 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: 1.150 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.510 Find NCS groups from input model: 0.160 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.006 0.097 15577 Z= 0.258 Angle : 0.820 32.288 22295 Z= 0.442 Chirality : 0.043 0.218 2530 Planarity : 0.005 0.040 1810 Dihedral : 26.071 156.048 6600 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.02 (0.24), residues: 1074 helix: 0.31 (0.19), residues: 651 sheet: -1.28 (0.98), residues: 22 loop : -2.31 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.022 0.002 TYR C 57 PHE 0.027 0.002 PHE C 25 TRP 0.017 0.002 TRP P 141 HIS 0.011 0.002 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00588 (15559) covalent geometry : angle 0.73196 (22271) hydrogen bonds : bond 0.18923 ( 864) hydrogen bonds : angle 5.03219 ( 2192) metal coordination : bond 0.03100 ( 16) metal coordination : angle 12.99331 ( 18) link_TRANS : bond 0.00152 ( 2) link_TRANS : angle 0.85670 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.8392 (mmt-90) cc_final: 0.8186 (mpt90) REVERT: D 90 THR cc_start: 0.8819 (p) cc_final: 0.8280 (p) REVERT: M 14 VAL cc_start: 0.8994 (t) cc_final: 0.8684 (t) REVERT: M 15 ILE cc_start: 0.8663 (pt) cc_final: 0.8315 (pt) REVERT: M 21 ILE cc_start: 0.8810 (mm) cc_final: 0.8471 (mm) REVERT: C 95 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8679 (ttmm) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1883 time to fit residues: 77.6092 Evaluate side-chains 249 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 0.0670 chunk 55 optimal weight: 5.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 64 ASN H 47 GLN H 84 ASN M 12 GLN M 74 GLN N 73 ASN G 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.088899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.054178 restraints weight = 42810.483| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.59 r_work: 0.2648 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15577 Z= 0.156 Angle : 0.622 9.425 22295 Z= 0.354 Chirality : 0.035 0.158 2530 Planarity : 0.004 0.037 1810 Dihedral : 28.594 156.022 4409 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.06 % Allowed : 10.33 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1074 helix: 1.85 (0.20), residues: 675 sheet: 1.01 (1.16), residues: 22 loop : -1.96 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 43 TYR 0.018 0.002 TYR D 40 PHE 0.020 0.001 PHE N 70 TRP 0.008 0.001 TRP P 93 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00323 (15559) covalent geometry : angle 0.60409 (22271) hydrogen bonds : bond 0.05547 ( 864) hydrogen bonds : angle 3.22756 ( 2192) metal coordination : bond 0.00897 ( 16) metal coordination : angle 5.27098 ( 18) link_TRANS : bond 0.00139 ( 2) link_TRANS : angle 0.35885 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 289 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8831 (tt0) cc_final: 0.8405 (tt0) REVERT: D 59 MET cc_start: 0.9182 (tpp) cc_final: 0.8862 (tmm) REVERT: D 105 GLU cc_start: 0.8530 (tp30) cc_final: 0.8311 (mm-30) REVERT: E 120 MET cc_start: 0.7698 (mtt) cc_final: 0.7417 (mtt) REVERT: H 46 LYS cc_start: 0.9414 (mmtt) cc_final: 0.9152 (mmtt) REVERT: M 32 LYS cc_start: 0.8241 (mttt) cc_final: 0.7988 (mtmt) REVERT: M 33 GLU cc_start: 0.9067 (pt0) cc_final: 0.8850 (pm20) REVERT: M 45 LYS cc_start: 0.9411 (tttm) cc_final: 0.9188 (tmmt) REVERT: P 30 MET cc_start: 0.7224 (tpp) cc_final: 0.6814 (mmp) REVERT: P 63 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8310 (tmtt) REVERT: N 96 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8811 (mmmm) REVERT: C 90 ASP cc_start: 0.8680 (t70) cc_final: 0.8234 (t70) REVERT: G 73 ASN cc_start: 0.8539 (m-40) cc_final: 0.8237 (t0) outliers start: 10 outliers final: 6 residues processed: 290 average time/residue: 0.1593 time to fit residues: 62.8601 Evaluate side-chains 254 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 248 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain G residue 36 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 12 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.085517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.050231 restraints weight = 42853.101| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.56 r_work: 0.2535 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15577 Z= 0.229 Angle : 0.625 10.610 22295 Z= 0.354 Chirality : 0.037 0.142 2530 Planarity : 0.004 0.034 1810 Dihedral : 28.819 158.221 4409 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.66 % Allowed : 15.76 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.42 (0.26), residues: 1074 helix: 2.30 (0.20), residues: 677 sheet: 1.64 (1.27), residues: 22 loop : -1.81 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 33 TYR 0.038 0.002 TYR D 83 PHE 0.012 0.001 PHE N 70 TRP 0.007 0.001 TRP P 93 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00521 (15559) covalent geometry : angle 0.60720 (22271) hydrogen bonds : bond 0.06276 ( 864) hydrogen bonds : angle 3.43742 ( 2192) metal coordination : bond 0.01264 ( 16) metal coordination : angle 5.19761 ( 18) link_TRANS : bond 0.00131 ( 2) link_TRANS : angle 0.26114 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8839 (tt0) cc_final: 0.8509 (tt0) REVERT: D 59 MET cc_start: 0.9269 (tpp) cc_final: 0.8950 (mmm) REVERT: D 93 GLU cc_start: 0.9218 (mp0) cc_final: 0.8429 (mp0) REVERT: D 105 GLU cc_start: 0.8882 (tp30) cc_final: 0.8589 (mm-30) REVERT: E 59 GLU cc_start: 0.8502 (pm20) cc_final: 0.8294 (pm20) REVERT: E 120 MET cc_start: 0.8402 (mtt) cc_final: 0.8130 (mtt) REVERT: F 25 ASN cc_start: 0.9192 (m-40) cc_final: 0.8827 (m110) REVERT: H 68 ASP cc_start: 0.9252 (t0) cc_final: 0.9026 (t0) REVERT: M 7 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7705 (mmm160) REVERT: M 10 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8951 (mm-30) REVERT: M 88 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8318 (tmmt) REVERT: N 79 ILE cc_start: 0.8685 (mt) cc_final: 0.8415 (mm) REVERT: N 96 LYS cc_start: 0.9042 (mmmt) cc_final: 0.8772 (mmmm) REVERT: C 90 ASP cc_start: 0.8980 (t70) cc_final: 0.8610 (t70) REVERT: G 73 ASN cc_start: 0.8746 (m-40) cc_final: 0.8406 (t0) outliers start: 25 outliers final: 18 residues processed: 271 average time/residue: 0.1495 time to fit residues: 55.3407 Evaluate side-chains 264 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 246 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 50.0000 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN H 84 ASN ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 HIS ** 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 = 0.3608 r_free = 0.3608 target = 0.086385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.051117 restraints weight = 43089.664| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.54 r_work: 0.2563 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15577 Z= 0.186 Angle : 0.581 8.038 22295 Z= 0.336 Chirality : 0.035 0.144 2530 Planarity : 0.004 0.036 1810 Dihedral : 28.647 160.572 4409 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.02 % Allowed : 17.89 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.27), residues: 1074 helix: 2.52 (0.20), residues: 677 sheet: 1.72 (1.32), residues: 22 loop : -1.66 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.019 0.002 TYR B 88 PHE 0.013 0.001 PHE N 70 TRP 0.009 0.001 TRP P 93 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00415 (15559) covalent geometry : angle 0.56931 (22271) hydrogen bonds : bond 0.05535 ( 864) hydrogen bonds : angle 3.17481 ( 2192) metal coordination : bond 0.00947 ( 16) metal coordination : angle 4.20066 ( 18) link_TRANS : bond 0.00112 ( 2) link_TRANS : angle 0.22208 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 255 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8851 (tt0) cc_final: 0.8478 (tt0) REVERT: B 88 TYR cc_start: 0.9291 (m-10) cc_final: 0.9028 (m-10) REVERT: D 59 MET cc_start: 0.9233 (tpp) cc_final: 0.8902 (mmm) REVERT: D 71 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8893 (tm-30) REVERT: D 105 GLU cc_start: 0.8715 (tp30) cc_final: 0.8408 (mm-30) REVERT: E 59 GLU cc_start: 0.8474 (pm20) cc_final: 0.8231 (pm20) REVERT: F 25 ASN cc_start: 0.9208 (m-40) cc_final: 0.8879 (m110) REVERT: M 7 ARG cc_start: 0.8230 (mmm160) cc_final: 0.7921 (mmm160) REVERT: M 13 ASN cc_start: 0.9000 (m110) cc_final: 0.8712 (m110) REVERT: M 88 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8307 (tmmt) REVERT: M 89 ILE cc_start: 0.7960 (mm) cc_final: 0.7462 (mm) REVERT: N 79 ILE cc_start: 0.8700 (mt) cc_final: 0.8430 (mm) REVERT: N 96 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8759 (mmmm) REVERT: C 90 ASP cc_start: 0.9001 (t70) cc_final: 0.8613 (t70) REVERT: G 73 ASN cc_start: 0.8576 (m-40) cc_final: 0.8279 (t0) outliers start: 19 outliers final: 16 residues processed: 263 average time/residue: 0.1585 time to fit residues: 57.0980 Evaluate side-chains 264 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 248 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 64 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 39 HIS H 84 ASN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.087892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.052810 restraints weight = 43338.321| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.68 r_work: 0.2591 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15577 Z= 0.151 Angle : 0.563 7.569 22295 Z= 0.327 Chirality : 0.034 0.144 2530 Planarity : 0.004 0.037 1810 Dihedral : 28.527 160.802 4409 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.77 % Allowed : 17.04 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.93 (0.27), residues: 1074 helix: 2.65 (0.20), residues: 679 sheet: 1.40 (1.23), residues: 22 loop : -1.50 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 33 TYR 0.019 0.001 TYR F 88 PHE 0.012 0.001 PHE N 70 TRP 0.009 0.001 TRP P 33 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00325 (15559) covalent geometry : angle 0.55283 (22271) hydrogen bonds : bond 0.05060 ( 864) hydrogen bonds : angle 2.98497 ( 2192) metal coordination : bond 0.00881 ( 16) metal coordination : angle 3.72395 ( 18) link_TRANS : bond 0.00056 ( 2) link_TRANS : angle 0.15640 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8751 (tt0) cc_final: 0.8347 (tt0) REVERT: D 68 ASP cc_start: 0.9411 (t70) cc_final: 0.8953 (t0) REVERT: D 71 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8903 (tm-30) REVERT: D 105 GLU cc_start: 0.8621 (tp30) cc_final: 0.8310 (mm-30) REVERT: E 59 GLU cc_start: 0.8266 (pm20) cc_final: 0.8031 (pm20) REVERT: E 77 ASP cc_start: 0.9166 (m-30) cc_final: 0.8925 (t0) REVERT: F 25 ASN cc_start: 0.9221 (m-40) cc_final: 0.8859 (m110) REVERT: H 42 TYR cc_start: 0.8687 (t80) cc_final: 0.8429 (t80) REVERT: M 29 GLU cc_start: 0.8737 (tt0) cc_final: 0.8513 (tt0) REVERT: M 33 GLU cc_start: 0.9164 (pt0) cc_final: 0.8831 (pm20) REVERT: M 45 LYS cc_start: 0.9480 (tttm) cc_final: 0.9266 (ttpt) REVERT: M 88 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8299 (tmmt) REVERT: M 89 ILE cc_start: 0.7937 (mm) cc_final: 0.7396 (mm) REVERT: N 79 ILE cc_start: 0.8591 (mt) cc_final: 0.8361 (mm) REVERT: N 96 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8765 (mmmm) REVERT: N 99 ARG cc_start: 0.9023 (mmp80) cc_final: 0.8819 (mmm160) REVERT: C 90 ASP cc_start: 0.8892 (t70) cc_final: 0.8409 (t70) REVERT: G 100 VAL cc_start: 0.9685 (t) cc_final: 0.9372 (p) outliers start: 26 outliers final: 18 residues processed: 276 average time/residue: 0.1665 time to fit residues: 62.6600 Evaluate side-chains 267 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 249 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 33 TRP Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN P 55 HIS G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.086555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.051160 restraints weight = 43180.876| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.66 r_work: 0.2555 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15577 Z= 0.185 Angle : 0.593 9.365 22295 Z= 0.341 Chirality : 0.035 0.145 2530 Planarity : 0.004 0.036 1810 Dihedral : 28.645 161.299 4409 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.56 % Allowed : 18.85 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.92 (0.27), residues: 1074 helix: 2.66 (0.20), residues: 678 sheet: 1.14 (1.23), residues: 22 loop : -1.49 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.035 0.002 TYR F 88 PHE 0.013 0.001 PHE N 70 TRP 0.008 0.001 TRP P 33 HIS 0.006 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00414 (15559) covalent geometry : angle 0.58371 (22271) hydrogen bonds : bond 0.05424 ( 864) hydrogen bonds : angle 3.08447 ( 2192) metal coordination : bond 0.00901 ( 16) metal coordination : angle 3.70323 ( 18) link_TRANS : bond 0.00104 ( 2) link_TRANS : angle 0.15227 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8931 (tm-30) REVERT: D 105 GLU cc_start: 0.8804 (tp30) cc_final: 0.8483 (mm-30) REVERT: E 59 GLU cc_start: 0.8349 (pm20) cc_final: 0.8038 (pm20) REVERT: E 77 ASP cc_start: 0.9142 (m-30) cc_final: 0.8910 (t0) REVERT: E 120 MET cc_start: 0.8124 (mtt) cc_final: 0.7872 (mtt) REVERT: F 25 ASN cc_start: 0.9215 (m-40) cc_final: 0.8857 (m110) REVERT: M 18 MET cc_start: 0.9231 (mmm) cc_final: 0.8927 (mmt) REVERT: M 29 GLU cc_start: 0.8768 (tt0) cc_final: 0.8535 (tt0) REVERT: M 42 ILE cc_start: 0.8269 (mm) cc_final: 0.8028 (mm) REVERT: M 88 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8272 (tmmt) REVERT: M 89 ILE cc_start: 0.8059 (mm) cc_final: 0.7468 (mm) REVERT: N 62 CYS cc_start: 0.9253 (t) cc_final: 0.8979 (t) REVERT: N 79 ILE cc_start: 0.8645 (mt) cc_final: 0.8418 (mm) REVERT: N 96 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8780 (mmmm) REVERT: C 90 ASP cc_start: 0.8939 (t70) cc_final: 0.8475 (t70) outliers start: 24 outliers final: 21 residues processed: 263 average time/residue: 0.1533 time to fit residues: 54.8762 Evaluate side-chains 263 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 30.0000 chunk 127 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 82 optimal weight: 0.0470 chunk 65 optimal weight: 9.9990 chunk 111 optimal weight: 0.0770 chunk 90 optimal weight: 40.0000 chunk 33 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN M 13 ASN P 55 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.088814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054060 restraints weight = 42925.376| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.67 r_work: 0.2639 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15577 Z= 0.144 Angle : 0.584 11.033 22295 Z= 0.334 Chirality : 0.034 0.178 2530 Planarity : 0.004 0.037 1810 Dihedral : 28.456 161.286 4409 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.56 % Allowed : 20.02 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.96 (0.26), residues: 1074 helix: 2.61 (0.20), residues: 677 sheet: 1.49 (1.16), residues: 21 loop : -1.31 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 112 TYR 0.038 0.002 TYR B 88 PHE 0.015 0.001 PHE N 70 TRP 0.030 0.002 TRP P 33 HIS 0.010 0.001 HIS N 116 Details of bonding type rmsd covalent geometry : bond 0.00306 (15559) covalent geometry : angle 0.57567 (22271) hydrogen bonds : bond 0.04798 ( 864) hydrogen bonds : angle 2.89616 ( 2192) metal coordination : bond 0.00782 ( 16) metal coordination : angle 3.44758 ( 18) link_TRANS : bond 0.00027 ( 2) link_TRANS : angle 0.13470 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 270 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.9446 (t70) cc_final: 0.8990 (t0) REVERT: D 71 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8907 (tm-30) REVERT: D 105 GLU cc_start: 0.8511 (tp30) cc_final: 0.8201 (mm-30) REVERT: E 59 GLU cc_start: 0.8207 (pm20) cc_final: 0.7868 (pm20) REVERT: E 77 ASP cc_start: 0.9149 (m-30) cc_final: 0.8940 (t0) REVERT: F 25 ASN cc_start: 0.9259 (m-40) cc_final: 0.8913 (m110) REVERT: H 42 TYR cc_start: 0.8651 (t80) cc_final: 0.8397 (t80) REVERT: M 18 MET cc_start: 0.9280 (mmm) cc_final: 0.9069 (mmm) REVERT: M 32 LYS cc_start: 0.8117 (mttt) cc_final: 0.7541 (ptpt) REVERT: M 33 GLU cc_start: 0.9141 (pt0) cc_final: 0.8635 (pm20) REVERT: M 45 LYS cc_start: 0.9445 (tttm) cc_final: 0.9205 (ttpt) REVERT: M 88 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8328 (ttpt) REVERT: M 89 ILE cc_start: 0.7988 (mm) cc_final: 0.7543 (mm) REVERT: N 104 MET cc_start: 0.8855 (mmm) cc_final: 0.8511 (mmm) REVERT: C 24 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8511 (mt0) REVERT: C 90 ASP cc_start: 0.8836 (t70) cc_final: 0.8289 (t70) REVERT: G 100 VAL cc_start: 0.9690 (t) cc_final: 0.9398 (p) outliers start: 24 outliers final: 18 residues processed: 282 average time/residue: 0.1484 time to fit residues: 57.1588 Evaluate side-chains 269 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 251 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 58 ARG Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 120 optimal weight: 0.0870 chunk 26 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS N 36 HIS N 55 ASN G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.085041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.049109 restraints weight = 43193.384| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.64 r_work: 0.2501 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15577 Z= 0.266 Angle : 0.662 10.884 22295 Z= 0.372 Chirality : 0.039 0.184 2530 Planarity : 0.004 0.044 1810 Dihedral : 28.913 162.602 4409 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.88 % Allowed : 20.55 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.78 (0.27), residues: 1074 helix: 2.51 (0.20), residues: 677 sheet: 0.85 (1.21), residues: 22 loop : -1.43 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 33 TYR 0.032 0.002 TYR F 88 PHE 0.016 0.001 PHE N 70 TRP 0.014 0.002 TRP P 33 HIS 0.008 0.002 HIS N 116 Details of bonding type rmsd covalent geometry : bond 0.00608 (15559) covalent geometry : angle 0.65037 (22271) hydrogen bonds : bond 0.06207 ( 864) hydrogen bonds : angle 3.35114 ( 2192) metal coordination : bond 0.00872 ( 16) metal coordination : angle 4.35482 ( 18) link_TRANS : bond 0.00203 ( 2) link_TRANS : angle 0.18098 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.8920 (tp30) cc_final: 0.8622 (mm-30) REVERT: E 59 GLU cc_start: 0.8484 (pm20) cc_final: 0.8131 (pm20) REVERT: F 25 ASN cc_start: 0.9189 (m-40) cc_final: 0.8832 (m110) REVERT: M 29 GLU cc_start: 0.8741 (tt0) cc_final: 0.8506 (pt0) REVERT: M 32 LYS cc_start: 0.8184 (mttt) cc_final: 0.7841 (mtmt) REVERT: M 33 GLU cc_start: 0.9243 (pt0) cc_final: 0.8911 (pm20) REVERT: M 45 LYS cc_start: 0.9465 (tttm) cc_final: 0.9226 (ttpt) REVERT: M 88 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8393 (ttpt) REVERT: M 89 ILE cc_start: 0.8076 (mm) cc_final: 0.7603 (mm) REVERT: N 43 ARG cc_start: 0.9235 (mtt-85) cc_final: 0.8986 (mtm-85) REVERT: C 90 ASP cc_start: 0.9026 (t70) cc_final: 0.8611 (t70) REVERT: G 15 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7906 (mtmm) outliers start: 27 outliers final: 20 residues processed: 261 average time/residue: 0.1549 time to fit residues: 54.1613 Evaluate side-chains 258 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 58 ARG Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 114 optimal weight: 0.0970 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 75 HIS ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.086001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.050372 restraints weight = 43009.750| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.64 r_work: 0.2539 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15577 Z= 0.198 Angle : 0.631 13.303 22295 Z= 0.357 Chirality : 0.036 0.200 2530 Planarity : 0.004 0.035 1810 Dihedral : 28.778 163.485 4409 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.13 % Allowed : 21.41 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.74 (0.27), residues: 1074 helix: 2.50 (0.20), residues: 676 sheet: 0.02 (1.20), residues: 24 loop : -1.43 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 99 TYR 0.042 0.002 TYR F 88 PHE 0.017 0.001 PHE N 70 TRP 0.018 0.002 TRP P 33 HIS 0.007 0.001 HIS N 116 Details of bonding type rmsd covalent geometry : bond 0.00447 (15559) covalent geometry : angle 0.62107 (22271) hydrogen bonds : bond 0.05502 ( 864) hydrogen bonds : angle 3.17991 ( 2192) metal coordination : bond 0.00719 ( 16) metal coordination : angle 4.02367 ( 18) link_TRANS : bond 0.00123 ( 2) link_TRANS : angle 0.13918 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9047 (m-30) cc_final: 0.8774 (t0) REVERT: D 105 GLU cc_start: 0.8820 (tp30) cc_final: 0.8517 (mm-30) REVERT: E 59 GLU cc_start: 0.8477 (pm20) cc_final: 0.8253 (pm20) REVERT: E 77 ASP cc_start: 0.9161 (m-30) cc_final: 0.8902 (t0) REVERT: F 25 ASN cc_start: 0.9197 (m-40) cc_final: 0.8863 (m110) REVERT: M 32 LYS cc_start: 0.8198 (mttt) cc_final: 0.7878 (mttt) REVERT: M 33 GLU cc_start: 0.9189 (pt0) cc_final: 0.8804 (pm20) REVERT: M 45 LYS cc_start: 0.9457 (tttm) cc_final: 0.9220 (ttpt) REVERT: M 88 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8398 (ttpt) REVERT: M 89 ILE cc_start: 0.8042 (mm) cc_final: 0.7582 (mm) REVERT: C 90 ASP cc_start: 0.8999 (t70) cc_final: 0.8570 (t70) REVERT: G 15 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7875 (mtmm) outliers start: 20 outliers final: 17 residues processed: 256 average time/residue: 0.1674 time to fit residues: 57.7439 Evaluate side-chains 261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 135 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 = 0.3597 r_free = 0.3597 target = 0.086100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.050404 restraints weight = 42791.886| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.64 r_work: 0.2546 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15577 Z= 0.191 Angle : 0.641 13.422 22295 Z= 0.362 Chirality : 0.036 0.202 2530 Planarity : 0.004 0.036 1810 Dihedral : 28.784 163.894 4409 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.92 % Allowed : 22.47 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.85 (0.27), residues: 1074 helix: 2.55 (0.20), residues: 674 sheet: 0.05 (1.24), residues: 24 loop : -1.29 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 99 TYR 0.019 0.001 TYR B 88 PHE 0.017 0.001 PHE N 70 TRP 0.015 0.002 TRP P 33 HIS 0.006 0.001 HIS N 116 Details of bonding type rmsd covalent geometry : bond 0.00431 (15559) covalent geometry : angle 0.63272 (22271) hydrogen bonds : bond 0.05463 ( 864) hydrogen bonds : angle 3.16813 ( 2192) metal coordination : bond 0.00823 ( 16) metal coordination : angle 3.63705 ( 18) link_TRANS : bond 0.00118 ( 2) link_TRANS : angle 0.15991 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9055 (m-30) cc_final: 0.8525 (t0) REVERT: D 105 GLU cc_start: 0.8786 (tp30) cc_final: 0.8492 (mm-30) REVERT: E 59 GLU cc_start: 0.8441 (pm20) cc_final: 0.8191 (pm20) REVERT: E 77 ASP cc_start: 0.9156 (m-30) cc_final: 0.8905 (t0) REVERT: F 25 ASN cc_start: 0.9188 (m-40) cc_final: 0.8841 (m110) REVERT: F 88 TYR cc_start: 0.8987 (m-80) cc_final: 0.8347 (m-80) REVERT: M 32 LYS cc_start: 0.8229 (mttt) cc_final: 0.7499 (ptpt) REVERT: M 33 GLU cc_start: 0.9200 (pt0) cc_final: 0.8726 (pm20) REVERT: M 45 LYS cc_start: 0.9456 (tttm) cc_final: 0.9210 (ttpt) REVERT: M 88 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8392 (ttpt) REVERT: M 89 ILE cc_start: 0.8027 (mm) cc_final: 0.7556 (mm) REVERT: N 62 CYS cc_start: 0.9284 (t) cc_final: 0.9070 (t) REVERT: C 90 ASP cc_start: 0.9007 (t70) cc_final: 0.8577 (t70) REVERT: G 15 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7885 (mtmm) outliers start: 18 outliers final: 18 residues processed: 254 average time/residue: 0.1588 time to fit residues: 54.4319 Evaluate side-chains 257 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 108 optimal weight: 0.0870 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 135 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 = 0.3636 r_free = 0.3636 target = 0.088245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.053215 restraints weight = 42804.829| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.66 r_work: 0.2621 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15577 Z= 0.151 Angle : 0.619 13.304 22295 Z= 0.352 Chirality : 0.035 0.193 2530 Planarity : 0.004 0.038 1810 Dihedral : 28.585 164.210 4409 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.49 % Allowed : 22.68 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.92 (0.27), residues: 1074 helix: 2.60 (0.20), residues: 672 sheet: 0.26 (1.25), residues: 24 loop : -1.22 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 99 TYR 0.016 0.001 TYR F 88 PHE 0.017 0.001 PHE N 70 TRP 0.010 0.001 TRP P 33 HIS 0.006 0.001 HIS N 116 Details of bonding type rmsd covalent geometry : bond 0.00326 (15559) covalent geometry : angle 0.61172 (22271) hydrogen bonds : bond 0.04948 ( 864) hydrogen bonds : angle 2.99451 ( 2192) metal coordination : bond 0.00866 ( 16) metal coordination : angle 3.36335 ( 18) link_TRANS : bond 0.00028 ( 2) link_TRANS : angle 0.18475 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3928.32 seconds wall clock time: 67 minutes 41.76 seconds (4061.76 seconds total)