Starting phenix.real_space_refine on Sat Jul 4 06:32:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lyb_23591/07_2026/7lyb_23591.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyb_23591/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7lyb_23591/07_2026/7lyb_23591.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lyb_23591/07_2026/7lyb_23591.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lyb_23591/07_2026/7lyb_23591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyb_23591/07_2026/7lyb_23591.map" model { file = "/net/cci-nas-00/data/ceres_data/7lyb_23591/07_2026/7lyb_23591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyb_23591/07_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-6108/lib/python3.11/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: 3.17, per 1000 atoms: 0.22 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: 1.05 Conformation dependent library (CDL) restraints added in 449.1 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: 1.32 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: 2.00 Time building geometry restraints manager: 1.48 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=" C1' DC I 36 " pdb=" N1 DC I 36 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" C6 DG J -36 " pdb=" O6 DG J -36 " ideal model delta sigma weight residual 1.237 1.203 0.034 9.00e-03 1.23e+04 1.43e+01 bond pdb=" C3' DC I 22 " pdb=" C2' DC I 22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG J 62 " pdb=" C2' DG J 62 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC I 33 " pdb=" C2' DC I 33 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.87e+00 ... (remaining 15554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 20642 1.62 - 3.24: 1519 3.24 - 4.85: 83 4.85 - 6.47: 14 6.47 - 8.09: 13 Bond angle restraints: 22271 Sorted by residual: angle pdb=" O4' DC J -26 " pdb=" C4' DC J -26 " pdb=" C3' DC J -26 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" O4 DT J 9 " pdb=" C4 DT J 9 " pdb=" C5 DT J 9 " ideal model delta sigma weight residual 124.90 121.81 3.09 7.00e-01 2.04e+00 1.95e+01 angle pdb=" O4' DG I 9 " pdb=" C4' DG I 9 " pdb=" C3' DG I 9 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT J 33 " pdb=" C4 DT J 33 " pdb=" O4 DT J 33 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+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: 1667 0.044 - 0.087: 638 0.087 - 0.131: 201 0.131 - 0.175: 19 0.175 - 0.218: 5 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: 1.580 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.580 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 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 : 0.007 0.097 15577 Z= 0.553 Angle : 0.929 32.288 22295 Z= 0.702 Chirality : 0.049 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/Z covalent geometry : bond 0.00691 / 0.55 (15559) covalent geometry : angle 0.85285 / 0.70 (22271) hydrogen bonds : bond 0.18923 / 12.73 ( 864) hydrogen bonds : angle 5.03219 / 3.59 ( 2192) metal coordination : bond 0.03100 / 2.22 ( 16) metal coordination : angle 12.99331 / 10.00 ( 18) link_TRANS : bond 0.00152 / 0.07 ( 2) link_TRANS : angle 0.85670 / 0.44 ( 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 : 0.428 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: 0.1500 time to fit residues: 62.4808 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 : 0.414 ------------------------------------------------------------------------------- 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: 30.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 0.0670 chunk 55 optimal weight: 10.0000 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS B 25 ASN D 47 GLN F 27 GLN F 64 ASN H 84 ASN M 12 GLN N 73 ASN G 24 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.087008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.051535 restraints weight = 42579.756| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.59 r_work: 0.2574 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15577 Z= 0.175 Angle : 0.725 14.346 22295 Z= 0.404 Chirality : 0.045 0.233 2530 Planarity : 0.005 0.037 1810 Dihedral : 29.380 159.880 4409 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.28 % Allowed : 10.76 % Favored : 87.97 % 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: 0.46 (0.25), residues: 1074 helix: 1.61 (0.20), residues: 669 sheet: 0.24 (1.08), residues: 22 loop : -2.17 (0.27), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 33 TYR 0.026 0.002 TYR H 83 PHE 0.029 0.002 PHE M 43 TRP 0.011 0.002 TRP P 93 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.18 (15559) covalent geometry : angle 0.68941 / 0.40 (22271) hydrogen bonds : bond 0.07389 / 4.89 ( 864) hydrogen bonds : angle 3.65940 / 2.63 ( 2192) metal coordination : bond 0.00928 / 0.52 ( 16) metal coordination : angle 7.90536 / 5.13 ( 18) link_TRANS : bond 0.00157 / 0.07 ( 2) link_TRANS : angle 0.37541 / 0.17 ( 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 289 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 277 time to evaluate : 0.496 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: B 88 TYR cc_start: 0.9334 (m-10) cc_final: 0.8967 (m-10) REVERT: D 90 THR cc_start: 0.9432 (p) cc_final: 0.9218 (t) REVERT: D 93 GLU cc_start: 0.8861 (mp0) cc_final: 0.8244 (mp0) REVERT: D 105 GLU cc_start: 0.8842 (tp30) cc_final: 0.8601 (mm-30) REVERT: E 120 MET cc_start: 0.8181 (mtt) cc_final: 0.7734 (mtt) REVERT: E 123 ASP cc_start: 0.9293 (m-30) cc_final: 0.8837 (m-30) REVERT: N 96 LYS cc_start: 0.9159 (mmmt) cc_final: 0.8828 (mmmm) REVERT: C 90 ASP cc_start: 0.8701 (t70) cc_final: 0.8336 (t70) REVERT: C 91 GLU cc_start: 0.8783 (tp30) cc_final: 0.8558 (tp30) REVERT: C 95 LYS cc_start: 0.9492 (ttmt) cc_final: 0.9290 (ttmm) outliers start: 12 outliers final: 8 residues processed: 281 average time/residue: 0.1408 time to fit residues: 54.2331 Evaluate side-chains 259 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 251 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain P residue 33 TRP 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 C residue 40 SER 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: 5.9990 chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 54 optimal weight: 30.0000 chunk 104 optimal weight: 7.9990 chunk 107 optimal weight: 0.0070 chunk 5 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN H 84 ASN P 7 ASN G 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.087168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.051652 restraints weight = 43373.632| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.64 r_work: 0.2576 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15577 Z= 0.153 Angle : 0.642 10.673 22295 Z= 0.366 Chirality : 0.042 0.225 2530 Planarity : 0.004 0.037 1810 Dihedral : 29.235 159.031 4409 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.45 % Allowed : 13.74 % Favored : 83.81 % 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: 1.14 (0.26), residues: 1074 helix: 2.08 (0.20), residues: 672 sheet: 1.19 (1.26), residues: 22 loop : -1.85 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 78 TYR 0.034 0.002 TYR H 83 PHE 0.019 0.001 PHE N 70 TRP 0.007 0.001 TRP P 93 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (15559) covalent geometry : angle 0.61992 / 0.37 (22271) hydrogen bonds : bond 0.06554 / 4.27 ( 864) hydrogen bonds : angle 3.40983 / 2.46 ( 2192) metal coordination : bond 0.00893 / 0.57 ( 16) metal coordination : angle 5.91673 / 3.90 ( 18) link_TRANS : bond 0.00102 / 0.05 ( 2) link_TRANS : angle 0.43733 / 0.19 ( 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 294 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9264 (t) REVERT: A 73 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8834 (tt0) REVERT: D 90 THR cc_start: 0.9412 (p) cc_final: 0.9030 (t) REVERT: D 93 GLU cc_start: 0.8956 (mp0) cc_final: 0.8188 (mp0) REVERT: D 105 GLU cc_start: 0.8737 (tp30) cc_final: 0.8503 (mm-30) REVERT: E 73 GLU cc_start: 0.9009 (tt0) cc_final: 0.8647 (tt0) REVERT: E 120 MET cc_start: 0.8147 (mtt) cc_final: 0.7520 (mtt) REVERT: E 123 ASP cc_start: 0.9321 (m-30) cc_final: 0.8913 (m-30) REVERT: F 25 ASN cc_start: 0.9247 (m-40) cc_final: 0.8614 (m110) REVERT: M 13 ASN cc_start: 0.9061 (m110) cc_final: 0.8832 (m110) REVERT: M 32 LYS cc_start: 0.8073 (mttt) cc_final: 0.7581 (mtmt) REVERT: M 33 GLU cc_start: 0.9189 (pt0) cc_final: 0.8894 (pm20) REVERT: M 88 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8470 (ttpt) REVERT: N 59 GLU cc_start: 0.9088 (pm20) cc_final: 0.8259 (pp20) REVERT: N 96 LYS cc_start: 0.9135 (mmmt) cc_final: 0.8831 (mmmm) REVERT: C 90 ASP cc_start: 0.8740 (t70) cc_final: 0.8272 (t70) REVERT: C 91 GLU cc_start: 0.8847 (tp30) cc_final: 0.8578 (tp30) REVERT: C 95 LYS cc_start: 0.9486 (ttmt) cc_final: 0.9266 (ttmm) outliers start: 23 outliers final: 11 residues processed: 282 average time/residue: 0.1260 time to fit residues: 49.2744 Evaluate side-chains 267 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 255 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain P residue 33 TRP 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 C residue 40 SER Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.086591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.051062 restraints weight = 42995.148| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.61 r_work: 0.2569 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15577 Z= 0.163 Angle : 0.631 8.209 22295 Z= 0.360 Chirality : 0.042 0.235 2530 Planarity : 0.004 0.037 1810 Dihedral : 29.216 160.748 4409 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.24 % Allowed : 16.08 % Favored : 81.68 % 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: 1.43 (0.26), residues: 1074 helix: 2.30 (0.20), residues: 675 sheet: 1.18 (1.24), residues: 22 loop : -1.72 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 33 TYR 0.046 0.002 TYR D 83 PHE 0.016 0.001 PHE N 70 TRP 0.007 0.001 TRP P 93 HIS 0.010 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (15559) covalent geometry : angle 0.61582 / 0.36 (22271) hydrogen bonds : bond 0.06269 / 4.07 ( 864) hydrogen bonds : angle 3.35618 / 2.43 ( 2192) metal coordination : bond 0.00984 / 0.54 ( 16) metal coordination : angle 4.82168 / 2.93 ( 18) link_TRANS : bond 0.00078 / 0.04 ( 2) link_TRANS : angle 0.29487 / 0.14 ( 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 281 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 260 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9467 (OUTLIER) cc_final: 0.9235 (t) REVERT: A 73 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8776 (tt0) REVERT: B 88 TYR cc_start: 0.9233 (m-80) cc_final: 0.9002 (m-80) REVERT: D 90 THR cc_start: 0.9399 (p) cc_final: 0.9066 (t) REVERT: D 93 GLU cc_start: 0.9016 (mp0) cc_final: 0.8311 (mp0) REVERT: D 105 GLU cc_start: 0.8716 (tp30) cc_final: 0.8482 (mm-30) REVERT: E 120 MET cc_start: 0.8228 (mtt) cc_final: 0.7602 (mtt) REVERT: E 123 ASP cc_start: 0.9303 (m-30) cc_final: 0.8947 (m-30) REVERT: F 25 ASN cc_start: 0.9227 (m-40) cc_final: 0.8821 (m110) REVERT: M 15 ILE cc_start: 0.8692 (pp) cc_final: 0.8444 (pp) REVERT: M 88 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8361 (ttpp) REVERT: M 89 ILE cc_start: 0.7974 (mm) cc_final: 0.7558 (mm) REVERT: N 96 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8841 (mmmm) REVERT: N 106 GLN cc_start: 0.9278 (mp10) cc_final: 0.8917 (mp10) REVERT: C 90 ASP cc_start: 0.8816 (t70) cc_final: 0.8342 (t70) REVERT: C 91 GLU cc_start: 0.8818 (tp30) cc_final: 0.8562 (tp30) REVERT: C 95 LYS cc_start: 0.9475 (ttmt) cc_final: 0.9252 (ttmm) outliers start: 21 outliers final: 15 residues processed: 265 average time/residue: 0.1280 time to fit residues: 47.1485 Evaluate side-chains 265 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 249 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR 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 H residue 48 VAL Chi-restraints excluded: chain P residue 33 TRP Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 62 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 30.0000 chunk 129 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS P 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.086230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.050949 restraints weight = 43199.587| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.60 r_work: 0.2552 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15577 Z= 0.181 Angle : 0.645 11.150 22295 Z= 0.363 Chirality : 0.042 0.250 2530 Planarity : 0.004 0.036 1810 Dihedral : 29.225 162.028 4409 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.45 % Allowed : 17.15 % Favored : 80.40 % 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: 1.56 (0.26), residues: 1074 helix: 2.39 (0.20), residues: 677 sheet: 0.96 (1.21), residues: 22 loop : -1.66 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.048 0.002 TYR D 83 PHE 0.025 0.002 PHE M 43 TRP 0.007 0.001 TRP N 34 HIS 0.009 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (15559) covalent geometry : angle 0.62663 / 0.36 (22271) hydrogen bonds : bond 0.06305 / 4.10 ( 864) hydrogen bonds : angle 3.34248 / 2.43 ( 2192) metal coordination : bond 0.01122 / 0.61 ( 16) metal coordination : angle 5.39248 / 3.23 ( 18) link_TRANS : bond 0.00126 / 0.07 ( 2) link_TRANS : angle 0.21521 / 0.10 ( 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 278 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9486 (OUTLIER) cc_final: 0.9278 (t) REVERT: A 73 GLU cc_start: 0.9292 (tm-30) cc_final: 0.8876 (tt0) REVERT: D 90 THR cc_start: 0.9374 (p) cc_final: 0.8995 (t) REVERT: D 93 GLU cc_start: 0.9076 (mp0) cc_final: 0.8326 (mp0) REVERT: D 105 GLU cc_start: 0.8781 (tp30) cc_final: 0.8536 (mm-30) REVERT: E 120 MET cc_start: 0.8300 (mtt) cc_final: 0.7980 (mtt) REVERT: F 25 ASN cc_start: 0.9197 (m-40) cc_final: 0.8772 (m110) REVERT: H 71 GLU cc_start: 0.9416 (tp30) cc_final: 0.9163 (tp30) REVERT: M 15 ILE cc_start: 0.8641 (pp) cc_final: 0.8256 (pp) REVERT: M 18 MET cc_start: 0.9249 (mmm) cc_final: 0.8980 (mmt) REVERT: M 42 ILE cc_start: 0.8481 (mp) cc_final: 0.7889 (mm) REVERT: M 88 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8314 (ttpp) REVERT: M 89 ILE cc_start: 0.7952 (mm) cc_final: 0.7471 (mm) REVERT: N 34 TRP cc_start: 0.7614 (OUTLIER) cc_final: 0.7169 (t-100) REVERT: N 79 ILE cc_start: 0.8778 (mt) cc_final: 0.8494 (mm) REVERT: N 96 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8805 (mmmm) REVERT: C 90 ASP cc_start: 0.8944 (t70) cc_final: 0.8500 (t70) REVERT: C 91 GLU cc_start: 0.8850 (tp30) cc_final: 0.8574 (tp30) REVERT: C 95 LYS cc_start: 0.9477 (ttmt) cc_final: 0.9237 (ttmm) outliers start: 23 outliers final: 17 residues processed: 262 average time/residue: 0.1219 time to fit residues: 43.8803 Evaluate side-chains 267 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 248 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 124 ILE 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 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain P residue 33 TRP Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 34 TRP Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 40 SER 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: 3.9990 chunk 55 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.086572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.051329 restraints weight = 43247.665| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.61 r_work: 0.2571 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15577 Z= 0.154 Angle : 0.611 9.008 22295 Z= 0.352 Chirality : 0.041 0.245 2530 Planarity : 0.004 0.036 1810 Dihedral : 29.160 162.979 4409 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.92 % Allowed : 18.10 % Favored : 79.98 % 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: 1.62 (0.26), residues: 1074 helix: 2.43 (0.20), residues: 678 sheet: 0.86 (1.20), residues: 22 loop : -1.61 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.037 0.002 TYR B 88 PHE 0.013 0.001 PHE N 70 TRP 0.008 0.001 TRP P 93 HIS 0.007 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (15559) covalent geometry : angle 0.60086 / 0.35 (22271) hydrogen bonds : bond 0.06014 / 3.90 ( 864) hydrogen bonds : angle 3.24075 / 2.35 ( 2192) metal coordination : bond 0.00964 / 0.54 ( 16) metal coordination : angle 3.90641 / 2.35 ( 18) link_TRANS : bond 0.00065 / 0.03 ( 2) link_TRANS : angle 0.23038 / 0.11 ( 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 277 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 0.428 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 58 THR cc_start: 0.9447 (OUTLIER) cc_final: 0.9242 (t) REVERT: A 73 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8882 (tt0) REVERT: D 90 THR cc_start: 0.9363 (p) cc_final: 0.9025 (t) REVERT: D 93 GLU cc_start: 0.9076 (mp0) cc_final: 0.8335 (mp0) REVERT: D 105 GLU cc_start: 0.8733 (tp30) cc_final: 0.8475 (mm-30) REVERT: F 25 ASN cc_start: 0.9227 (m-40) cc_final: 0.8823 (m110) REVERT: H 71 GLU cc_start: 0.9436 (tp30) cc_final: 0.9054 (tp30) REVERT: H 83 TYR cc_start: 0.8023 (m-80) cc_final: 0.7696 (m-80) REVERT: M 42 ILE cc_start: 0.8520 (mp) cc_final: 0.7917 (mm) REVERT: M 88 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8421 (ttpp) REVERT: M 89 ILE cc_start: 0.7906 (mm) cc_final: 0.7643 (mm) REVERT: N 79 ILE cc_start: 0.8771 (mt) cc_final: 0.8499 (mm) REVERT: N 96 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8810 (mmmm) REVERT: C 90 ASP cc_start: 0.8961 (t70) cc_final: 0.8497 (t70) REVERT: C 91 GLU cc_start: 0.8842 (tp30) cc_final: 0.8560 (tp30) REVERT: C 95 LYS cc_start: 0.9463 (ttmt) cc_final: 0.9212 (ttmm) REVERT: G 73 ASN cc_start: 0.8869 (m-40) cc_final: 0.8216 (t0) outliers start: 18 outliers final: 13 residues processed: 266 average time/residue: 0.1303 time to fit residues: 48.0352 Evaluate side-chains 264 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 250 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 124 ILE 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 M residue 47 CYS Chi-restraints excluded: chain P residue 33 TRP 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 C residue 79 ILE 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: 9.9990 chunk 127 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 111 optimal weight: 0.0870 chunk 90 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.087020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.051972 restraints weight = 42794.542| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.56 r_work: 0.2592 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15577 Z= 0.143 Angle : 0.608 10.541 22295 Z= 0.353 Chirality : 0.041 0.245 2530 Planarity : 0.004 0.037 1810 Dihedral : 29.117 163.650 4409 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.13 % Allowed : 18.85 % Favored : 79.02 % 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 (0.26), residues: 1074 helix: 2.50 (0.20), residues: 674 sheet: 0.90 (1.20), residues: 22 loop : -1.52 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.060 0.002 TYR B 88 PHE 0.014 0.001 PHE N 70 TRP 0.008 0.001 TRP P 93 HIS 0.007 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (15559) covalent geometry : angle 0.59782 / 0.35 (22271) hydrogen bonds : bond 0.05810 / 3.77 ( 864) hydrogen bonds : angle 3.17015 / 2.31 ( 2192) metal coordination : bond 0.00885 / 0.57 ( 16) metal coordination : angle 3.91800 / 2.21 ( 18) link_TRANS : bond 0.00049 / 0.03 ( 2) link_TRANS : angle 0.20926 / 0.10 ( 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 281 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 261 time to evaluate : 0.256 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: 0.9303 (tm-30) cc_final: 0.8909 (tt0) REVERT: D 105 GLU cc_start: 0.8660 (tp30) cc_final: 0.8393 (mm-30) REVERT: F 25 ASN cc_start: 0.9226 (m-40) cc_final: 0.8825 (m110) REVERT: H 33 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6330 (tpt170) REVERT: H 105 GLU cc_start: 0.8806 (tp30) cc_final: 0.8574 (tp30) REVERT: M 33 GLU cc_start: 0.8872 (pm20) cc_final: 0.8657 (pm20) REVERT: M 42 ILE cc_start: 0.8553 (mp) cc_final: 0.7856 (mm) REVERT: M 88 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8366 (ttpp) REVERT: M 89 ILE cc_start: 0.7902 (mm) cc_final: 0.7355 (mm) REVERT: N 79 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8519 (mm) REVERT: N 96 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8824 (mmmm) REVERT: N 100 GLN cc_start: 0.8210 (tm-30) cc_final: 0.8002 (tm-30) REVERT: N 104 MET cc_start: 0.8818 (mmm) cc_final: 0.8520 (mmm) REVERT: C 90 ASP cc_start: 0.8956 (t70) cc_final: 0.8483 (t70) REVERT: C 91 GLU cc_start: 0.8854 (tp30) cc_final: 0.8639 (tp30) REVERT: C 95 LYS cc_start: 0.9456 (ttmt) cc_final: 0.9242 (ttmm) REVERT: G 73 ASN cc_start: 0.8820 (m-40) cc_final: 0.8218 (t0) outliers start: 20 outliers final: 16 residues processed: 271 average time/residue: 0.1302 time to fit residues: 48.7905 Evaluate side-chains 265 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 124 ILE 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 H residue 33 ARG Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain P residue 33 TRP Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain G residue 62 ILE 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: 5.9990 chunk 31 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN N 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.085466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.050259 restraints weight = 42935.112| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.53 r_work: 0.2542 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15577 Z= 0.221 Angle : 0.669 10.128 22295 Z= 0.377 Chirality : 0.043 0.273 2530 Planarity : 0.004 0.036 1810 Dihedral : 29.255 165.129 4409 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.88 % Allowed : 19.38 % Favored : 77.74 % 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: 1.62 (0.27), residues: 1074 helix: 2.44 (0.20), residues: 677 sheet: 0.76 (1.20), residues: 22 loop : -1.60 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 33 TYR 0.079 0.003 TYR B 88 PHE 0.015 0.001 PHE N 70 TRP 0.006 0.001 TRP P 93 HIS 0.006 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (15559) covalent geometry : angle 0.66177 / 0.38 (22271) hydrogen bonds : bond 0.06353 / 4.13 ( 864) hydrogen bonds : angle 3.41872 / 2.49 ( 2192) metal coordination : bond 0.01072 / 0.55 ( 16) metal coordination : angle 3.46040 / 2.02 ( 18) link_TRANS : bond 0.00207 / 0.11 ( 2) link_TRANS : angle 0.26457 / 0.13 ( 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 269 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9359 (tm-30) cc_final: 0.8903 (tt0) REVERT: D 79 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8643 (mtm180) REVERT: D 105 GLU cc_start: 0.8811 (tp30) cc_final: 0.8550 (mm-30) REVERT: F 25 ASN cc_start: 0.9228 (m-40) cc_final: 0.8827 (m110) REVERT: H 83 TYR cc_start: 0.7832 (m-80) cc_final: 0.7513 (m-80) REVERT: H 105 GLU cc_start: 0.8928 (tp30) cc_final: 0.8702 (tp30) REVERT: M 29 GLU cc_start: 0.8786 (tt0) cc_final: 0.8553 (tt0) REVERT: M 88 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8299 (ttpp) REVERT: M 89 ILE cc_start: 0.7965 (mm) cc_final: 0.7363 (mm) REVERT: N 62 CYS cc_start: 0.9180 (t) cc_final: 0.8911 (t) REVERT: N 79 ILE cc_start: 0.8749 (mt) cc_final: 0.8479 (mm) REVERT: C 24 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8376 (mt0) REVERT: C 90 ASP cc_start: 0.8974 (t70) cc_final: 0.8547 (t70) REVERT: C 91 GLU cc_start: 0.8935 (tp30) cc_final: 0.8627 (tp30) REVERT: C 95 LYS cc_start: 0.9481 (ttmt) cc_final: 0.9224 (ttmm) REVERT: G 73 ASN cc_start: 0.8902 (m-40) cc_final: 0.8276 (t0) outliers start: 27 outliers final: 19 residues processed: 254 average time/residue: 0.1320 time to fit residues: 45.9362 Evaluate side-chains 253 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 79 ARG 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 98 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain P residue 33 TRP 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 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: 0.7980 chunk 63 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN H 84 ASN P 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.085959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.050662 restraints weight = 43029.921| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.54 r_work: 0.2557 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2972 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= 0.171 Angle : 0.640 9.205 22295 Z= 0.367 Chirality : 0.042 0.258 2530 Planarity : 0.004 0.035 1810 Dihedral : 29.229 165.637 4409 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.56 % Allowed : 20.13 % Favored : 77.32 % 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: 1.66 (0.27), residues: 1074 helix: 2.46 (0.20), residues: 677 sheet: 0.68 (1.19), residues: 22 loop : -1.56 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.070 0.002 TYR B 88 PHE 0.015 0.001 PHE N 70 TRP 0.008 0.001 TRP P 93 HIS 0.006 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (15559) covalent geometry : angle 0.63339 / 0.37 (22271) hydrogen bonds : bond 0.06058 / 3.94 ( 864) hydrogen bonds : angle 3.28808 / 2.39 ( 2192) metal coordination : bond 0.00835 / 0.49 ( 16) metal coordination : angle 3.38605 / 1.98 ( 18) link_TRANS : bond 0.00104 / 0.05 ( 2) link_TRANS : angle 0.18682 / 0.08 ( 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 271 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9362 (tm-30) cc_final: 0.8937 (tt0) REVERT: D 105 GLU cc_start: 0.8756 (tp30) cc_final: 0.8495 (mm-30) REVERT: F 25 ASN cc_start: 0.9221 (m-40) cc_final: 0.8814 (m110) REVERT: H 105 GLU cc_start: 0.8887 (tp30) cc_final: 0.8666 (tp30) REVERT: M 29 GLU cc_start: 0.8796 (tt0) cc_final: 0.8543 (tt0) REVERT: M 65 LYS cc_start: 0.8663 (ptmm) cc_final: 0.8417 (pptt) REVERT: M 88 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8287 (tmmt) REVERT: M 89 ILE cc_start: 0.7972 (mm) cc_final: 0.7199 (mm) REVERT: N 62 CYS cc_start: 0.9193 (t) cc_final: 0.8939 (t) REVERT: N 79 ILE cc_start: 0.8741 (mt) cc_final: 0.8482 (mm) REVERT: C 90 ASP cc_start: 0.9000 (t70) cc_final: 0.8588 (t70) REVERT: C 91 GLU cc_start: 0.8900 (tp30) cc_final: 0.8673 (tp30) REVERT: C 95 LYS cc_start: 0.9471 (ttmt) cc_final: 0.9245 (ttmm) REVERT: G 73 ASN cc_start: 0.8868 (m-40) cc_final: 0.8322 (t0) outliers start: 24 outliers final: 20 residues processed: 257 average time/residue: 0.1463 time to fit residues: 51.8625 Evaluate side-chains 260 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN 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 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain P residue 21 CYS 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 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: 10.0000 chunk 68 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 53 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 126 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN H 84 ASN ** 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 = 0.3620 r_free = 0.3620 target = 0.086891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.051883 restraints weight = 43201.023| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.55 r_work: 0.2589 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15577 Z= 0.146 Angle : 0.635 11.889 22295 Z= 0.367 Chirality : 0.041 0.250 2530 Planarity : 0.004 0.038 1810 Dihedral : 29.159 165.984 4409 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.24 % Allowed : 20.98 % Favored : 76.78 % 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: 2.52 (0.20), residues: 673 sheet: 0.96 (1.14), residues: 21 loop : -1.41 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 52 TYR 0.062 0.002 TYR B 88 PHE 0.016 0.001 PHE N 70 TRP 0.049 0.004 TRP P 33 HIS 0.006 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (15559) covalent geometry : angle 0.62571 / 0.37 (22271) hydrogen bonds : bond 0.05766 / 3.75 ( 864) hydrogen bonds : angle 3.25811 / 2.37 ( 2192) metal coordination : bond 0.00846 / 0.56 ( 16) metal coordination : angle 3.95246 / 2.20 ( 18) link_TRANS : bond 0.00041 / 0.02 ( 2) link_TRANS : angle 0.16129 / 0.08 ( 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 271 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.468 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: 0.9365 (tm-30) cc_final: 0.8961 (tt0) REVERT: D 59 MET cc_start: 0.9254 (tpp) cc_final: 0.8805 (tmm) REVERT: D 105 GLU cc_start: 0.8679 (tp30) cc_final: 0.8417 (mm-30) REVERT: F 25 ASN cc_start: 0.9218 (m-40) cc_final: 0.8829 (m110) REVERT: H 105 GLU cc_start: 0.8820 (tp30) cc_final: 0.8592 (tp30) REVERT: M 29 GLU cc_start: 0.8816 (tt0) cc_final: 0.8560 (tt0) REVERT: M 65 LYS cc_start: 0.8646 (ptmm) cc_final: 0.8381 (pptt) REVERT: M 88 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8266 (tmmt) REVERT: M 89 ILE cc_start: 0.7959 (mm) cc_final: 0.7164 (mm) REVERT: N 62 CYS cc_start: 0.9187 (t) cc_final: 0.8946 (t) REVERT: N 79 ILE cc_start: 0.8720 (mt) cc_final: 0.8469 (mm) REVERT: N 96 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8813 (mmmm) REVERT: C 90 ASP cc_start: 0.8966 (t70) cc_final: 0.8525 (t70) REVERT: C 91 GLU cc_start: 0.8889 (tp30) cc_final: 0.8646 (tp30) REVERT: C 95 LYS cc_start: 0.9464 (ttmt) cc_final: 0.9233 (ttmm) REVERT: G 73 ASN cc_start: 0.8819 (m-40) cc_final: 0.8325 (t0) outliers start: 21 outliers final: 17 residues processed: 259 average time/residue: 0.1427 time to fit residues: 51.0631 Evaluate side-chains 260 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN 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 77 LYS Chi-restraints excluded: chain B residue 96 THR 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 47 CYS Chi-restraints excluded: chain P residue 21 CYS 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 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: 3.9990 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 109 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 93 GLN ** 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 = 0.3621 r_free = 0.3621 target = 0.086849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.051866 restraints weight = 42972.859| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.56 r_work: 0.2593 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3201 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= 0.148 Angle : 0.628 10.383 22295 Z= 0.365 Chirality : 0.041 0.255 2530 Planarity : 0.004 0.036 1810 Dihedral : 29.164 166.409 4409 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.92 % Allowed : 20.87 % Favored : 77.21 % 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: 1.77 (0.26), residues: 1074 helix: 2.50 (0.20), residues: 673 sheet: 0.96 (1.12), residues: 21 loop : -1.40 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 52 TYR 0.060 0.002 TYR B 88 PHE 0.017 0.001 PHE N 70 TRP 0.028 0.002 TRP P 33 HIS 0.006 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (15559) covalent geometry : angle 0.62158 / 0.36 (22271) hydrogen bonds : bond 0.05744 / 3.73 ( 864) hydrogen bonds : angle 3.26949 / 2.38 ( 2192) metal coordination : bond 0.00943 / 0.64 ( 16) metal coordination : angle 3.34886 / 1.92 ( 18) link_TRANS : bond 0.00069 / 0.04 ( 2) link_TRANS : angle 0.15733 / 0.08 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.29 seconds wall clock time: 58 minutes 35.38 seconds (3515.38 seconds total)