Starting phenix.real_space_refine on Sat Sep 12 22:50:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lyb_23591/09_2026/7lyb_23591.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyb_23591/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lyb_23591/09_2026/7lyb_23591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyb_23591/09_2026/7lyb_23591.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lyb_23591/09_2026/7lyb_23591.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lyb_23591/09_2026/7lyb_23591.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lyb_23591/09_2026/7lyb_23591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyb_23591/09_2026/7lyb_23591.map" } 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-2.2.1-6174/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: 3.07, per 1000 atoms: 0.21 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: 1.21 Conformation dependent library (CDL) restraints added in 446.4 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: 2.01 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: 2.52 Time building geometry restraints manager: 1.65 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: 20599 1.62 - 3.24: 1560 3.24 - 4.85: 85 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.880 ------------------------------------------------------------------------------- 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 : 0.935 32.288 22295 Z= 0.708 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 0.85933 / 0.71 (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: 0.1801 time to fit residues: 75.1412 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 : 0.353 ------------------------------------------------------------------------------- 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: 20.0000 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 = 0.3620 r_free = 0.3620 target = 0.087354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.052203 restraints weight = 42791.607| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.59 r_work: 0.2584 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15577 Z= 0.174 Angle : 0.743 14.029 22295 Z= 0.411 Chirality : 0.045 0.231 2530 Planarity : 0.005 0.046 1810 Dihedral : 29.278 158.485 4409 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.49 % Allowed : 10.97 % Favored : 87.54 % 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: 0.40 (0.25), residues: 1074 helix: 1.54 (0.20), residues: 669 sheet: 0.30 (1.07), residues: 22 loop : -2.14 (0.27), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 33 TYR 0.024 0.002 TYR H 83 PHE 0.030 0.002 PHE M 43 TRP 0.011 0.001 TRP P 93 HIS 0.013 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (15559) covalent geometry : angle 0.71170 / 0.41 (22271) hydrogen bonds : bond 0.07285 / 4.83 ( 864) hydrogen bonds : angle 3.63225 / 2.61 ( 2192) metal coordination : bond 0.00917 / 0.51 ( 16) metal coordination : angle 7.58318 / 4.69 ( 18) link_TRANS : bond 0.00239 / 0.11 ( 2) link_TRANS : angle 0.39238 / 0.18 ( 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 292 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 278 time to evaluate : 0.433 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 120 MET cc_start: 0.8613 (mtm) cc_final: 0.8413 (mtt) REVERT: B 88 TYR cc_start: 0.9318 (m-10) cc_final: 0.8935 (m-10) REVERT: D 90 THR cc_start: 0.9429 (p) cc_final: 0.9223 (t) REVERT: D 93 GLU cc_start: 0.8908 (mp0) cc_final: 0.8281 (mp0) REVERT: E 120 MET cc_start: 0.8134 (mtt) cc_final: 0.7711 (mtt) REVERT: E 123 ASP cc_start: 0.9273 (m-30) cc_final: 0.8808 (m-30) REVERT: M 14 VAL cc_start: 0.9218 (t) cc_final: 0.8641 (t) REVERT: M 15 ILE cc_start: 0.8683 (pt) cc_final: 0.8364 (pt) REVERT: N 96 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8825 (mmmm) REVERT: C 90 ASP cc_start: 0.8702 (t70) cc_final: 0.8333 (t70) REVERT: C 91 GLU cc_start: 0.8793 (tp30) cc_final: 0.8565 (tp30) outliers start: 14 outliers final: 9 residues processed: 284 average time/residue: 0.1512 time to fit residues: 59.2992 Evaluate side-chains 258 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 249 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 82 LEU 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: 5.9990 chunk 113 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN H 84 ASN G 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.085483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.049496 restraints weight = 43322.538| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.63 r_work: 0.2522 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15577 Z= 0.220 Angle : 0.705 11.073 22295 Z= 0.388 Chirality : 0.045 0.263 2530 Planarity : 0.004 0.035 1810 Dihedral : 29.287 158.869 4409 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.34 % Allowed : 14.91 % Favored : 82.75 % 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: 1.00 (0.26), residues: 1074 helix: 2.03 (0.20), residues: 670 sheet: 1.11 (1.23), residues: 22 loop : -2.00 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 52 TYR 0.036 0.002 TYR H 83 PHE 0.019 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 0.00459 / 0.22 (15559) covalent geometry : angle 0.68018 / 0.39 (22271) hydrogen bonds : bond 0.07127 / 4.67 ( 864) hydrogen bonds : angle 3.64327 / 2.63 ( 2192) metal coordination : bond 0.00941 / 0.51 ( 16) metal coordination : angle 6.54380 / 4.24 ( 18) link_TRANS : bond 0.00147 / 0.08 ( 2) link_TRANS : angle 0.33871 / 0.17 ( 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 278 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8858 (tt0) REVERT: B 88 TYR cc_start: 0.9281 (m-10) cc_final: 0.8970 (m-80) REVERT: D 83 TYR cc_start: 0.8682 (m-10) cc_final: 0.8175 (m-80) REVERT: D 90 THR cc_start: 0.9404 (p) cc_final: 0.9061 (t) REVERT: D 93 GLU cc_start: 0.8997 (mp0) cc_final: 0.8275 (mp0) REVERT: F 25 ASN cc_start: 0.9211 (m-40) cc_final: 0.8860 (m-40) REVERT: M 14 VAL cc_start: 0.9197 (t) cc_final: 0.8883 (t) REVERT: M 18 MET cc_start: 0.9392 (mmt) cc_final: 0.9111 (mmt) REVERT: N 79 ILE cc_start: 0.8585 (mt) cc_final: 0.8316 (mm) REVERT: N 96 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8825 (mmmm) REVERT: C 90 ASP cc_start: 0.8868 (t70) cc_final: 0.8469 (t70) outliers start: 22 outliers final: 18 residues processed: 266 average time/residue: 0.1565 time to fit residues: 57.1477 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 : 0.429 ------------------------------------------------------------------------------- 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 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 73 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain M residue 40 ASP 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 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 117 optimal weight: 0.0070 chunk 77 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN P 7 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 = 0.3602 r_free = 0.3602 target = 0.086066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.050688 restraints weight = 43044.865| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.59 r_work: 0.2546 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2300 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= 0.167 Angle : 0.653 8.436 22295 Z= 0.368 Chirality : 0.043 0.255 2530 Planarity : 0.004 0.036 1810 Dihedral : 29.199 160.441 4409 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.45 % Allowed : 15.55 % Favored : 82.00 % 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: 1.33 (0.26), residues: 1074 helix: 2.26 (0.20), residues: 672 sheet: 1.13 (1.23), residues: 22 loop : -1.81 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG N 43 TYR 0.034 0.002 TYR H 83 PHE 0.014 0.001 PHE N 70 TRP 0.007 0.001 TRP P 93 HIS 0.008 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (15559) covalent geometry : angle 0.63655 / 0.37 (22271) hydrogen bonds : bond 0.06471 / 4.22 ( 864) hydrogen bonds : angle 3.43473 / 2.49 ( 2192) metal coordination : bond 0.01049 / 0.59 ( 16) metal coordination : angle 5.12260 / 3.20 ( 18) link_TRANS : bond 0.00078 / 0.04 ( 2) link_TRANS : angle 0.31186 / 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 287 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9501 (OUTLIER) cc_final: 0.9270 (t) REVERT: A 73 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8802 (tt0) REVERT: B 88 TYR cc_start: 0.9291 (m-10) cc_final: 0.8989 (m-80) REVERT: D 83 TYR cc_start: 0.8724 (m-10) cc_final: 0.8322 (m-80) REVERT: D 90 THR cc_start: 0.9395 (p) cc_final: 0.8969 (t) REVERT: D 93 GLU cc_start: 0.9034 (mp0) cc_final: 0.8240 (mp0) REVERT: F 25 ASN cc_start: 0.9217 (m-40) cc_final: 0.8897 (m-40) REVERT: M 88 LYS cc_start: 0.8578 (mttm) cc_final: 0.8166 (tmmt) REVERT: M 89 ILE cc_start: 0.7997 (mm) cc_final: 0.7472 (mm) REVERT: N 41 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8312 (mp) REVERT: N 79 ILE cc_start: 0.8575 (mt) cc_final: 0.8310 (mm) REVERT: N 96 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8837 (mmmm) REVERT: N 106 GLN cc_start: 0.9299 (mp10) cc_final: 0.9016 (mp10) REVERT: C 90 ASP cc_start: 0.8900 (t70) cc_final: 0.8486 (t70) outliers start: 23 outliers final: 16 residues processed: 273 average time/residue: 0.1527 time to fit residues: 57.3559 Evaluate side-chains 268 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 H residue 48 VAL Chi-restraints excluded: chain M residue 21 ILE 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 94 ASP Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU 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: 20.0000 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 30.0000 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS ** 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 = 0.3618 r_free = 0.3618 target = 0.086736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.051157 restraints weight = 43202.565| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.63 r_work: 0.2565 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2515 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= 0.150 Angle : 0.640 11.378 22295 Z= 0.361 Chirality : 0.042 0.261 2530 Planarity : 0.004 0.037 1810 Dihedral : 29.108 161.375 4409 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.56 % Allowed : 16.29 % Favored : 81.15 % 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: 1.59 (0.26), residues: 1074 helix: 2.44 (0.20), residues: 673 sheet: 1.39 (1.17), residues: 21 loop : -1.67 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 52 TYR 0.034 0.001 TYR H 83 PHE 0.017 0.001 PHE M 43 TRP 0.008 0.001 TRP P 93 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (15559) covalent geometry : angle 0.61917 / 0.36 (22271) hydrogen bonds : bond 0.06120 / 3.97 ( 864) hydrogen bonds : angle 3.26720 / 2.38 ( 2192) metal coordination : bond 0.01105 / 0.63 ( 16) metal coordination : angle 5.77270 / 3.17 ( 18) link_TRANS : bond 0.00063 / 0.03 ( 2) link_TRANS : angle 0.27672 / 0.12 ( 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 279 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9489 (p) cc_final: 0.9264 (t) REVERT: A 73 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8857 (tt0) REVERT: B 88 TYR cc_start: 0.9346 (m-10) cc_final: 0.8907 (m-80) REVERT: D 83 TYR cc_start: 0.8709 (m-10) cc_final: 0.8277 (m-80) REVERT: D 90 THR cc_start: 0.9359 (p) cc_final: 0.8984 (t) REVERT: D 93 GLU cc_start: 0.9037 (mp0) cc_final: 0.8294 (mp0) REVERT: F 25 ASN cc_start: 0.9216 (m-40) cc_final: 0.8840 (m110) REVERT: M 42 ILE cc_start: 0.8595 (mp) cc_final: 0.8097 (mm) REVERT: M 88 LYS cc_start: 0.8562 (mttm) cc_final: 0.8158 (tmmt) REVERT: M 89 ILE cc_start: 0.8073 (mm) cc_final: 0.7518 (mm) REVERT: N 45 GLU cc_start: 0.9361 (OUTLIER) cc_final: 0.8981 (tp30) REVERT: N 96 LYS cc_start: 0.9109 (mmmt) cc_final: 0.8846 (mmmm) REVERT: C 90 ASP cc_start: 0.8900 (t70) cc_final: 0.8442 (t70) outliers start: 24 outliers final: 17 residues processed: 262 average time/residue: 0.1532 time to fit residues: 55.4820 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 : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 M residue 21 ILE Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 95 LYS 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: 20.0000 chunk 55 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 7 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 = 0.3593 r_free = 0.3593 target = 0.085559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.050380 restraints weight = 42864.862| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.57 r_work: 0.2539 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15577 Z= 0.198 Angle : 0.663 12.588 22295 Z= 0.370 Chirality : 0.043 0.282 2530 Planarity : 0.004 0.036 1810 Dihedral : 29.164 162.943 4409 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.45 % Allowed : 18.00 % Favored : 79.55 % 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: 1.59 (0.26), residues: 1074 helix: 2.46 (0.20), residues: 676 sheet: 1.18 (1.15), residues: 21 loop : -1.73 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 33 TYR 0.018 0.002 TYR D 83 PHE 0.013 0.002 PHE N 70 TRP 0.007 0.001 TRP P 93 HIS 0.007 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.20 (15559) covalent geometry : angle 0.64958 / 0.37 (22271) hydrogen bonds : bond 0.06386 / 4.16 ( 864) hydrogen bonds : angle 3.37030 / 2.45 ( 2192) metal coordination : bond 0.01089 / 0.57 ( 16) metal coordination : angle 4.76066 / 2.66 ( 18) link_TRANS : bond 0.00165 / 0.08 ( 2) link_TRANS : angle 0.23807 / 0.12 ( 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 268 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9506 (OUTLIER) cc_final: 0.9276 (t) REVERT: A 73 GLU cc_start: 0.9289 (tm-30) cc_final: 0.8852 (tt0) REVERT: B 88 TYR cc_start: 0.9398 (m-10) cc_final: 0.8908 (m-80) REVERT: D 83 TYR cc_start: 0.8759 (m-10) cc_final: 0.8336 (m-10) REVERT: D 90 THR cc_start: 0.9338 (p) cc_final: 0.8914 (t) REVERT: D 93 GLU cc_start: 0.9089 (mp0) cc_final: 0.8310 (mp0) REVERT: F 25 ASN cc_start: 0.9221 (m-40) cc_final: 0.8849 (m110) REVERT: H 33 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6738 (tpt170) REVERT: M 42 ILE cc_start: 0.8649 (mp) cc_final: 0.8093 (mm) REVERT: M 88 LYS cc_start: 0.8549 (mttm) cc_final: 0.8125 (tmmt) REVERT: M 89 ILE cc_start: 0.7990 (mm) cc_final: 0.7416 (mm) REVERT: N 34 TRP cc_start: 0.7608 (OUTLIER) cc_final: 0.7058 (t-100) REVERT: N 45 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8475 (mm-30) REVERT: N 58 ARG cc_start: 0.7411 (pmt170) cc_final: 0.7088 (pmt170) REVERT: N 59 GLU cc_start: 0.8880 (pm20) cc_final: 0.6781 (pm20) REVERT: N 79 ILE cc_start: 0.8561 (mt) cc_final: 0.8317 (mm) REVERT: N 104 MET cc_start: 0.8872 (mmm) cc_final: 0.8496 (mmm) REVERT: C 90 ASP cc_start: 0.8975 (t70) cc_final: 0.8552 (t70) REVERT: G 73 ASN cc_start: 0.8893 (m-40) cc_final: 0.8204 (t0) outliers start: 23 outliers final: 14 residues processed: 257 average time/residue: 0.1553 time to fit residues: 54.9698 Evaluate side-chains 255 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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 56 PHE Chi-restraints excluded: chain N residue 34 TRP Chi-restraints excluded: chain N residue 45 GLU 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 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 6.9990 chunk 127 optimal weight: 0.0270 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 65 optimal weight: 30.0000 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.085663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.050464 restraints weight = 42319.380| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.56 r_work: 0.2545 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15577 Z= 0.180 Angle : 0.652 11.727 22295 Z= 0.367 Chirality : 0.043 0.282 2530 Planarity : 0.004 0.036 1810 Dihedral : 29.151 163.935 4409 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.88 % Allowed : 17.78 % Favored : 79.34 % 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: 1.70 (0.26), residues: 1074 helix: 2.55 (0.20), residues: 673 sheet: 1.13 (1.17), residues: 21 loop : -1.64 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.015 0.002 TYR F 88 PHE 0.014 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 0.00361 / 0.18 (15559) covalent geometry : angle 0.63845 / 0.37 (22271) hydrogen bonds : bond 0.06214 / 4.04 ( 864) hydrogen bonds : angle 3.29756 / 2.41 ( 2192) metal coordination : bond 0.00965 / 0.53 ( 16) metal coordination : angle 4.65316 / 2.57 ( 18) link_TRANS : bond 0.00125 / 0.06 ( 2) link_TRANS : angle 0.19752 / 0.09 ( 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 276 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.425 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: 0.9359 (tm-30) cc_final: 0.8870 (tt0) REVERT: B 88 TYR cc_start: 0.9426 (m-10) cc_final: 0.8957 (m-80) REVERT: D 83 TYR cc_start: 0.8750 (m-10) cc_final: 0.8351 (m-10) REVERT: D 90 THR cc_start: 0.9327 (p) cc_final: 0.8932 (t) REVERT: D 93 GLU cc_start: 0.9091 (mp0) cc_final: 0.8306 (mp0) REVERT: F 25 ASN cc_start: 0.9221 (m-40) cc_final: 0.8853 (m110) REVERT: H 33 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6779 (tpt170) REVERT: M 42 ILE cc_start: 0.8569 (mp) cc_final: 0.8032 (mm) REVERT: M 65 LYS cc_start: 0.8626 (ptmm) cc_final: 0.8384 (pptt) REVERT: M 88 LYS cc_start: 0.8590 (mttm) cc_final: 0.8164 (tmmt) REVERT: M 89 ILE cc_start: 0.8009 (mm) cc_final: 0.7440 (mm) REVERT: N 62 CYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8938 (t) REVERT: C 90 ASP cc_start: 0.8985 (t70) cc_final: 0.8556 (t70) REVERT: G 73 ASN cc_start: 0.8902 (m-40) cc_final: 0.8248 (t0) outliers start: 27 outliers final: 20 residues processed: 262 average time/residue: 0.1544 time to fit residues: 55.6117 Evaluate side-chains 267 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 E residue 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER 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 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: 4.9990 chunk 31 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 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: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN ** 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 = 0.3582 r_free = 0.3582 target = 0.084990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.049700 restraints weight = 42777.901| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.56 r_work: 0.2521 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15577 Z= 0.225 Angle : 0.688 11.277 22295 Z= 0.382 Chirality : 0.044 0.298 2530 Planarity : 0.004 0.036 1810 Dihedral : 29.217 165.290 4409 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.88 % Allowed : 18.32 % Favored : 78.81 % 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: 1.61 (0.27), residues: 1074 helix: 2.48 (0.20), residues: 676 sheet: 0.72 (1.21), residues: 22 loop : -1.71 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 33 TYR 0.056 0.002 TYR F 88 PHE 0.011 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 0.00474 / 0.22 (15559) covalent geometry : angle 0.67696 / 0.38 (22271) hydrogen bonds : bond 0.06480 / 4.22 ( 864) hydrogen bonds : angle 3.40153 / 2.49 ( 2192) metal coordination : bond 0.01164 / 0.61 ( 16) metal coordination : angle 4.38719 / 2.45 ( 18) link_TRANS : bond 0.00211 / 0.11 ( 2) link_TRANS : angle 0.21960 / 0.11 ( 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 : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9365 (tm-30) cc_final: 0.8893 (tt0) REVERT: B 88 TYR cc_start: 0.9435 (m-10) cc_final: 0.8885 (m-80) REVERT: D 83 TYR cc_start: 0.8814 (m-10) cc_final: 0.8353 (m-10) REVERT: D 90 THR cc_start: 0.9331 (p) cc_final: 0.8930 (t) REVERT: D 93 GLU cc_start: 0.9124 (mp0) cc_final: 0.8325 (mp0) REVERT: F 25 ASN cc_start: 0.9222 (m-40) cc_final: 0.8845 (m110) REVERT: F 53 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8807 (mm-30) REVERT: M 29 GLU cc_start: 0.8618 (tt0) cc_final: 0.8360 (tt0) REVERT: M 42 ILE cc_start: 0.8547 (mp) cc_final: 0.7965 (mm) REVERT: M 65 LYS cc_start: 0.8595 (ptmm) cc_final: 0.8351 (pptt) REVERT: M 88 LYS cc_start: 0.8573 (mttm) cc_final: 0.8155 (tmmt) REVERT: M 89 ILE cc_start: 0.8018 (mm) cc_final: 0.7428 (mm) REVERT: N 45 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.8581 (mm-30) REVERT: N 58 ARG cc_start: 0.7517 (pmt170) cc_final: 0.7072 (pmt170) REVERT: N 62 CYS cc_start: 0.9138 (t) cc_final: 0.8790 (t) REVERT: N 79 ILE cc_start: 0.8572 (mt) cc_final: 0.8338 (mm) REVERT: C 24 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8439 (mt0) REVERT: C 90 ASP cc_start: 0.9033 (t70) cc_final: 0.8653 (t70) REVERT: G 73 ASN cc_start: 0.8939 (m-40) cc_final: 0.8304 (t0) outliers start: 27 outliers final: 24 residues processed: 255 average time/residue: 0.1558 time to fit residues: 54.4498 Evaluate side-chains 263 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 E residue 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 45 GLU 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 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: 0.9990 chunk 63 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 114 optimal weight: 0.0980 chunk 56 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 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 = 0.3580 r_free = 0.3580 target = 0.084842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.049480 restraints weight = 42460.929| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.56 r_work: 0.2522 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2891 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= 0.215 Angle : 0.686 11.104 22295 Z= 0.382 Chirality : 0.044 0.298 2530 Planarity : 0.004 0.035 1810 Dihedral : 29.241 166.055 4409 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.88 % Allowed : 18.53 % 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: 1.67 (0.27), residues: 1074 helix: 2.53 (0.20), residues: 673 sheet: 0.70 (1.22), residues: 22 loop : -1.65 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 29 TYR 0.071 0.002 TYR F 88 PHE 0.015 0.001 PHE N 70 TRP 0.009 0.001 TRP N 91 HIS 0.006 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (15559) covalent geometry : angle 0.67501 / 0.38 (22271) hydrogen bonds : bond 0.06447 / 4.20 ( 864) hydrogen bonds : angle 3.38760 / 2.48 ( 2192) metal coordination : bond 0.01052 / 0.56 ( 16) metal coordination : angle 4.29225 / 2.35 ( 18) link_TRANS : bond 0.00181 / 0.09 ( 2) link_TRANS : angle 0.16764 / 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 269 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9367 (tm-30) cc_final: 0.8948 (tt0) REVERT: B 88 TYR cc_start: 0.9439 (m-10) cc_final: 0.8933 (m-80) REVERT: D 59 MET cc_start: 0.9388 (tpp) cc_final: 0.8978 (tmm) REVERT: D 83 TYR cc_start: 0.8813 (m-10) cc_final: 0.8376 (m-10) REVERT: D 90 THR cc_start: 0.9329 (p) cc_final: 0.8936 (t) REVERT: D 93 GLU cc_start: 0.9132 (mp0) cc_final: 0.8350 (mp0) REVERT: F 25 ASN cc_start: 0.9217 (m-40) cc_final: 0.8840 (m110) REVERT: F 53 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8820 (mm-30) REVERT: M 18 MET cc_start: 0.9290 (mmt) cc_final: 0.9065 (mmm) REVERT: M 29 GLU cc_start: 0.8671 (tt0) cc_final: 0.8412 (tt0) REVERT: M 42 ILE cc_start: 0.8535 (mp) cc_final: 0.7976 (mm) REVERT: M 65 LYS cc_start: 0.8669 (ptmm) cc_final: 0.8410 (pptt) REVERT: M 88 LYS cc_start: 0.8590 (mttm) cc_final: 0.8159 (tmmt) REVERT: M 89 ILE cc_start: 0.8067 (mm) cc_final: 0.7493 (mm) REVERT: N 62 CYS cc_start: 0.9161 (t) cc_final: 0.8834 (t) REVERT: N 79 ILE cc_start: 0.8601 (mt) cc_final: 0.8383 (mm) REVERT: C 24 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8436 (mt0) REVERT: C 90 ASP cc_start: 0.9066 (t70) cc_final: 0.8701 (t70) REVERT: G 73 ASN cc_start: 0.8953 (m-40) cc_final: 0.8349 (t0) outliers start: 27 outliers final: 25 residues processed: 254 average time/residue: 0.1620 time to fit residues: 56.1352 Evaluate side-chains 264 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 E residue 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 32 HIS 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 15 LYS 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=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: 0.9990 chunk 30 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 GLN ** 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 = 0.3584 r_free = 0.3584 target = 0.084978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.049461 restraints weight = 42728.471| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.57 r_work: 0.2524 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2969 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= 0.196 Angle : 0.680 11.258 22295 Z= 0.381 Chirality : 0.044 0.295 2530 Planarity : 0.004 0.036 1810 Dihedral : 29.230 166.794 4409 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.98 % Allowed : 18.74 % Favored : 78.27 % 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: 2.53 (0.20), residues: 674 sheet: 1.04 (1.24), residues: 21 loop : -1.61 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 5 TYR 0.073 0.002 TYR F 88 PHE 0.015 0.002 PHE N 70 TRP 0.044 0.003 TRP P 33 HIS 0.005 0.001 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (15559) covalent geometry : angle 0.67032 / 0.38 (22271) hydrogen bonds : bond 0.06322 / 4.12 ( 864) hydrogen bonds : angle 3.34470 / 2.45 ( 2192) metal coordination : bond 0.01022 / 0.58 ( 16) metal coordination : angle 3.99566 / 2.22 ( 18) link_TRANS : bond 0.00152 / 0.08 ( 2) link_TRANS : angle 0.14070 / 0.07 ( 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 269 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9403 (tm-30) cc_final: 0.8948 (tt0) REVERT: B 88 TYR cc_start: 0.9445 (m-10) cc_final: 0.8832 (m-80) REVERT: D 59 MET cc_start: 0.9367 (tpp) cc_final: 0.8943 (tmm) REVERT: D 83 TYR cc_start: 0.8818 (m-10) cc_final: 0.8361 (m-10) REVERT: D 90 THR cc_start: 0.9319 (p) cc_final: 0.8924 (t) REVERT: D 93 GLU cc_start: 0.9128 (mp0) cc_final: 0.8351 (mp0) REVERT: F 25 ASN cc_start: 0.9222 (m-40) cc_final: 0.8872 (m110) REVERT: F 53 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8827 (mm-30) REVERT: M 7 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8316 (tpm170) REVERT: M 18 MET cc_start: 0.9275 (mmt) cc_final: 0.9049 (mmm) REVERT: M 29 GLU cc_start: 0.8675 (tt0) cc_final: 0.8418 (tt0) REVERT: M 42 ILE cc_start: 0.8470 (mp) cc_final: 0.7940 (mm) REVERT: M 65 LYS cc_start: 0.8677 (ptmm) cc_final: 0.8415 (pptt) REVERT: M 88 LYS cc_start: 0.8598 (mttm) cc_final: 0.8192 (tmmt) REVERT: M 89 ILE cc_start: 0.8039 (mm) cc_final: 0.7452 (mm) REVERT: N 45 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.8596 (mm-30) REVERT: N 62 CYS cc_start: 0.9144 (t) cc_final: 0.8820 (t) REVERT: N 79 ILE cc_start: 0.8575 (mt) cc_final: 0.8364 (mm) REVERT: C 24 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8435 (mt0) REVERT: C 90 ASP cc_start: 0.9080 (t70) cc_final: 0.8724 (t70) REVERT: G 73 ASN cc_start: 0.8936 (m-40) cc_final: 0.8346 (t0) outliers start: 28 outliers final: 25 residues processed: 254 average time/residue: 0.1595 time to fit residues: 55.1779 Evaluate side-chains 265 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 E residue 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 45 GLU 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 15 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 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 = 0.3600 r_free = 0.3600 target = 0.085798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.050468 restraints weight = 42511.484| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.57 r_work: 0.2553 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3080 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= 0.158 Angle : 0.657 11.313 22295 Z= 0.373 Chirality : 0.042 0.285 2530 Planarity : 0.004 0.038 1810 Dihedral : 29.166 167.222 4409 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.45 % Allowed : 19.49 % Favored : 78.06 % 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: 1.82 (0.27), residues: 1074 helix: 2.61 (0.20), residues: 673 sheet: 0.85 (1.22), residues: 21 loop : -1.51 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 52 TYR 0.076 0.002 TYR F 88 PHE 0.016 0.001 PHE N 70 TRP 0.025 0.002 TRP P 33 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (15559) covalent geometry : angle 0.64630 / 0.37 (22271) hydrogen bonds : bond 0.05992 / 3.89 ( 864) hydrogen bonds : angle 3.24975 / 2.38 ( 2192) metal coordination : bond 0.01008 / 0.63 ( 16) metal coordination : angle 4.14862 / 2.28 ( 18) link_TRANS : bond 0.00066 / 0.03 ( 2) link_TRANS : angle 0.12119 / 0.06 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4062.37 seconds wall clock time: 70 minutes 2.32 seconds (4202.32 seconds total)