Starting phenix.real_space_refine on Fri Jul 3 13:32:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e8d_31015/07_2026/7e8d_31015.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8d_31015/07_2026/7e8d_31015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7e8d_31015/07_2026/7e8d_31015.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e8d_31015/07_2026/7e8d_31015.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e8d_31015/07_2026/7e8d_31015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8d_31015/07_2026/7e8d_31015.map" model { file = "/net/cci-nas-00/data/ceres_data/7e8d_31015/07_2026/7e8d_31015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8d_31015/07_2026/7e8d_31015.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 344 5.49 5 S 36 5.16 5 C 8248 2.51 5 N 2766 2.21 5 O 3455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 14852 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 845 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 3504 Classifications: {'DNA': 172} Link IDs: {'rna3p': 171} Chain: "J" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 3548 Classifications: {'DNA': 172} Link IDs: {'rna3p': 171} Chain: "K" Number of atoms: 1714 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1709 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 204} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 218, 1709 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 204} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1743 Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14390 SG CYS K1144 42.120 51.544 56.429 1.00114.62 S ATOM 14749 SG CYS K1191 42.466 50.214 52.961 1.00118.29 S ATOM 14760 SG CYS K1193 45.111 49.280 55.494 1.00118.84 S ATOM 14789 SG CYS K1198 41.809 47.729 55.847 1.00118.80 S ATOM 13361 SG CYS K1016 58.936 85.318 59.757 1.00 85.99 S ATOM 13375 SG CYS K1018 60.570 83.394 62.687 1.00 92.56 S ATOM 13436 SG CYS K1026 61.418 82.746 59.075 1.00 89.86 S ATOM 13480 SG CYS K1032 58.078 81.605 60.455 1.00 81.97 S ATOM 13436 SG CYS K1026 61.418 82.746 59.075 1.00 89.86 S ATOM 13557 SG CYS K1041 58.478 83.005 56.585 1.00 88.34 S ATOM 13596 SG CYS K1046 61.568 85.205 56.581 1.00 92.31 S ATOM 13638 SG CYS K1052 61.850 81.503 55.483 1.00 93.46 S Time building chain proxies: 2.83, per 1000 atoms: 0.19 Number of scatterers: 14852 At special positions: 0 Unit cell: (87.15, 168.49, 142.76, 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 3 29.99 S 36 16.00 P 344 15.00 O 3455 8.00 N 2766 7.00 C 8248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 382.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1301 " pdb="ZN ZN K1301 " - pdb=" SG CYS K1193 " pdb="ZN ZN K1301 " - pdb=" SG CYS K1191 " pdb="ZN ZN K1301 " - pdb=" SG CYS K1198 " pdb="ZN ZN K1301 " - pdb=" SG CYS K1144 " pdb=" ZN K1302 " pdb="ZN ZN K1302 " - pdb=" SG CYS K1026 " pdb="ZN ZN K1302 " - pdb=" SG CYS K1016 " pdb="ZN ZN K1302 " - pdb=" SG CYS K1018 " pdb="ZN ZN K1302 " - pdb=" SG CYS K1032 " pdb=" ZN K1303 " pdb="ZN ZN K1303 " - pdb=" SG CYS K1026 " pdb="ZN ZN K1303 " - pdb=" SG CYS K1046 " pdb="ZN ZN K1303 " - pdb=" SG CYS K1041 " pdb="ZN ZN K1303 " - pdb=" SG CYS K1052 " Number of angles added : 18 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 58.7% alpha, 6.2% beta 172 base pairs and 318 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.730A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.243A 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: 3.706A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.842A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.399A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.604A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 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 removed outlier: 3.631A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.368A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.688A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 1009 through 1013 removed outlier: 3.933A pdb=" N ILE K1013 " --> pdb=" O ILE K1010 " (cutoff:3.500A) Processing helix chain 'K' and resid 1032 through 1037 removed outlier: 3.803A pdb=" N LEU K1037 " --> pdb=" O LEU K1033 " (cutoff:3.500A) Processing helix chain 'K' and resid 1098 through 1112 Processing helix chain 'K' and resid 1135 through 1140 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.784A 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 'C' and resid 42 through 43 removed outlier: 6.969A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.661A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.937A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.019A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 992 through 993 Processing sheet with id=AB3, first strand: chain 'K' and resid 998 through 999 removed outlier: 7.023A pdb=" N LYS K 998 " --> pdb=" O LEU K1096 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG K1126 " --> pdb=" O ILE K1122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 1065 through 1069 removed outlier: 4.770A pdb=" N LEU K1077 " --> pdb=" O LEU K1175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 1088 through 1092 removed outlier: 6.726A pdb=" N PHE K1088 " --> pdb=" O ALA K1165 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA K1165 " --> pdb=" O PHE K1088 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL K1161 " --> pdb=" O TYR K1092 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 444 hydrogen bonds 884 hydrogen bond angles 0 basepair planarities 172 basepair parallelities 318 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2521 1.33 - 1.45: 5349 1.45 - 1.57: 7222 1.57 - 1.69: 686 1.69 - 1.81: 52 Bond restraints: 15830 Sorted by residual: bond pdb=" C3' DG I 101 " pdb=" O3' DG I 101 " ideal model delta sigma weight residual 1.435 1.372 0.063 1.30e-02 5.92e+03 2.37e+01 bond pdb=" C3' DA J 60 " pdb=" O3' DA J 60 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.03e+01 bond pdb=" C3' DA I 60 " pdb=" O3' DA I 60 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.66e+01 bond pdb=" C3' DG J 101 " pdb=" O3' DG J 101 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.61e+01 bond pdb=" C3' DG J 68 " pdb=" O3' DG J 68 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.53e+01 ... (remaining 15825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 21308 1.70 - 3.40: 1455 3.40 - 5.10: 85 5.10 - 6.79: 11 6.79 - 8.49: 2 Bond angle restraints: 22861 Sorted by residual: angle pdb=" O4' DG J 94 " pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.52e+01 angle pdb=" O4' DC I 140 " pdb=" C4' DC I 140 " pdb=" C3' DC I 140 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.34e+01 angle pdb=" N3 DT J 17 " pdb=" C4 DT J 17 " pdb=" O4 DT J 17 " ideal model delta sigma weight residual 119.90 122.74 -2.84 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT I 142 " pdb=" C4 DT I 142 " pdb=" O4 DT I 142 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N3 DT J 24 " pdb=" C4 DT J 24 " pdb=" O4 DT J 24 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 ... (remaining 22856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 6846 35.23 - 70.46: 1759 70.46 - 105.68: 20 105.68 - 140.91: 1 140.91 - 176.14: 7 Dihedral angle restraints: 8633 sinusoidal: 5787 harmonic: 2846 Sorted by residual: dihedral pdb=" CA LYS C 15 " pdb=" C LYS C 15 " pdb=" N THR C 16 " pdb=" CA THR C 16 " ideal model delta harmonic sigma weight residual 180.00 148.55 31.45 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA ASN K1186 " pdb=" C ASN K1186 " pdb=" N GLU K1187 " pdb=" CA GLU K1187 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASN K1180 " pdb=" C ASN K1180 " pdb=" N LEU K1181 " pdb=" CA LEU K1181 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 8630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1641 0.047 - 0.093: 714 0.093 - 0.140: 199 0.140 - 0.187: 21 0.187 - 0.233: 5 Chirality restraints: 2580 Sorted by residual: chirality pdb=" C3' DA I 41 " pdb=" C4' DA I 41 " pdb=" O3' DA I 41 " pdb=" C2' DA I 41 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C3' DT I 77 " pdb=" C4' DT I 77 " pdb=" O3' DT I 77 " pdb=" C2' DT I 77 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C1' SFG K1304 " pdb=" C2' SFG K1304 " pdb=" N9 SFG K1304 " pdb=" O4' SFG K1304 " both_signs ideal model delta sigma weight residual False 2.38 2.57 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 2577 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.030 2.00e-02 2.50e+03 1.34e-02 4.90e+00 pdb=" N9 DA I 20 " 0.031 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 100 " -0.024 2.00e-02 2.50e+03 1.12e-02 3.47e+00 pdb=" N9 DA J 100 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA J 100 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 100 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA J 100 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA J 100 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA J 100 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA J 100 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA J 100 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA J 100 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA J 100 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 48 " 0.024 2.00e-02 2.50e+03 1.15e-02 3.32e+00 pdb=" N1 DT I 48 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DT I 48 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 48 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 48 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 48 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT I 48 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT I 48 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT I 48 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 48 " -0.002 2.00e-02 2.50e+03 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 288 2.64 - 3.20: 12341 3.20 - 3.77: 27657 3.77 - 4.33: 38159 4.33 - 4.90: 53341 Nonbonded interactions: 131786 Sorted by model distance: nonbonded pdb=" NH2 ARG C 11 " pdb=" O2 DT I 117 " model vdw 2.070 3.120 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.234 3.040 nonbonded pdb=" OE2 GLU K1101 " pdb=" NE ARG K1105 " model vdw 2.251 3.120 ... (remaining 131781 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' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 11 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 98 or (resid 99 and (name N or nam \ e CA or name C or name O or name CB )) or resid 100 through 119)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 124) } 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=0.50 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.190 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:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.071 15842 Z= 0.845 Angle : 0.865 11.195 22879 Z= 0.722 Chirality : 0.054 0.233 2580 Planarity : 0.004 0.044 1709 Dihedral : 28.802 176.140 6801 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 1.95 % Allowed : 6.20 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.71 (0.25), residues: 966 helix: 0.52 (0.21), residues: 561 sheet: -2.44 (0.68), residues: 38 loop : -1.79 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 134 TYR 0.013 0.002 TYR A 54 PHE 0.012 0.002 PHE K1088 TRP 0.010 0.003 TRP K1075 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01079 / 0.85 (15830) covalent geometry : angle 0.85787 / 0.72 (22861) hydrogen bonds : bond 0.11535 / 8.14 ( 891) hydrogen bonds : angle 4.61703 / 3.43 ( 2189) metal coordination : bond 0.00821 / 0.46 ( 12) metal coordination : angle 3.95529 / 2.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8247 (ttpp) REVERT: D 71 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7467 (mt-10) REVERT: D 113 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: H 34 LYS cc_start: 0.8575 (mptt) cc_final: 0.8279 (mmtm) REVERT: K 1126 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7658 (mtm110) outliers start: 15 outliers final: 7 residues processed: 196 average time/residue: 0.6915 time to fit residues: 145.7312 Evaluate side-chains 176 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1115 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN K1110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.139935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094988 restraints weight = 26998.234| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.37 r_work: 0.3171 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15842 Z= 0.208 Angle : 0.725 10.832 22879 Z= 0.406 Chirality : 0.052 0.338 2580 Planarity : 0.005 0.068 1709 Dihedral : 32.453 176.280 4873 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.19 % Allowed : 13.14 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 966 helix: 1.32 (0.21), residues: 565 sheet: -2.32 (0.69), residues: 38 loop : -1.58 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 11 TYR 0.011 0.002 TYR B 51 PHE 0.016 0.002 PHE K1051 TRP 0.009 0.002 TRP K1075 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 (15830) covalent geometry : angle 0.71729 / 0.41 (22861) hydrogen bonds : bond 0.05779 / 4.09 ( 891) hydrogen bonds : angle 3.48711 / 2.58 ( 2189) metal coordination : bond 0.00626 / 0.33 ( 12) metal coordination : angle 3.72059 / 2.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.285 Fit side-chains REVERT: A 53 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7673 (ttp-110) REVERT: D 113 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: H 34 LYS cc_start: 0.8831 (mptt) cc_final: 0.8627 (mptt) outliers start: 17 outliers final: 8 residues processed: 184 average time/residue: 0.6737 time to fit residues: 133.1846 Evaluate side-chains 183 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 104 optimal weight: 50.0000 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 95 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.141430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096692 restraints weight = 27482.505| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.40 r_work: 0.3203 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15842 Z= 0.152 Angle : 0.682 9.815 22879 Z= 0.387 Chirality : 0.050 0.338 2580 Planarity : 0.005 0.105 1709 Dihedral : 32.297 175.288 4870 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.34 % Allowed : 14.96 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 966 helix: 1.77 (0.21), residues: 567 sheet: -2.35 (0.69), residues: 38 loop : -1.43 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K1060 TYR 0.010 0.001 TYR B 51 PHE 0.011 0.001 PHE K1139 TRP 0.007 0.001 TRP K1075 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (15830) covalent geometry : angle 0.67582 / 0.39 (22861) hydrogen bonds : bond 0.04932 / 3.49 ( 891) hydrogen bonds : angle 3.27936 / 2.42 ( 2189) metal coordination : bond 0.00516 / 0.27 ( 12) metal coordination : angle 3.42890 / 2.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.407 Fit side-chains REVERT: D 113 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: G 75 LYS cc_start: 0.8932 (mmtp) cc_final: 0.8636 (mmmt) REVERT: H 34 LYS cc_start: 0.8778 (mptt) cc_final: 0.8575 (mptt) REVERT: H 68 ASP cc_start: 0.9146 (t70) cc_final: 0.8938 (t70) REVERT: H 113 GLU cc_start: 0.8258 (tt0) cc_final: 0.8018 (tt0) outliers start: 10 outliers final: 5 residues processed: 185 average time/residue: 0.7034 time to fit residues: 139.9059 Evaluate side-chains 182 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain K residue 1093 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN E 108 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.138949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093573 restraints weight = 26587.297| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.33 r_work: 0.3151 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15842 Z= 0.277 Angle : 0.743 10.126 22879 Z= 0.409 Chirality : 0.054 0.344 2580 Planarity : 0.005 0.047 1709 Dihedral : 32.372 174.351 4869 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.95 % Allowed : 15.82 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 966 helix: 1.68 (0.21), residues: 567 sheet: -2.33 (0.70), residues: 38 loop : -1.52 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 11 TYR 0.011 0.002 TYR C 57 PHE 0.016 0.002 PHE K1051 TRP 0.008 0.002 TRP K1075 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.28 (15830) covalent geometry : angle 0.73629 / 0.41 (22861) hydrogen bonds : bond 0.06361 / 4.45 ( 891) hydrogen bonds : angle 3.29772 / 2.43 ( 2189) metal coordination : bond 0.00731 / 0.40 ( 12) metal coordination : angle 3.55452 / 2.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8701 (mtpt) REVERT: C 15 LYS cc_start: 0.8400 (ttpt) cc_final: 0.8193 (ttpp) REVERT: D 113 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8158 (tt0) outliers start: 15 outliers final: 7 residues processed: 183 average time/residue: 0.6849 time to fit residues: 134.4696 Evaluate side-chains 183 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1093 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 50.0000 chunk 42 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.140896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095443 restraints weight = 33176.716| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.49 r_work: 0.3169 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15842 Z= 0.154 Angle : 0.701 12.831 22879 Z= 0.390 Chirality : 0.051 0.338 2580 Planarity : 0.005 0.052 1709 Dihedral : 32.333 174.422 4869 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.70 % Allowed : 17.27 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 966 helix: 1.93 (0.21), residues: 561 sheet: -2.36 (0.70), residues: 38 loop : -1.41 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K1060 TYR 0.010 0.001 TYR C 57 PHE 0.031 0.002 PHE K1028 TRP 0.005 0.001 TRP K1075 HIS 0.004 0.001 HIS K1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (15830) covalent geometry : angle 0.69363 / 0.39 (22861) hydrogen bonds : bond 0.05165 / 3.66 ( 891) hydrogen bonds : angle 3.22310 / 2.38 ( 2189) metal coordination : bond 0.00602 / 0.32 ( 12) metal coordination : angle 3.57702 / 2.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.357 Fit side-chains REVERT: B 77 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8613 (mtpt) REVERT: D 93 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: D 113 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: H 34 LYS cc_start: 0.8823 (mptt) cc_final: 0.8531 (mmtm) outliers start: 13 outliers final: 5 residues processed: 184 average time/residue: 0.6251 time to fit residues: 123.6763 Evaluate side-chains 185 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 1093 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN K1044 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.141067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.096460 restraints weight = 24674.261| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.35 r_work: 0.3213 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15842 Z= 0.164 Angle : 0.691 10.682 22879 Z= 0.384 Chirality : 0.050 0.346 2580 Planarity : 0.004 0.048 1709 Dihedral : 32.256 174.328 4867 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.15 % Favored : 95.75 % Rotamer: Outliers : 1.95 % Allowed : 17.52 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.27), residues: 966 helix: 2.07 (0.21), residues: 561 sheet: -2.36 (0.70), residues: 38 loop : -1.35 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K1060 TYR 0.011 0.001 TYR B 51 PHE 0.020 0.002 PHE K1201 TRP 0.005 0.001 TRP K1075 HIS 0.003 0.001 HIS K1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (15830) covalent geometry : angle 0.68457 / 0.38 (22861) hydrogen bonds : bond 0.04912 / 3.47 ( 891) hydrogen bonds : angle 3.16894 / 2.34 ( 2189) metal coordination : bond 0.00507 / 0.26 ( 12) metal coordination : angle 3.39610 / 2.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.558 Fit side-chains REVERT: B 77 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8649 (mtpt) REVERT: D 93 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: D 113 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: G 107 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.9010 (m) REVERT: H 34 LYS cc_start: 0.8833 (mptt) cc_final: 0.8542 (mmtm) outliers start: 15 outliers final: 8 residues processed: 181 average time/residue: 0.6646 time to fit residues: 129.4826 Evaluate side-chains 186 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1126 ARG Chi-restraints excluded: chain K residue 1176 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 66 optimal weight: 0.7980 chunk 86 optimal weight: 50.0000 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 50.0000 chunk 16 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN K1044 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.140348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.095319 restraints weight = 25110.819| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.37 r_work: 0.3195 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15842 Z= 0.209 Angle : 0.699 9.508 22879 Z= 0.388 Chirality : 0.051 0.351 2580 Planarity : 0.005 0.049 1709 Dihedral : 32.167 173.305 4867 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.07 % Allowed : 17.15 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 966 helix: 2.06 (0.21), residues: 561 sheet: -2.37 (0.70), residues: 38 loop : -1.36 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 42 TYR 0.011 0.001 TYR B 51 PHE 0.019 0.002 PHE K1028 TRP 0.006 0.002 TRP K1075 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 (15830) covalent geometry : angle 0.69264 / 0.39 (22861) hydrogen bonds : bond 0.05403 / 3.78 ( 891) hydrogen bonds : angle 3.14515 / 2.32 ( 2189) metal coordination : bond 0.00620 / 0.33 ( 12) metal coordination : angle 3.44908 / 2.32 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7546 (ttp-110) REVERT: B 77 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8685 (mtpt) REVERT: D 113 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: G 99 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8756 (mtpt) outliers start: 16 outliers final: 9 residues processed: 186 average time/residue: 0.6908 time to fit residues: 138.0950 Evaluate side-chains 188 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1126 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN K1044 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.141049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095592 restraints weight = 32149.460| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.48 r_work: 0.3183 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15842 Z= 0.153 Angle : 0.689 10.544 22879 Z= 0.384 Chirality : 0.050 0.350 2580 Planarity : 0.004 0.050 1709 Dihedral : 32.159 173.198 4867 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.82 % Allowed : 17.88 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.27), residues: 966 helix: 2.17 (0.21), residues: 561 sheet: -2.37 (0.70), residues: 38 loop : -1.32 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 42 TYR 0.011 0.001 TYR C 57 PHE 0.023 0.002 PHE K1028 TRP 0.005 0.001 TRP K1075 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (15830) covalent geometry : angle 0.68213 / 0.38 (22861) hydrogen bonds : bond 0.05108 / 3.59 ( 891) hydrogen bonds : angle 3.13104 / 2.31 ( 2189) metal coordination : bond 0.00510 / 0.27 ( 12) metal coordination : angle 3.46242 / 2.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.390 Fit side-chains REVERT: B 77 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8694 (mtpt) REVERT: D 113 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: H 34 LYS cc_start: 0.8835 (mptt) cc_final: 0.8569 (mmtm) outliers start: 14 outliers final: 10 residues processed: 181 average time/residue: 0.6416 time to fit residues: 125.2914 Evaluate side-chains 186 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1126 ARG Chi-restraints excluded: chain K residue 1176 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 50.0000 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 50.0000 chunk 58 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN K1044 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.141147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.096315 restraints weight = 25897.781| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.36 r_work: 0.3205 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15842 Z= 0.156 Angle : 0.684 12.165 22879 Z= 0.380 Chirality : 0.049 0.350 2580 Planarity : 0.005 0.064 1709 Dihedral : 32.131 173.301 4867 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.70 % Allowed : 18.00 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.27), residues: 966 helix: 2.18 (0.21), residues: 561 sheet: -2.32 (0.70), residues: 38 loop : -1.31 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K1060 TYR 0.010 0.001 TYR B 51 PHE 0.017 0.002 PHE K1051 TRP 0.005 0.001 TRP K1075 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (15830) covalent geometry : angle 0.67762 / 0.38 (22861) hydrogen bonds : bond 0.04903 / 3.45 ( 891) hydrogen bonds : angle 3.10700 / 2.29 ( 2189) metal coordination : bond 0.00495 / 0.26 ( 12) metal coordination : angle 3.39390 / 2.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.279 Fit side-chains REVERT: B 77 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8687 (mtpt) REVERT: D 113 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: H 34 LYS cc_start: 0.8834 (mptt) cc_final: 0.8550 (mmtm) outliers start: 13 outliers final: 9 residues processed: 178 average time/residue: 0.6943 time to fit residues: 132.6405 Evaluate side-chains 184 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1126 ARG Chi-restraints excluded: chain K residue 1176 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 60 optimal weight: 0.0370 chunk 54 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 29 optimal weight: 0.7980 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN K1044 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.141600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.096092 restraints weight = 30658.049| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.42 r_work: 0.3195 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15842 Z= 0.147 Angle : 0.680 11.911 22879 Z= 0.379 Chirality : 0.049 0.350 2580 Planarity : 0.005 0.075 1709 Dihedral : 32.111 173.189 4867 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.58 % Allowed : 17.76 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.27), residues: 966 helix: 2.23 (0.21), residues: 561 sheet: -2.30 (0.70), residues: 38 loop : -1.29 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K1084 TYR 0.011 0.001 TYR B 51 PHE 0.013 0.002 PHE K1028 TRP 0.005 0.001 TRP K1075 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (15830) covalent geometry : angle 0.67357 / 0.38 (22861) hydrogen bonds : bond 0.04790 / 3.37 ( 891) hydrogen bonds : angle 3.09430 / 2.28 ( 2189) metal coordination : bond 0.00487 / 0.26 ( 12) metal coordination : angle 3.38150 / 2.27 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.416 Fit side-chains REVERT: B 77 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8708 (mtpt) REVERT: D 113 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: H 34 LYS cc_start: 0.8842 (mptt) cc_final: 0.8578 (mmtm) outliers start: 12 outliers final: 10 residues processed: 181 average time/residue: 0.7070 time to fit residues: 137.6258 Evaluate side-chains 185 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1126 ARG Chi-restraints excluded: chain K residue 1176 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 chunk 92 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.141751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.096669 restraints weight = 32938.728| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.53 r_work: 0.3203 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15842 Z= 0.143 Angle : 0.677 12.186 22879 Z= 0.378 Chirality : 0.049 0.351 2580 Planarity : 0.005 0.088 1709 Dihedral : 32.091 173.169 4867 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.58 % Allowed : 18.00 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.27), residues: 966 helix: 2.25 (0.21), residues: 561 sheet: -2.29 (0.70), residues: 38 loop : -1.27 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K1060 TYR 0.010 0.001 TYR B 51 PHE 0.012 0.001 PHE K1028 TRP 0.005 0.001 TRP K1075 HIS 0.003 0.001 HIS K1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (15830) covalent geometry : angle 0.67099 / 0.38 (22861) hydrogen bonds : bond 0.04707 / 3.32 ( 891) hydrogen bonds : angle 3.08518 / 2.27 ( 2189) metal coordination : bond 0.00471 / 0.24 ( 12) metal coordination : angle 3.36013 / 2.25 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5892.85 seconds wall clock time: 100 minutes 34.81 seconds (6034.81 seconds total)