Starting phenix.real_space_refine on Sat Sep 12 06:58:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e8d_31015/09_2026/7e8d_31015.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8d_31015/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7e8d_31015/09_2026/7e8d_31015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8d_31015/09_2026/7e8d_31015.map" model { file = "/net/cci-nas-00/data/ceres_data/7e8d_31015/09_2026/7e8d_31015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8d_31015/09_2026/7e8d_31015.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7e8d_31015/09_2026/7e8d_31015.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e8d_31015/09_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-2.2.1-6174/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: 3.80, per 1000 atoms: 0.26 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: 1.29 Conformation dependent library (CDL) restraints added in 498.6 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: 2.12 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: 3.36 Time building geometry restraints manager: 1.71 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: 21277 1.70 - 3.40: 1482 3.40 - 5.10: 89 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.940 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- 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= 0.847 Angle : 0.872 11.195 22879 Z= 0.728 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 0.86501 / 0.73 (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 : 0.296 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: 0.8032 time to fit residues: 168.8668 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 : 0.486 ------------------------------------------------------------------------------- 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 = 0.139848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094870 restraints weight = 27011.543| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.35 r_work: 0.3168 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 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 = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15842 Z= 0.202 Angle : 0.740 10.832 22879 Z= 0.410 Chirality : 0.054 0.358 2580 Planarity : 0.005 0.066 1709 Dihedral : 32.375 175.170 4873 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.19 % Allowed : 12.77 % Favored : 85.04 % 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: 0.16 (0.26), residues: 966 helix: 1.31 (0.21), residues: 565 sheet: -2.33 (0.68), residues: 38 loop : -1.58 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 (15830) covalent geometry : angle 0.73339 / 0.41 (22861) hydrogen bonds : bond 0.05782 / 4.09 ( 891) hydrogen bonds : angle 3.48596 / 2.58 ( 2189) metal coordination : bond 0.00648 / 0.34 ( 12) metal coordination : angle 3.71391 / 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 : 0.417 Fit side-chains REVERT: A 53 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7673 (ttp-110) REVERT: D 113 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8035 (tt0) outliers start: 17 outliers final: 8 residues processed: 184 average time/residue: 0.8072 time to fit residues: 159.8034 Evaluate side-chains 182 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 104 optimal weight: 50.0000 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 95 GLN E 108 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.141888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097219 restraints weight = 27739.134| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.40 r_work: 0.3207 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15842 Z= 0.144 Angle : 0.710 9.997 22879 Z= 0.397 Chirality : 0.052 0.355 2580 Planarity : 0.006 0.101 1709 Dihedral : 32.235 174.731 4870 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.34 % Allowed : 15.21 % Favored : 83.45 % 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: 0.69 (0.26), residues: 966 helix: 1.78 (0.21), residues: 567 sheet: -2.35 (0.69), residues: 38 loop : -1.41 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K1081 TYR 0.015 0.001 TYR G 39 PHE 0.013 0.001 PHE K1139 TRP 0.006 0.001 TRP K1075 HIS 0.003 0.001 HIS K1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (15830) covalent geometry : angle 0.70390 / 0.40 (22861) hydrogen bonds : bond 0.04912 / 3.49 ( 891) hydrogen bonds : angle 3.32370 / 2.46 ( 2189) metal coordination : bond 0.00508 / 0.28 ( 12) metal coordination : angle 3.49424 / 2.32 ( 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 190 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.377 Fit side-chains REVERT: D 113 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: G 75 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8635 (mmmt) REVERT: H 68 ASP cc_start: 0.9117 (t70) cc_final: 0.8896 (t70) REVERT: H 113 GLU cc_start: 0.8241 (tt0) cc_final: 0.7990 (tt0) outliers start: 10 outliers final: 5 residues processed: 185 average time/residue: 0.7488 time to fit residues: 149.1089 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 : 0.394 ------------------------------------------------------------------------------- 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: 5.9990 chunk 78 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN ** H 49 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 = 0.4018 r_free = 0.4018 target = 0.138763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093444 restraints weight = 26539.195| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.35 r_work: 0.3153 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 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: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15842 Z= 0.302 Angle : 0.776 10.149 22879 Z= 0.421 Chirality : 0.056 0.365 2580 Planarity : 0.005 0.051 1709 Dihedral : 32.314 173.594 4869 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.23 % Rotamer: Outliers : 2.07 % Allowed : 15.33 % Favored : 82.60 % 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: 0.52 (0.26), residues: 966 helix: 1.66 (0.21), residues: 567 sheet: -2.33 (0.70), residues: 38 loop : -1.54 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 11 TYR 0.012 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 B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.30 (15830) covalent geometry : angle 0.76941 / 0.42 (22861) hydrogen bonds : bond 0.06494 / 4.54 ( 891) hydrogen bonds : angle 3.33271 / 2.46 ( 2189) metal coordination : bond 0.00774 / 0.44 ( 12) metal coordination : angle 3.57858 / 2.35 ( 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 194 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.414 Fit side-chains REVERT: B 77 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8879 (mmtp) REVERT: C 15 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8215 (ttpp) REVERT: D 113 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8138 (tt0) outliers start: 16 outliers final: 7 residues processed: 184 average time/residue: 0.8220 time to fit residues: 162.3807 Evaluate side-chains 184 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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: 0.7980 chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 42 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.140148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094610 restraints weight = 33023.612| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.50 r_work: 0.3155 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- 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 = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15842 Z= 0.179 Angle : 0.736 12.049 22879 Z= 0.403 Chirality : 0.053 0.359 2580 Planarity : 0.005 0.048 1709 Dihedral : 32.297 173.624 4869 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.07 % Allowed : 16.55 % Favored : 81.39 % 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: 0.67 (0.26), residues: 966 helix: 1.79 (0.21), residues: 567 sheet: -2.33 (0.71), residues: 38 loop : -1.48 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K1060 TYR 0.011 0.001 TYR B 51 PHE 0.028 0.002 PHE K1028 TRP 0.006 0.002 TRP K1075 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (15830) covalent geometry : angle 0.72934 / 0.40 (22861) hydrogen bonds : bond 0.05563 / 3.92 ( 891) hydrogen bonds : angle 3.26775 / 2.42 ( 2189) metal coordination : bond 0.00642 / 0.34 ( 12) metal coordination : angle 3.64691 / 2.42 ( 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 198 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.421 Fit side-chains REVERT: D 93 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: D 113 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: H 68 ASP cc_start: 0.9168 (t70) cc_final: 0.8947 (t70) outliers start: 16 outliers final: 9 residues processed: 185 average time/residue: 0.7965 time to fit residues: 158.4025 Evaluate side-chains 188 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 104 GLN 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 Chi-restraints excluded: chain K residue 1126 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.141278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096461 restraints weight = 24875.407| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.37 r_work: 0.3209 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1306 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= 0.146 Angle : 0.715 11.150 22879 Z= 0.393 Chirality : 0.051 0.363 2580 Planarity : 0.005 0.051 1709 Dihedral : 32.216 173.523 4869 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.85 % Rotamer: Outliers : 1.70 % Allowed : 17.64 % 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: 0.92 (0.27), residues: 966 helix: 2.05 (0.21), residues: 561 sheet: -2.31 (0.70), residues: 38 loop : -1.41 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 11 TYR 0.011 0.001 TYR B 51 PHE 0.027 0.002 PHE K1139 TRP 0.006 0.001 TRP K1075 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (15830) covalent geometry : angle 0.70822 / 0.39 (22861) hydrogen bonds : bond 0.04929 / 3.49 ( 891) hydrogen bonds : angle 3.19903 / 2.36 ( 2189) metal coordination : bond 0.00544 / 0.29 ( 12) metal coordination : angle 3.52606 / 2.33 ( 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: 13 poor density : 177 time to evaluate : 0.306 Fit side-chains REVERT: D 93 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: D 113 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: H 68 ASP cc_start: 0.9157 (t70) cc_final: 0.8952 (t70) outliers start: 13 outliers final: 7 residues processed: 181 average time/residue: 0.7813 time to fit residues: 152.1792 Evaluate side-chains 185 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 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: 0.8980 chunk 86 optimal weight: 50.0000 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 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: 1.9990 chunk 115 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN G 24 GLN K1044 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.141317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.096506 restraints weight = 25522.012| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.40 r_work: 0.3214 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 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 = 0.3053 r_free = 0.3053 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: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1440 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= 0.173 Angle : 0.692 9.515 22879 Z= 0.384 Chirality : 0.050 0.374 2580 Planarity : 0.004 0.050 1709 Dihedral : 32.001 172.286 4868 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.82 % Allowed : 17.64 % 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: 1.08 (0.27), residues: 966 helix: 2.18 (0.21), residues: 561 sheet: -2.36 (0.69), residues: 38 loop : -1.34 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 42 TYR 0.010 0.001 TYR B 51 PHE 0.021 0.002 PHE K1028 TRP 0.005 0.001 TRP K1075 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (15830) covalent geometry : angle 0.68570 / 0.38 (22861) hydrogen bonds : bond 0.04941 / 3.46 ( 891) hydrogen bonds : angle 3.08979 / 2.28 ( 2189) metal coordination : bond 0.00521 / 0.27 ( 12) metal coordination : angle 3.28300 / 2.17 ( 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 191 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.329 Fit side-chains REVERT: D 113 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8123 (tt0) outliers start: 14 outliers final: 8 residues processed: 183 average time/residue: 0.7976 time to fit residues: 157.0015 Evaluate side-chains 184 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.141978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.096287 restraints weight = 33335.684| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.45 r_work: 0.3196 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 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 = 0.3053 r_free = 0.3053 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: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15842 Z= 0.143 Angle : 0.684 10.719 22879 Z= 0.381 Chirality : 0.050 0.373 2580 Planarity : 0.004 0.055 1709 Dihedral : 31.981 172.181 4867 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.34 % Allowed : 19.22 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.27), residues: 966 helix: 2.27 (0.21), residues: 561 sheet: -2.35 (0.69), residues: 38 loop : -1.29 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K1060 TYR 0.010 0.001 TYR B 51 PHE 0.023 0.002 PHE K1028 TRP 0.004 0.001 TRP K1075 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (15830) covalent geometry : angle 0.67857 / 0.38 (22861) hydrogen bonds : bond 0.04703 / 3.31 ( 891) hydrogen bonds : angle 3.08187 / 2.27 ( 2189) metal coordination : bond 0.00469 / 0.24 ( 12) metal coordination : angle 3.27091 / 2.18 ( 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 187 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.409 Fit side-chains REVERT: D 113 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: H 68 ASP cc_start: 0.9185 (t70) cc_final: 0.8934 (t70) outliers start: 10 outliers final: 8 residues processed: 181 average time/residue: 0.8065 time to fit residues: 156.7992 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 : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 71 GLU Chi-restraints excluded: chain H residue 101 LEU 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: 1.9990 chunk 7 optimal weight: 0.0270 chunk 116 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 50.0000 chunk 58 optimal weight: 3.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.141820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096800 restraints weight = 25833.199| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.37 r_work: 0.3217 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 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 = 0.3064 r_free = 0.3064 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: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1633 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= 0.165 Angle : 0.683 10.203 22879 Z= 0.378 Chirality : 0.049 0.381 2580 Planarity : 0.004 0.050 1709 Dihedral : 31.854 171.705 4867 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.34 % Allowed : 18.73 % Favored : 79.93 % 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: 1.24 (0.27), residues: 966 helix: 2.30 (0.21), residues: 561 sheet: -2.34 (0.68), residues: 38 loop : -1.24 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K1084 TYR 0.009 0.001 TYR B 51 PHE 0.016 0.001 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 0.00318 / 0.17 (15830) covalent geometry : angle 0.67693 / 0.38 (22861) hydrogen bonds : bond 0.04747 / 3.32 ( 891) hydrogen bonds : angle 3.04136 / 2.24 ( 2189) metal coordination : bond 0.00478 / 0.25 ( 12) metal coordination : angle 3.29297 / 2.22 ( 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 189 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.362 Fit side-chains REVERT: C 73 ASN cc_start: 0.8229 (m110) cc_final: 0.7900 (t160) REVERT: D 113 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: H 34 LYS cc_start: 0.8642 (mmpt) cc_final: 0.8337 (mmtt) outliers start: 10 outliers final: 7 residues processed: 182 average time/residue: 0.7972 time to fit residues: 155.9636 Evaluate side-chains 183 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 71 GLU 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: 0.2980 chunk 74 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 60 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.142076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096421 restraints weight = 30750.538| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.40 r_work: 0.3211 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 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 = 0.3052 r_free = 0.3052 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: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15842 Z= 0.152 Angle : 0.684 11.349 22879 Z= 0.378 Chirality : 0.049 0.380 2580 Planarity : 0.005 0.059 1709 Dihedral : 31.848 171.656 4867 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.97 % Allowed : 19.71 % Favored : 79.32 % 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: 1.30 (0.27), residues: 966 helix: 2.34 (0.21), residues: 561 sheet: -2.32 (0.68), residues: 38 loop : -1.19 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K1060 TYR 0.010 0.001 TYR G 57 PHE 0.017 0.002 PHE K1117 TRP 0.004 0.001 TRP K1075 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (15830) covalent geometry : angle 0.67799 / 0.38 (22861) hydrogen bonds : bond 0.04638 / 3.25 ( 891) hydrogen bonds : angle 3.03696 / 2.24 ( 2189) metal coordination : bond 0.00462 / 0.24 ( 12) metal coordination : angle 3.25069 / 2.19 ( 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 184 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.431 Fit side-chains REVERT: C 73 ASN cc_start: 0.8235 (m110) cc_final: 0.7907 (t160) REVERT: H 34 LYS cc_start: 0.8657 (mmpt) cc_final: 0.8411 (mmtt) REVERT: H 68 ASP cc_start: 0.9168 (t70) cc_final: 0.8953 (t70) outliers start: 7 outliers final: 7 residues processed: 180 average time/residue: 0.8297 time to fit residues: 160.3187 Evaluate side-chains 181 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 174 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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: 10.0000 chunk 116 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 0.0370 chunk 92 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 33 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN C 104 GLN K1044 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.142446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.096656 restraints weight = 32995.827| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.46 r_work: 0.3207 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 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 = 0.3053 r_free = 0.3053 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: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15842 Z= 0.134 Angle : 0.679 11.778 22879 Z= 0.377 Chirality : 0.049 0.380 2580 Planarity : 0.004 0.053 1709 Dihedral : 31.838 171.565 4864 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.97 % Allowed : 20.07 % Favored : 78.95 % 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: 1.34 (0.27), residues: 966 helix: 2.36 (0.21), residues: 561 sheet: -2.31 (0.68), residues: 38 loop : -1.16 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 42 TYR 0.010 0.001 TYR G 57 PHE 0.017 0.002 PHE K1051 TRP 0.004 0.001 TRP K1075 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (15830) covalent geometry : angle 0.67284 / 0.38 (22861) hydrogen bonds : bond 0.04545 / 3.19 ( 891) hydrogen bonds : angle 3.03438 / 2.24 ( 2189) metal coordination : bond 0.00421 / 0.22 ( 12) metal coordination : angle 3.26079 / 2.20 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6917.09 seconds wall clock time: 117 minutes 59.84 seconds (7079.84 seconds total)