Starting phenix.real_space_refine on Fri Sep 11 19:36:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m1x_23626/09_2026/7m1x_23626.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m1x_23626/09_2026/7m1x_23626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m1x_23626/09_2026/7m1x_23626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m1x_23626/09_2026/7m1x_23626.map" model { file = "/net/cci-nas-00/data/ceres_data/7m1x_23626/09_2026/7m1x_23626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m1x_23626/09_2026/7m1x_23626.cif" } resolution = 3.7 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 272 5.49 5 S 12 5.16 5 C 6350 2.51 5 N 2156 2.21 5 O 2685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 11475 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2806 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "J" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2770 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "A" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 780 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 781 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 715 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Time building chain proxies: 2.45, per 1000 atoms: 0.21 Number of scatterers: 11475 At special positions: 0 Unit cell: (102.3, 121, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 272 15.00 O 2685 8.00 N 2156 7.00 C 6350 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: 0.96 Conformation dependent library (CDL) restraints added in 265.8 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 74.3% alpha, 1.9% beta 135 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 445 through 457 Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.607A pdb=" N PHE A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 514 removed outlier: 3.627A pdb=" N ALA A 514 " --> pdb=" O CYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.780A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.842A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.526A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 824 Processing helix chain 'C' and resid 828 through 838 Processing helix chain 'C' and resid 847 through 875 removed outlier: 4.054A pdb=" N ALA C 851 " --> pdb=" O GLY C 847 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 875 " --> pdb=" O ASN C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 893 removed outlier: 3.529A pdb=" N ASP C 893 " --> pdb=" O ALA C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 900 Processing helix chain 'D' and resid 1234 through 1246 Processing helix chain 'D' and resid 1252 through 1281 Processing helix chain 'D' and resid 1287 through 1299 removed outlier: 3.697A pdb=" N ILE D1291 " --> pdb=" O THR D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1300 through 1320 Processing helix chain 'E' and resid 644 through 657 Processing helix chain 'E' and resid 663 through 679 removed outlier: 4.259A pdb=" N ASP E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE E 678 " --> pdb=" O ILE E 674 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E 679 " --> pdb=" O ALA E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 714 Processing helix chain 'E' and resid 720 through 732 Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.707A pdb=" N ILE F 229 " --> pdb=" O ILE F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 249 through 276 removed outlier: 4.193A pdb=" N GLU F 253 " --> pdb=" O LEU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 293 removed outlier: 3.512A pdb=" N VAL F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 1018 through 1023 Processing helix chain 'G' and resid 1028 through 1039 removed outlier: 3.709A pdb=" N SER G1038 " --> pdb=" O ARG G1034 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG G1039 " --> pdb=" O HIS G1035 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1077 removed outlier: 3.796A pdb=" N VAL G1052 " --> pdb=" O ALA G1048 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR G1053 " --> pdb=" O THR G1049 " (cutoff:3.500A) Processing helix chain 'G' and resid 1082 through 1093 Processing helix chain 'G' and resid 1093 through 1100 removed outlier: 3.737A pdb=" N ASP G1097 " --> pdb=" O ASP G1093 " (cutoff:3.500A) Processing helix chain 'H' and resid 1434 through 1446 Processing helix chain 'H' and resid 1452 through 1481 Processing helix chain 'H' and resid 1487 through 1499 removed outlier: 3.698A pdb=" N ILE H1491 " --> pdb=" O THR H1487 " (cutoff:3.500A) Processing helix chain 'H' and resid 1500 through 1520 Processing sheet with id=AA1, first strand: chain 'A' and resid 483 through 484 removed outlier: 6.999A pdb=" N ARG A 483 " --> 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 'C' and resid 845 through 846 removed outlier: 7.216A pdb=" N ARG C 845 " --> pdb=" O ILE D1286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 880 through 881 Processing sheet with id=AA4, first strand: chain 'E' and resid 683 through 684 removed outlier: 7.173A pdb=" N ARG E 683 " --> pdb=" O VAL F 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 718 through 719 Processing sheet with id=AA6, first strand: chain 'G' and resid 1045 through 1046 removed outlier: 7.156A pdb=" N ARG G1045 " --> pdb=" O ILE H1486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 1080 through 1081 399 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 225 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1924 1.33 - 1.45: 4086 1.45 - 1.56: 5656 1.56 - 1.68: 542 1.68 - 1.80: 22 Bond restraints: 12230 Sorted by residual: bond pdb=" C3' DC J -57 " pdb=" C2' DC J -57 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DT I -59 " pdb=" C2' DT I -59 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DA I -62 " pdb=" C2' DA I -62 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT I -32 " pdb=" O3' DT I -32 " ideal model delta sigma weight residual 1.435 1.477 -0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" C3' DG J 27 " pdb=" O3' DG J 27 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.87e+00 ... (remaining 12225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15944 1.55 - 3.09: 1567 3.09 - 4.64: 137 4.64 - 6.19: 22 6.19 - 7.73: 8 Bond angle restraints: 17678 Sorted by residual: angle pdb=" N VAL A 517 " pdb=" CA VAL A 517 " pdb=" C VAL A 517 " ideal model delta sigma weight residual 113.20 107.72 5.48 9.60e-01 1.09e+00 3.25e+01 angle pdb=" O4' DA I -71 " pdb=" C4' DA I -71 " pdb=" C3' DA I -71 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.30e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.77 -2.87 6.00e-01 2.78e+00 2.29e+01 angle pdb=" N3 DT J 55 " pdb=" C4 DT J 55 " pdb=" O4 DT J 55 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" O4' DC J 45 " pdb=" C4' DC J 45 " pdb=" C3' DC J 45 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 ... (remaining 17673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 5212 35.46 - 70.92: 1413 70.92 - 106.37: 16 106.37 - 141.83: 2 141.83 - 177.29: 3 Dihedral angle restraints: 6646 sinusoidal: 4484 harmonic: 2162 Sorted by residual: dihedral pdb=" CA THR C 841 " pdb=" C THR C 841 " pdb=" N SER C 842 " pdb=" CA SER C 842 " ideal model delta harmonic sigma weight residual -180.00 -142.85 -37.15 0 5.00e+00 4.00e-02 5.52e+01 dihedral pdb=" CA PRO H1500 " pdb=" C PRO H1500 " pdb=" N GLY H1501 " pdb=" CA GLY H1501 " ideal model delta harmonic sigma weight residual 180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA PRO D1300 " pdb=" C PRO D1300 " pdb=" N GLY D1301 " pdb=" CA GLY D1301 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 6643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1403 0.047 - 0.094: 486 0.094 - 0.141: 109 0.141 - 0.187: 18 0.187 - 0.234: 3 Chirality restraints: 2019 Sorted by residual: chirality pdb=" C3' DT I 15 " pdb=" C4' DT I 15 " pdb=" O3' DT I 15 " pdb=" C2' DT I 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C3' DT I -32 " pdb=" C4' DT I -32 " pdb=" O3' DT I -32 " pdb=" C2' DT I -32 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 2016 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 882 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO C 883 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 883 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 883 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 14 " 0.028 2.00e-02 2.50e+03 1.36e-02 4.63e+00 pdb=" N1 DT I 14 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DT I 14 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DT I 14 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT I 14 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 14 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT I 14 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT I 14 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 14 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 14 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G1082 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO G1083 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO G1083 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G1083 " -0.030 5.00e-02 4.00e+02 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2360 2.78 - 3.31: 10154 3.31 - 3.84: 23712 3.84 - 4.37: 25913 4.37 - 4.90: 36424 Nonbonded interactions: 98563 Sorted by model distance: nonbonded pdb=" OG SER G1073 " pdb=" O VAL G1078 " model vdw 2.244 3.040 nonbonded pdb=" OG SER C 842 " pdb=" O THR G1041 " model vdw 2.254 3.040 nonbonded pdb=" O ILE E 719 " pdb=" OG SER F 247 " model vdw 2.265 3.040 nonbonded pdb=" O GLY C 906 " pdb=" OG1 THR E 658 " model vdw 2.288 3.040 nonbonded pdb=" O SER C 916 " pdb=" OG SER C 916 " model vdw 2.298 3.040 ... (remaining 98558 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 641 through 735) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 223 through 302) } ncs_group { reference = (chain 'C' and resid 816 through 910) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.230 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 : 0.008 0.046 12230 Z= 0.661 Angle : 0.924 7.733 17678 Z= 0.787 Chirality : 0.050 0.234 2019 Planarity : 0.005 0.065 1290 Dihedral : 29.133 177.288 5250 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.48 % Favored : 94.38 % Rotamer: Outliers : 2.27 % Allowed : 6.63 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.27), residues: 730 helix: -0.21 (0.20), residues: 526 sheet: None (None), residues: 0 loop : -3.11 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1031 TYR 0.015 0.002 TYR C 860 PHE 0.018 0.002 PHE A 478 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.66 (12230) covalent geometry : angle 0.92404 / 0.79 (17678) hydrogen bonds : bond 0.09819 / 10.92 ( 746) hydrogen bonds : angle 4.08767 / 5.47 ( 1879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 346 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 GLN cc_start: 0.9232 (tt0) cc_final: 0.8532 (tm-30) REVERT: A 473 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8427 (tm-30) REVERT: A 476 GLN cc_start: 0.9020 (tp40) cc_final: 0.8672 (tm-30) REVERT: A 493 GLN cc_start: 0.8856 (tt0) cc_final: 0.8594 (tt0) REVERT: A 520 MET cc_start: 0.8227 (mtt) cc_final: 0.7452 (mtp) REVERT: A 522 LYS cc_start: 0.8580 (pttt) cc_final: 0.8332 (ptpp) REVERT: A 534 ARG cc_start: 0.8265 (ptp90) cc_final: 0.7827 (ttp80) REVERT: B 29 ILE cc_start: 0.9491 (mm) cc_final: 0.9288 (mm) REVERT: B 46 ILE cc_start: 0.8745 (mt) cc_final: 0.8533 (mt) REVERT: B 52 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8685 (tp30) REVERT: B 74 GLU cc_start: 0.9313 (tt0) cc_final: 0.9084 (tt0) REVERT: B 88 TYR cc_start: 0.8668 (m-10) cc_final: 0.8382 (m-80) REVERT: B 92 ARG cc_start: 0.8810 (tmm-80) cc_final: 0.8522 (mtp-110) REVERT: B 98 TYR cc_start: 0.9137 (m-10) cc_final: 0.8870 (m-80) REVERT: C 821 GLN cc_start: 0.9179 (mp10) cc_final: 0.8942 (mp10) REVERT: C 839 ARG cc_start: 0.8535 (mtt90) cc_final: 0.8275 (mtm-85) REVERT: C 853 TYR cc_start: 0.8956 (t80) cc_final: 0.8402 (t80) REVERT: C 887 GLN cc_start: 0.9200 (tp40) cc_final: 0.8866 (tp-100) REVERT: C 901 LYS cc_start: 0.9030 (pttp) cc_final: 0.8402 (tptp) REVERT: C 912 HIS cc_start: 0.8481 (t70) cc_final: 0.7714 (t-90) REVERT: D 1248 ASP cc_start: 0.8506 (p0) cc_final: 0.8278 (p0) REVERT: D 1265 ASP cc_start: 0.8648 (t70) cc_final: 0.8421 (t0) REVERT: D 1268 GLU cc_start: 0.8987 (tp30) cc_final: 0.8663 (tp30) REVERT: D 1277 LEU cc_start: 0.9197 (tp) cc_final: 0.8990 (tp) REVERT: D 1279 HIS cc_start: 0.8670 (t-90) cc_final: 0.8224 (t70) REVERT: D 1281 ASN cc_start: 0.9413 (t0) cc_final: 0.8995 (t0) REVERT: D 1303 LEU cc_start: 0.9047 (tp) cc_final: 0.8844 (tp) REVERT: D 1317 LYS cc_start: 0.9242 (ttmm) cc_final: 0.8957 (ttmt) REVERT: E 659 GLU cc_start: 0.8390 (pp20) cc_final: 0.8096 (pp20) REVERT: E 660 LEU cc_start: 0.8873 (mm) cc_final: 0.8495 (mm) REVERT: E 661 LEU cc_start: 0.8987 (mt) cc_final: 0.8705 (mt) REVERT: E 668 GLN cc_start: 0.9271 (tt0) cc_final: 0.7955 (tm-30) REVERT: E 690 MET cc_start: 0.9194 (tpt) cc_final: 0.8969 (tpp) REVERT: E 693 GLN cc_start: 0.9034 (tt0) cc_final: 0.8761 (tp40) REVERT: E 706 ASP cc_start: 0.9207 (t70) cc_final: 0.8985 (t70) REVERT: E 718 THR cc_start: 0.8792 (p) cc_final: 0.7902 (p) REVERT: E 722 LYS cc_start: 0.8969 (pttt) cc_final: 0.8706 (pttm) REVERT: E 723 ASP cc_start: 0.8840 (m-30) cc_final: 0.8613 (m-30) REVERT: E 725 GLN cc_start: 0.9256 (mt0) cc_final: 0.8959 (mt0) REVERT: F 231 LYS cc_start: 0.8817 (tttt) cc_final: 0.8486 (ttpt) REVERT: F 243 VAL cc_start: 0.9290 (t) cc_final: 0.9034 (p) REVERT: F 244 LYS cc_start: 0.8900 (tttt) cc_final: 0.8292 (tttt) REVERT: F 246 ILE cc_start: 0.9137 (mt) cc_final: 0.8817 (pt) REVERT: F 249 LEU cc_start: 0.9427 (mt) cc_final: 0.9036 (mm) REVERT: F 258 LEU cc_start: 0.9632 (tp) cc_final: 0.9404 (tp) REVERT: F 274 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8933 (tm-30) REVERT: F 291 LYS cc_start: 0.9158 (tttp) cc_final: 0.8816 (ttpt) REVERT: G 1059 GLU cc_start: 0.8798 (tt0) cc_final: 0.8557 (tt0) REVERT: G 1084 ARG cc_start: 0.8739 (tpt170) cc_final: 0.8512 (tpp80) REVERT: G 1087 GLN cc_start: 0.9156 (tp40) cc_final: 0.8930 (tp40) REVERT: G 1088 LEU cc_start: 0.9347 (mm) cc_final: 0.8951 (mm) REVERT: G 1093 ASP cc_start: 0.8276 (t70) cc_final: 0.8011 (t0) REVERT: H 1433 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8615 (m) REVERT: H 1465 ASP cc_start: 0.9202 (t70) cc_final: 0.8849 (t0) REVERT: H 1468 GLU cc_start: 0.8762 (tp30) cc_final: 0.8351 (tt0) REVERT: H 1486 ILE cc_start: 0.8916 (mt) cc_final: 0.8684 (mt) REVERT: H 1505 LYS cc_start: 0.9207 (tmmt) cc_final: 0.8997 (mttm) outliers start: 14 outliers final: 5 residues processed: 354 average time/residue: 0.1333 time to fit residues: 63.2586 Evaluate side-chains 286 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 280 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1253 SER Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1453 SER Chi-restraints excluded: chain H residue 1488 SER Chi-restraints excluded: chain H residue 1495 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN A 476 GLN B 25 ASN B 93 GLN D1246 HIS E 655 GLN E 668 GLN E 693 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1087 GLN H1446 HIS H1481 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.096187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068920 restraints weight = 32991.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071034 restraints weight = 16124.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.072454 restraints weight = 10840.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.073316 restraints weight = 8681.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073806 restraints weight = 7677.446| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12230 Z= 0.161 Angle : 0.707 7.957 17678 Z= 0.411 Chirality : 0.049 0.264 2019 Planarity : 0.005 0.056 1290 Dihedral : 32.123 175.904 3809 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.85 % Allowed : 22.82 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.06 (0.29), residues: 730 helix: 1.03 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -3.09 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 529 TYR 0.023 0.002 TYR D1318 PHE 0.006 0.001 PHE E 667 HIS 0.006 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (12230) covalent geometry : angle 0.70695 / 0.41 (17678) hydrogen bonds : bond 0.04644 / 5.16 ( 746) hydrogen bonds : angle 3.37668 / 4.47 ( 1879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 320 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8065 (pp20) cc_final: 0.7402 (pp20) REVERT: A 461 LEU cc_start: 0.8820 (mm) cc_final: 0.8516 (mm) REVERT: A 468 GLN cc_start: 0.9055 (tt0) cc_final: 0.8515 (tm-30) REVERT: A 473 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 520 MET cc_start: 0.8229 (mtt) cc_final: 0.7799 (mtp) REVERT: B 52 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8467 (tp30) REVERT: B 81 VAL cc_start: 0.9343 (t) cc_final: 0.8987 (p) REVERT: B 92 ARG cc_start: 0.8664 (tmm-80) cc_final: 0.8101 (tmm-80) REVERT: C 826 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7887 (mm110) REVERT: C 839 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7926 (mtm-85) REVERT: C 867 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8555 (tm-30) REVERT: C 887 GLN cc_start: 0.9253 (tp40) cc_final: 0.8890 (tp-100) REVERT: C 900 ILE cc_start: 0.8879 (mp) cc_final: 0.8665 (mp) REVERT: C 901 LYS cc_start: 0.8905 (pttp) cc_final: 0.8346 (tptp) REVERT: C 912 HIS cc_start: 0.8286 (t70) cc_final: 0.7678 (t-90) REVERT: D 1248 ASP cc_start: 0.8264 (p0) cc_final: 0.8056 (p0) REVERT: D 1268 GLU cc_start: 0.8893 (tp30) cc_final: 0.8524 (tp30) REVERT: D 1279 HIS cc_start: 0.8588 (t-90) cc_final: 0.8092 (t70) REVERT: D 1281 ASN cc_start: 0.9350 (t0) cc_final: 0.8914 (t0) REVERT: D 1317 LYS cc_start: 0.9302 (ttmm) cc_final: 0.8986 (ttmt) REVERT: E 699 TYR cc_start: 0.9153 (t80) cc_final: 0.8888 (t80) REVERT: E 705 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8431 (tm-30) REVERT: E 718 THR cc_start: 0.8816 (p) cc_final: 0.8615 (p) REVERT: E 722 LYS cc_start: 0.8997 (pttt) cc_final: 0.8758 (pttm) REVERT: E 723 ASP cc_start: 0.8433 (m-30) cc_final: 0.8184 (m-30) REVERT: E 725 GLN cc_start: 0.9178 (mt0) cc_final: 0.8917 (mt0) REVERT: E 733 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7806 (mt-10) REVERT: F 231 LYS cc_start: 0.8882 (tttt) cc_final: 0.8646 (ttpt) REVERT: F 243 VAL cc_start: 0.9396 (t) cc_final: 0.9184 (p) REVERT: F 244 LYS cc_start: 0.9027 (tttt) cc_final: 0.8452 (tttt) REVERT: F 249 LEU cc_start: 0.9253 (mt) cc_final: 0.8991 (mm) REVERT: F 252 GLU cc_start: 0.8740 (mp0) cc_final: 0.8513 (mp0) REVERT: F 274 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8752 (tm-30) REVERT: F 284 MET cc_start: 0.8929 (tpp) cc_final: 0.8453 (mmm) REVERT: F 291 LYS cc_start: 0.9123 (tttp) cc_final: 0.8775 (ttpt) REVERT: G 1034 ARG cc_start: 0.9373 (tmm160) cc_final: 0.8167 (ttm170) REVERT: G 1045 ARG cc_start: 0.9346 (ptm160) cc_final: 0.9009 (ptm160) REVERT: G 1084 ARG cc_start: 0.8901 (tpt170) cc_final: 0.8621 (tpp80) REVERT: G 1087 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8844 (tp40) REVERT: G 1088 LEU cc_start: 0.9350 (mm) cc_final: 0.9032 (mm) REVERT: H 1468 GLU cc_start: 0.8660 (tp30) cc_final: 0.8288 (tt0) REVERT: H 1486 ILE cc_start: 0.9043 (mt) cc_final: 0.8732 (mt) outliers start: 30 outliers final: 22 residues processed: 334 average time/residue: 0.1207 time to fit residues: 55.8059 Evaluate side-chains 310 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 288 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1253 SER Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1054 SER Chi-restraints excluded: chain H residue 1453 SER Chi-restraints excluded: chain H residue 1488 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 27 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN B 75 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 GLN E 668 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.094252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065952 restraints weight = 33972.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.068034 restraints weight = 17102.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069446 restraints weight = 11696.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.070239 restraints weight = 9437.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.070737 restraints weight = 8426.926| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 12230 Z= 0.259 Angle : 0.754 7.997 17678 Z= 0.428 Chirality : 0.049 0.280 2019 Planarity : 0.005 0.054 1290 Dihedral : 31.996 174.233 3807 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.96 % Allowed : 26.86 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.47 (0.30), residues: 730 helix: 1.44 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -3.00 (0.35), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 240 TYR 0.026 0.003 TYR B 98 PHE 0.017 0.002 PHE D1267 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.26 (12230) covalent geometry : angle 0.75439 / 0.43 (17678) hydrogen bonds : bond 0.05045 / 5.62 ( 746) hydrogen bonds : angle 3.50746 / 4.64 ( 1879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8113 (pp20) cc_final: 0.7313 (pp20) REVERT: A 468 GLN cc_start: 0.9125 (tt0) cc_final: 0.8642 (tm-30) REVERT: A 473 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8409 (tm-30) REVERT: A 485 GLN cc_start: 0.8856 (mt0) cc_final: 0.8469 (mt0) REVERT: A 520 MET cc_start: 0.8316 (mtt) cc_final: 0.7857 (mtp) REVERT: A 533 GLU cc_start: 0.8241 (pt0) cc_final: 0.7964 (pt0) REVERT: B 52 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8630 (tp30) REVERT: B 88 TYR cc_start: 0.8658 (m-10) cc_final: 0.8273 (m-10) REVERT: C 821 GLN cc_start: 0.9119 (mp10) cc_final: 0.8593 (mp10) REVERT: C 839 ARG cc_start: 0.8265 (mtt90) cc_final: 0.7996 (mtm-85) REVERT: C 853 TYR cc_start: 0.8903 (t80) cc_final: 0.8270 (t80) REVERT: C 867 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8667 (tm-30) REVERT: C 887 GLN cc_start: 0.9230 (tp40) cc_final: 0.8117 (tp-100) REVERT: C 901 LYS cc_start: 0.8900 (pttp) cc_final: 0.8414 (tptp) REVERT: C 912 HIS cc_start: 0.8330 (t70) cc_final: 0.7773 (t-90) REVERT: D 1268 GLU cc_start: 0.8968 (tp30) cc_final: 0.8500 (tp30) REVERT: D 1279 HIS cc_start: 0.8635 (t-90) cc_final: 0.8415 (t-90) REVERT: D 1281 ASN cc_start: 0.9365 (t0) cc_final: 0.8962 (t0) REVERT: D 1317 LYS cc_start: 0.9373 (ttmm) cc_final: 0.9032 (ttmt) REVERT: D 1318 TYR cc_start: 0.9441 (t80) cc_final: 0.9133 (t80) REVERT: E 668 GLN cc_start: 0.9077 (tt0) cc_final: 0.8160 (tm-30) REVERT: E 693 GLN cc_start: 0.9184 (tp40) cc_final: 0.8794 (tp40) REVERT: E 705 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8422 (tm-30) REVERT: E 720 MET cc_start: 0.8676 (tpp) cc_final: 0.8131 (mmm) REVERT: E 722 LYS cc_start: 0.9061 (pttt) cc_final: 0.8767 (ptpp) REVERT: E 723 ASP cc_start: 0.8518 (m-30) cc_final: 0.8231 (m-30) REVERT: E 725 GLN cc_start: 0.9282 (mt0) cc_final: 0.8985 (mt0) REVERT: E 733 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7679 (pt0) REVERT: F 244 LYS cc_start: 0.9040 (tttt) cc_final: 0.8499 (tttt) REVERT: F 274 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8670 (tm-30) REVERT: F 277 LYS cc_start: 0.9554 (mttm) cc_final: 0.9230 (mmtp) REVERT: F 284 MET cc_start: 0.8951 (tpp) cc_final: 0.8412 (mmm) REVERT: F 291 LYS cc_start: 0.9169 (tttp) cc_final: 0.8851 (ttpt) REVERT: G 1087 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8754 (tp-100) REVERT: H 1486 ILE cc_start: 0.9059 (mt) cc_final: 0.8749 (mt) outliers start: 43 outliers final: 31 residues processed: 299 average time/residue: 0.1207 time to fit residues: 50.0329 Evaluate side-chains 304 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1233 SER Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1253 SER Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1054 SER Chi-restraints excluded: chain G residue 1068 LEU Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1453 SER Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1488 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 30.0000 chunk 16 optimal weight: 30.0000 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.096736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.069262 restraints weight = 33383.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.071431 restraints weight = 16220.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.072857 restraints weight = 10864.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.073724 restraints weight = 8676.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074203 restraints weight = 7669.201| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 12230 Z= 0.165 Angle : 0.675 7.176 17678 Z= 0.394 Chirality : 0.047 0.277 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.837 174.639 3807 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.99 % Allowed : 29.29 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.82 (0.30), residues: 730 helix: 1.71 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -2.93 (0.36), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1034 TYR 0.019 0.002 TYR H1480 PHE 0.010 0.001 PHE E 667 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (12230) covalent geometry : angle 0.67541 / 0.39 (17678) hydrogen bonds : bond 0.04360 / 4.88 ( 746) hydrogen bonds : angle 3.20155 / 4.26 ( 1879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 289 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7995 (pp20) cc_final: 0.7283 (pp20) REVERT: A 468 GLN cc_start: 0.9084 (tt0) cc_final: 0.8504 (tm-30) REVERT: A 473 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 485 GLN cc_start: 0.8816 (mt0) cc_final: 0.8426 (mt0) REVERT: A 493 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: A 509 LEU cc_start: 0.9470 (mt) cc_final: 0.9182 (mp) REVERT: A 520 MET cc_start: 0.8277 (mtt) cc_final: 0.7802 (mtp) REVERT: A 533 GLU cc_start: 0.8236 (pt0) cc_final: 0.7945 (pt0) REVERT: B 52 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8539 (tp30) REVERT: C 821 GLN cc_start: 0.9083 (mp10) cc_final: 0.8829 (mp10) REVERT: C 853 TYR cc_start: 0.8803 (t80) cc_final: 0.8131 (t80) REVERT: C 867 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8611 (tm-30) REVERT: C 875 ASP cc_start: 0.8834 (m-30) cc_final: 0.8321 (p0) REVERT: C 884 ARG cc_start: 0.8952 (tpt170) cc_final: 0.8616 (tpt170) REVERT: C 887 GLN cc_start: 0.9168 (tp40) cc_final: 0.8146 (tp-100) REVERT: C 901 LYS cc_start: 0.8870 (pttp) cc_final: 0.8368 (tptp) REVERT: C 912 HIS cc_start: 0.8351 (t70) cc_final: 0.7713 (t-90) REVERT: D 1268 GLU cc_start: 0.9029 (tp30) cc_final: 0.8682 (tp30) REVERT: D 1281 ASN cc_start: 0.9358 (t0) cc_final: 0.8960 (t0) REVERT: D 1317 LYS cc_start: 0.9344 (ttmm) cc_final: 0.8974 (ttmt) REVERT: D 1318 TYR cc_start: 0.9450 (t80) cc_final: 0.9155 (t80) REVERT: E 656 LYS cc_start: 0.9089 (ptpp) cc_final: 0.8806 (ptpp) REVERT: E 668 GLN cc_start: 0.8948 (tt0) cc_final: 0.7983 (tm-30) REVERT: E 693 GLN cc_start: 0.9044 (tp40) cc_final: 0.8615 (tp40) REVERT: E 694 GLU cc_start: 0.8968 (tp30) cc_final: 0.8761 (tp30) REVERT: E 699 TYR cc_start: 0.9200 (t80) cc_final: 0.8963 (t80) REVERT: E 705 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8416 (tm-30) REVERT: E 720 MET cc_start: 0.8813 (tpp) cc_final: 0.8352 (mmm) REVERT: E 722 LYS cc_start: 0.8937 (pttt) cc_final: 0.8635 (ptpp) REVERT: E 723 ASP cc_start: 0.8431 (m-30) cc_final: 0.8187 (m-30) REVERT: E 725 GLN cc_start: 0.9204 (mt0) cc_final: 0.8915 (mt0) REVERT: E 733 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7803 (pt0) REVERT: F 225 ASN cc_start: 0.8841 (m-40) cc_final: 0.8510 (m110) REVERT: F 244 LYS cc_start: 0.9074 (tttt) cc_final: 0.8579 (tttt) REVERT: F 247 SER cc_start: 0.9206 (p) cc_final: 0.8943 (t) REVERT: F 274 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8676 (tm-30) REVERT: F 277 LYS cc_start: 0.9533 (mttm) cc_final: 0.9236 (mmtp) REVERT: G 1084 ARG cc_start: 0.9054 (tpt170) cc_final: 0.8532 (tpp80) REVERT: G 1087 GLN cc_start: 0.9156 (tp-100) cc_final: 0.8756 (tp-100) REVERT: G 1088 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9020 (mm) REVERT: H 1486 ILE cc_start: 0.8908 (mt) cc_final: 0.8667 (mt) REVERT: H 1490 GLU cc_start: 0.9080 (mp0) cc_final: 0.8855 (pm20) REVERT: H 1505 LYS cc_start: 0.9048 (mttt) cc_final: 0.8770 (mttm) outliers start: 37 outliers final: 25 residues processed: 303 average time/residue: 0.1154 time to fit residues: 48.7563 Evaluate side-chains 305 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1233 SER Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1088 LEU Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1488 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 40.0000 chunk 88 optimal weight: 0.0030 chunk 93 optimal weight: 0.0050 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.6606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.097911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.070543 restraints weight = 33295.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.072746 restraints weight = 15998.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074186 restraints weight = 10660.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.075047 restraints weight = 8512.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.075261 restraints weight = 7531.356| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12230 Z= 0.144 Angle : 0.665 7.958 17678 Z= 0.386 Chirality : 0.046 0.282 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.737 174.603 3804 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.37 % Allowed : 32.04 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.91 (0.30), residues: 730 helix: 1.74 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -2.80 (0.36), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1031 TYR 0.020 0.002 TYR D1280 PHE 0.024 0.002 PHE B 61 HIS 0.004 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (12230) covalent geometry : angle 0.66458 / 0.39 (17678) hydrogen bonds : bond 0.04217 / 4.74 ( 746) hydrogen bonds : angle 3.05721 / 4.09 ( 1879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 302 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8009 (pp20) cc_final: 0.7344 (pp20) REVERT: A 468 GLN cc_start: 0.9039 (tt0) cc_final: 0.8474 (tm-30) REVERT: A 473 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8221 (tm-30) REVERT: A 520 MET cc_start: 0.8195 (mtt) cc_final: 0.7714 (mtp) REVERT: A 533 GLU cc_start: 0.8221 (pt0) cc_final: 0.7969 (pt0) REVERT: B 52 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8471 (tp30) REVERT: B 61 PHE cc_start: 0.9331 (t80) cc_final: 0.9062 (t80) REVERT: B 88 TYR cc_start: 0.8365 (m-10) cc_final: 0.8107 (m-80) REVERT: C 821 GLN cc_start: 0.9096 (mp10) cc_final: 0.8829 (mp10) REVERT: C 853 TYR cc_start: 0.8751 (t80) cc_final: 0.8149 (t80) REVERT: C 867 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8617 (tm-30) REVERT: C 875 ASP cc_start: 0.8836 (m-30) cc_final: 0.8324 (p0) REVERT: C 884 ARG cc_start: 0.8947 (tpt170) cc_final: 0.8634 (tpt170) REVERT: C 887 GLN cc_start: 0.9159 (tp40) cc_final: 0.8153 (tp-100) REVERT: C 901 LYS cc_start: 0.8803 (pttp) cc_final: 0.8319 (tptp) REVERT: C 912 HIS cc_start: 0.8331 (t70) cc_final: 0.7679 (t-90) REVERT: D 1268 GLU cc_start: 0.9007 (tp30) cc_final: 0.8604 (tp30) REVERT: D 1279 HIS cc_start: 0.8615 (t-90) cc_final: 0.8337 (t70) REVERT: D 1281 ASN cc_start: 0.9331 (t0) cc_final: 0.8873 (t0) REVERT: D 1317 LYS cc_start: 0.9357 (ttmm) cc_final: 0.8982 (ttmt) REVERT: E 656 LYS cc_start: 0.9040 (ptpp) cc_final: 0.8810 (ptpp) REVERT: E 676 GLN cc_start: 0.8908 (tp40) cc_final: 0.8656 (tp40) REVERT: E 693 GLN cc_start: 0.9018 (tp40) cc_final: 0.8592 (tp40) REVERT: E 699 TYR cc_start: 0.9163 (t80) cc_final: 0.8901 (t80) REVERT: E 705 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8407 (tm-30) REVERT: E 708 ASN cc_start: 0.9347 (t0) cc_final: 0.9111 (t0) REVERT: E 720 MET cc_start: 0.8872 (tpp) cc_final: 0.8338 (mmm) REVERT: E 722 LYS cc_start: 0.8878 (pttt) cc_final: 0.8654 (ptpp) REVERT: E 733 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7532 (pt0) REVERT: F 225 ASN cc_start: 0.8820 (m110) cc_final: 0.8588 (m110) REVERT: F 244 LYS cc_start: 0.9198 (tttt) cc_final: 0.8554 (tttt) REVERT: F 247 SER cc_start: 0.9193 (p) cc_final: 0.8947 (t) REVERT: F 274 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8634 (tm-30) REVERT: F 277 LYS cc_start: 0.9520 (mttm) cc_final: 0.9220 (mmtp) REVERT: F 298 TYR cc_start: 0.9092 (m-80) cc_final: 0.8889 (m-80) REVERT: G 1045 ARG cc_start: 0.9340 (ptm160) cc_final: 0.9077 (ptm-80) REVERT: G 1084 ARG cc_start: 0.9038 (tpt170) cc_final: 0.8523 (tpp80) REVERT: G 1087 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8768 (tp-100) REVERT: G 1088 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8995 (mm) REVERT: H 1468 GLU cc_start: 0.8714 (tp30) cc_final: 0.8458 (tt0) REVERT: H 1486 ILE cc_start: 0.8820 (mt) cc_final: 0.8613 (mt) REVERT: H 1490 GLU cc_start: 0.9073 (mp0) cc_final: 0.8742 (mp0) outliers start: 27 outliers final: 21 residues processed: 309 average time/residue: 0.1150 time to fit residues: 49.8645 Evaluate side-chains 310 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 287 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1233 SER Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain G residue 1088 LEU Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1477 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN F 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.097244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.069941 restraints weight = 33581.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.072078 restraints weight = 16239.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.073535 restraints weight = 10855.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.074377 restraints weight = 8658.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.074849 restraints weight = 7661.104| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12230 Z= 0.169 Angle : 0.677 9.735 17678 Z= 0.388 Chirality : 0.046 0.277 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.745 174.452 3803 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.15 % Allowed : 32.20 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.31), residues: 730 helix: 1.79 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -2.76 (0.37), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1031 TYR 0.017 0.002 TYR C 860 PHE 0.018 0.002 PHE B 61 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (12230) covalent geometry : angle 0.67656 / 0.39 (17678) hydrogen bonds : bond 0.04307 / 4.83 ( 746) hydrogen bonds : angle 3.13115 / 4.17 ( 1879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 GLN cc_start: 0.9068 (tt0) cc_final: 0.8832 (tm-30) REVERT: A 473 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8376 (tm-30) REVERT: A 520 MET cc_start: 0.8212 (mtt) cc_final: 0.7708 (mtp) REVERT: B 81 VAL cc_start: 0.9532 (t) cc_final: 0.9256 (m) REVERT: B 88 TYR cc_start: 0.8425 (m-10) cc_final: 0.7852 (m-80) REVERT: C 821 GLN cc_start: 0.9094 (mt0) cc_final: 0.8816 (mp10) REVERT: C 853 TYR cc_start: 0.8808 (t80) cc_final: 0.8192 (t80) REVERT: C 867 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8782 (tm-30) REVERT: C 875 ASP cc_start: 0.8856 (m-30) cc_final: 0.8345 (p0) REVERT: C 887 GLN cc_start: 0.9168 (tp40) cc_final: 0.8878 (tp-100) REVERT: C 901 LYS cc_start: 0.8807 (pttp) cc_final: 0.8331 (tptp) REVERT: C 912 HIS cc_start: 0.8317 (t70) cc_final: 0.7712 (t-90) REVERT: D 1265 ASP cc_start: 0.8478 (t0) cc_final: 0.8262 (t0) REVERT: D 1268 GLU cc_start: 0.9062 (tp30) cc_final: 0.8609 (tp30) REVERT: D 1281 ASN cc_start: 0.9313 (t0) cc_final: 0.8907 (t0) REVERT: D 1317 LYS cc_start: 0.9340 (ttmm) cc_final: 0.8965 (ttmt) REVERT: E 656 LYS cc_start: 0.9057 (ptpp) cc_final: 0.8853 (ptpp) REVERT: E 693 GLN cc_start: 0.9060 (tp40) cc_final: 0.8593 (tp40) REVERT: E 694 GLU cc_start: 0.8865 (tp30) cc_final: 0.8547 (tp30) REVERT: E 699 TYR cc_start: 0.9161 (t80) cc_final: 0.8885 (t80) REVERT: E 705 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8454 (tm-30) REVERT: E 730 ILE cc_start: 0.9291 (mt) cc_final: 0.9028 (mm) REVERT: E 733 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7592 (pt0) REVERT: F 244 LYS cc_start: 0.9209 (tttt) cc_final: 0.8638 (tttt) REVERT: F 247 SER cc_start: 0.8968 (p) cc_final: 0.8767 (t) REVERT: F 274 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8662 (tm-30) REVERT: G 1084 ARG cc_start: 0.9043 (tpt170) cc_final: 0.8543 (tpp80) REVERT: G 1087 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8754 (tp-100) REVERT: G 1088 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9006 (mm) REVERT: H 1468 GLU cc_start: 0.8762 (tp30) cc_final: 0.8495 (tt0) REVERT: H 1486 ILE cc_start: 0.8884 (mt) cc_final: 0.8557 (mt) REVERT: H 1490 GLU cc_start: 0.9046 (mp0) cc_final: 0.8826 (mp0) outliers start: 38 outliers final: 29 residues processed: 300 average time/residue: 0.1140 time to fit residues: 48.1157 Evaluate side-chains 298 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 267 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1233 SER Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1082 THR Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain G residue 1088 LEU Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1477 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 16 optimal weight: 30.0000 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 13 optimal weight: 50.0000 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 30.0000 chunk 85 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.097740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.070724 restraints weight = 33394.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.072915 restraints weight = 16140.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.074381 restraints weight = 10737.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.075268 restraints weight = 8527.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.075787 restraints weight = 7503.360| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 12230 Z= 0.149 Angle : 0.677 16.040 17678 Z= 0.386 Chirality : 0.045 0.280 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.691 174.706 3803 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.02 % Allowed : 33.82 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.06 (0.31), residues: 730 helix: 1.84 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -2.81 (0.37), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1031 TYR 0.024 0.002 TYR F 298 PHE 0.027 0.002 PHE B 61 HIS 0.005 0.001 HIS E 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (12230) covalent geometry : angle 0.67703 / 0.39 (17678) hydrogen bonds : bond 0.04187 / 4.71 ( 746) hydrogen bonds : angle 3.04488 / 4.05 ( 1879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8002 (pp20) cc_final: 0.7305 (pp20) REVERT: A 460 LEU cc_start: 0.8721 (mm) cc_final: 0.7918 (tp) REVERT: A 468 GLN cc_start: 0.9053 (tt0) cc_final: 0.8816 (tm-30) REVERT: A 473 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8361 (tm-30) REVERT: A 520 MET cc_start: 0.8163 (mtt) cc_final: 0.7651 (mtp) REVERT: B 61 PHE cc_start: 0.9339 (t80) cc_final: 0.9085 (t80) REVERT: B 88 TYR cc_start: 0.8398 (m-10) cc_final: 0.7858 (m-80) REVERT: C 821 GLN cc_start: 0.9082 (mt0) cc_final: 0.8797 (mp10) REVERT: C 853 TYR cc_start: 0.8669 (t80) cc_final: 0.7962 (t80) REVERT: C 867 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8759 (tm-30) REVERT: C 875 ASP cc_start: 0.8849 (m-30) cc_final: 0.8332 (p0) REVERT: C 887 GLN cc_start: 0.9155 (tp40) cc_final: 0.8869 (tp-100) REVERT: C 901 LYS cc_start: 0.8747 (pttp) cc_final: 0.8234 (tptp) REVERT: C 912 HIS cc_start: 0.8302 (t70) cc_final: 0.7690 (t-90) REVERT: D 1232 GLU cc_start: 0.7781 (tp30) cc_final: 0.7502 (tp30) REVERT: D 1268 GLU cc_start: 0.9067 (tp30) cc_final: 0.8623 (tp30) REVERT: D 1279 HIS cc_start: 0.8643 (t-90) cc_final: 0.8365 (t70) REVERT: D 1281 ASN cc_start: 0.9304 (t0) cc_final: 0.8899 (t0) REVERT: D 1317 LYS cc_start: 0.9329 (ttmm) cc_final: 0.8955 (ttmt) REVERT: E 668 GLN cc_start: 0.8981 (tt0) cc_final: 0.8075 (tm-30) REVERT: E 674 ILE cc_start: 0.9618 (mm) cc_final: 0.9358 (mt) REVERT: E 676 GLN cc_start: 0.8883 (tp40) cc_final: 0.8660 (tp40) REVERT: E 693 GLN cc_start: 0.9020 (tp40) cc_final: 0.8557 (tp40) REVERT: E 699 TYR cc_start: 0.9157 (t80) cc_final: 0.8895 (t80) REVERT: E 705 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8441 (tm-30) REVERT: E 708 ASN cc_start: 0.9330 (t0) cc_final: 0.9099 (t0) REVERT: E 733 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7422 (pt0) REVERT: F 244 LYS cc_start: 0.9203 (tttt) cc_final: 0.8607 (tttt) REVERT: F 274 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8633 (tm-30) REVERT: G 1026 GLN cc_start: 0.8618 (mm110) cc_final: 0.8038 (mp10) REVERT: G 1045 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.8910 (ptm160) REVERT: G 1084 ARG cc_start: 0.9037 (tpt170) cc_final: 0.8537 (tpp80) REVERT: G 1087 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8740 (tp-100) REVERT: G 1088 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8983 (mm) REVERT: H 1468 GLU cc_start: 0.8759 (tp30) cc_final: 0.8493 (tt0) REVERT: H 1486 ILE cc_start: 0.8830 (mt) cc_final: 0.8491 (mt) REVERT: H 1490 GLU cc_start: 0.9015 (mp0) cc_final: 0.8759 (mp0) outliers start: 31 outliers final: 25 residues processed: 296 average time/residue: 0.1112 time to fit residues: 46.4949 Evaluate side-chains 305 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1045 ARG Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain G residue 1088 LEU Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1509 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 52 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.098160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070978 restraints weight = 33612.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.073138 restraints weight = 16254.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.074600 restraints weight = 10822.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.075433 restraints weight = 8612.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.075950 restraints weight = 7630.109| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12230 Z= 0.154 Angle : 0.670 10.247 17678 Z= 0.384 Chirality : 0.045 0.278 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.668 174.562 3803 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.50 % Allowed : 34.47 % Favored : 60.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.99 (0.31), residues: 730 helix: 1.77 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -2.75 (0.37), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 529 TYR 0.023 0.002 TYR D1237 PHE 0.024 0.002 PHE B 61 HIS 0.004 0.001 HIS E 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (12230) covalent geometry : angle 0.67003 / 0.38 (17678) hydrogen bonds : bond 0.04208 / 4.75 ( 746) hydrogen bonds : angle 3.08325 / 4.15 ( 1879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 284 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8036 (pp20) cc_final: 0.7404 (pp20) REVERT: A 468 GLN cc_start: 0.9030 (tt0) cc_final: 0.8801 (tm-30) REVERT: A 473 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 493 GLN cc_start: 0.9174 (tt0) cc_final: 0.8954 (tp40) REVERT: A 520 MET cc_start: 0.8156 (mtt) cc_final: 0.7626 (mtp) REVERT: B 88 TYR cc_start: 0.8408 (m-10) cc_final: 0.7917 (m-80) REVERT: C 821 GLN cc_start: 0.9096 (mt0) cc_final: 0.8794 (mp10) REVERT: C 853 TYR cc_start: 0.8665 (t80) cc_final: 0.8044 (t80) REVERT: C 867 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8759 (tm-30) REVERT: C 875 ASP cc_start: 0.8830 (m-30) cc_final: 0.8314 (p0) REVERT: C 887 GLN cc_start: 0.9160 (tp40) cc_final: 0.8871 (tp-100) REVERT: C 901 LYS cc_start: 0.8730 (pttp) cc_final: 0.8207 (tptp) REVERT: C 912 HIS cc_start: 0.8295 (t70) cc_final: 0.7725 (t-90) REVERT: D 1231 LYS cc_start: 0.9117 (tppt) cc_final: 0.8774 (tptt) REVERT: D 1268 GLU cc_start: 0.9065 (tp30) cc_final: 0.8577 (tp30) REVERT: D 1279 HIS cc_start: 0.8643 (t-90) cc_final: 0.8356 (t70) REVERT: D 1281 ASN cc_start: 0.9281 (t0) cc_final: 0.8882 (t0) REVERT: D 1317 LYS cc_start: 0.9347 (ttmm) cc_final: 0.8979 (ttmt) REVERT: D 1318 TYR cc_start: 0.9382 (t80) cc_final: 0.9081 (t80) REVERT: E 674 ILE cc_start: 0.9607 (mm) cc_final: 0.9362 (mt) REVERT: E 676 GLN cc_start: 0.8877 (tp40) cc_final: 0.8656 (tp40) REVERT: E 693 GLN cc_start: 0.9032 (tp40) cc_final: 0.8571 (tp40) REVERT: E 699 TYR cc_start: 0.9167 (t80) cc_final: 0.8907 (t80) REVERT: E 705 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8566 (tm-30) REVERT: E 733 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7363 (pt0) REVERT: F 244 LYS cc_start: 0.9195 (tttt) cc_final: 0.8819 (tttt) REVERT: F 274 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8593 (tm-30) REVERT: G 1026 GLN cc_start: 0.8630 (mm110) cc_final: 0.8054 (mp10) REVERT: G 1084 ARG cc_start: 0.9033 (tpt170) cc_final: 0.8534 (tpp80) REVERT: G 1087 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8751 (tp-100) REVERT: G 1088 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8974 (mm) REVERT: H 1468 GLU cc_start: 0.8759 (tp30) cc_final: 0.8491 (tt0) REVERT: H 1486 ILE cc_start: 0.8866 (mt) cc_final: 0.8609 (mt) REVERT: H 1490 GLU cc_start: 0.9000 (mp0) cc_final: 0.8655 (mp0) outliers start: 34 outliers final: 28 residues processed: 295 average time/residue: 0.1096 time to fit residues: 45.7580 Evaluate side-chains 310 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 280 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1017 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain G residue 1088 LEU Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1509 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.0050 chunk 38 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.099181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.072061 restraints weight = 33161.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074260 restraints weight = 16184.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.075740 restraints weight = 10810.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.076610 restraints weight = 8605.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.077106 restraints weight = 7603.896| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 12230 Z= 0.149 Angle : 0.683 16.050 17678 Z= 0.388 Chirality : 0.044 0.283 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.610 174.778 3803 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 5.34 % Allowed : 33.98 % Favored : 60.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.31), residues: 730 helix: 1.71 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.64 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 845 TYR 0.024 0.002 TYR D1237 PHE 0.023 0.002 PHE B 61 HIS 0.004 0.001 HIS E 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (12230) covalent geometry : angle 0.68292 / 0.39 (17678) hydrogen bonds : bond 0.04189 / 4.73 ( 746) hydrogen bonds : angle 3.07218 / 4.10 ( 1879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7886 (pp20) cc_final: 0.7608 (pp20) REVERT: A 468 GLN cc_start: 0.9014 (tt0) cc_final: 0.8812 (tm-30) REVERT: A 473 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 520 MET cc_start: 0.8099 (mtt) cc_final: 0.7569 (mtp) REVERT: A 528 ARG cc_start: 0.8479 (mtp-110) cc_final: 0.8188 (mtp-110) REVERT: B 61 PHE cc_start: 0.9337 (t80) cc_final: 0.9084 (t80) REVERT: B 88 TYR cc_start: 0.8392 (m-10) cc_final: 0.7997 (m-80) REVERT: C 821 GLN cc_start: 0.9101 (mt0) cc_final: 0.8807 (mp10) REVERT: C 853 TYR cc_start: 0.8629 (t80) cc_final: 0.8008 (t80) REVERT: C 867 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8747 (tm-30) REVERT: C 875 ASP cc_start: 0.8811 (m-30) cc_final: 0.8314 (p0) REVERT: C 887 GLN cc_start: 0.9151 (tp40) cc_final: 0.8905 (tp-100) REVERT: C 901 LYS cc_start: 0.8672 (pttp) cc_final: 0.8267 (tptp) REVERT: C 912 HIS cc_start: 0.8271 (t70) cc_final: 0.7708 (t-90) REVERT: D 1231 LYS cc_start: 0.9111 (tppt) cc_final: 0.8790 (tptt) REVERT: D 1268 GLU cc_start: 0.9036 (tp30) cc_final: 0.8566 (tp30) REVERT: D 1279 HIS cc_start: 0.8607 (t-90) cc_final: 0.8351 (t70) REVERT: D 1281 ASN cc_start: 0.9232 (t0) cc_final: 0.8858 (t0) REVERT: D 1317 LYS cc_start: 0.9348 (ttmm) cc_final: 0.8975 (ttmt) REVERT: E 668 GLN cc_start: 0.8972 (tt0) cc_final: 0.7839 (tm-30) REVERT: E 674 ILE cc_start: 0.9593 (mm) cc_final: 0.9365 (mt) REVERT: E 676 GLN cc_start: 0.8843 (tp40) cc_final: 0.8640 (tp40) REVERT: E 693 GLN cc_start: 0.9010 (tp40) cc_final: 0.8545 (tp40) REVERT: E 694 GLU cc_start: 0.8923 (tp30) cc_final: 0.8680 (tp30) REVERT: E 699 TYR cc_start: 0.9185 (t80) cc_final: 0.8934 (t80) REVERT: E 705 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8635 (tm-30) REVERT: E 720 MET cc_start: 0.8914 (mmm) cc_final: 0.8526 (mmp) REVERT: E 733 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7341 (pt0) REVERT: F 244 LYS cc_start: 0.9192 (tttt) cc_final: 0.8815 (tttt) REVERT: F 274 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8562 (tm-30) REVERT: G 1045 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.8920 (ptm160) REVERT: G 1084 ARG cc_start: 0.9022 (tpt170) cc_final: 0.8524 (tpp80) REVERT: G 1087 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8728 (tp-100) REVERT: G 1088 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8972 (mm) REVERT: H 1468 GLU cc_start: 0.8780 (tp30) cc_final: 0.8455 (tt0) REVERT: H 1486 ILE cc_start: 0.8851 (mt) cc_final: 0.8604 (mt) REVERT: H 1490 GLU cc_start: 0.8979 (mp0) cc_final: 0.8637 (mp0) outliers start: 33 outliers final: 26 residues processed: 300 average time/residue: 0.1095 time to fit residues: 46.5236 Evaluate side-chains 306 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 719 ILE Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1045 ARG Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain G residue 1088 LEU Chi-restraints excluded: chain H residue 1433 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 94 optimal weight: 0.1980 chunk 91 optimal weight: 0.0030 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 30.0000 chunk 13 optimal weight: 50.0000 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071167 restraints weight = 33758.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.073339 restraints weight = 16292.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.074815 restraints weight = 10825.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.075702 restraints weight = 8581.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.076182 restraints weight = 7552.463| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 12230 Z= 0.165 Angle : 0.703 16.783 17678 Z= 0.395 Chirality : 0.044 0.279 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.623 174.505 3803 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.69 % Allowed : 36.73 % Favored : 58.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.31), residues: 730 helix: 1.74 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.70 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 731 TYR 0.019 0.002 TYR D1237 PHE 0.021 0.002 PHE A 467 HIS 0.004 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (12230) covalent geometry : angle 0.70262 / 0.40 (17678) hydrogen bonds : bond 0.04253 / 4.82 ( 746) hydrogen bonds : angle 3.22098 / 4.26 ( 1879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 GLN cc_start: 0.9063 (tt0) cc_final: 0.8449 (tm-30) REVERT: A 473 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8360 (tm-30) REVERT: A 520 MET cc_start: 0.8130 (mtt) cc_final: 0.7498 (mtp) REVERT: B 88 TYR cc_start: 0.8427 (m-10) cc_final: 0.8049 (m-80) REVERT: C 821 GLN cc_start: 0.9128 (mt0) cc_final: 0.8914 (mp10) REVERT: C 853 TYR cc_start: 0.8626 (t80) cc_final: 0.8007 (t80) REVERT: C 867 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8800 (tm-30) REVERT: C 875 ASP cc_start: 0.8853 (m-30) cc_final: 0.8339 (p0) REVERT: C 887 GLN cc_start: 0.9106 (tp40) cc_final: 0.8826 (tp-100) REVERT: C 901 LYS cc_start: 0.8698 (pttp) cc_final: 0.8267 (tptp) REVERT: C 912 HIS cc_start: 0.8296 (t70) cc_final: 0.7692 (t-90) REVERT: D 1231 LYS cc_start: 0.9111 (tppt) cc_final: 0.8773 (tptt) REVERT: D 1268 GLU cc_start: 0.9103 (tp30) cc_final: 0.8613 (tp30) REVERT: D 1279 HIS cc_start: 0.8657 (t-90) cc_final: 0.8373 (t70) REVERT: D 1281 ASN cc_start: 0.9226 (t0) cc_final: 0.8864 (t0) REVERT: D 1317 LYS cc_start: 0.9330 (ttmm) cc_final: 0.8999 (ttmt) REVERT: E 674 ILE cc_start: 0.9593 (mm) cc_final: 0.9356 (mt) REVERT: E 676 GLN cc_start: 0.8877 (tp40) cc_final: 0.8659 (tp40) REVERT: E 693 GLN cc_start: 0.9057 (tp40) cc_final: 0.8499 (tp40) REVERT: E 694 GLU cc_start: 0.8910 (tp30) cc_final: 0.8655 (tp30) REVERT: E 699 TYR cc_start: 0.9177 (t80) cc_final: 0.8917 (t80) REVERT: E 708 ASN cc_start: 0.9140 (t0) cc_final: 0.8874 (t0) REVERT: E 720 MET cc_start: 0.8817 (mmm) cc_final: 0.8563 (mmt) REVERT: E 733 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7304 (pt0) REVERT: F 244 LYS cc_start: 0.9158 (tttt) cc_final: 0.8727 (tttt) REVERT: F 252 GLU cc_start: 0.8750 (mp0) cc_final: 0.8077 (tp30) REVERT: F 274 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8583 (tm-30) REVERT: G 1084 ARG cc_start: 0.9017 (tpt170) cc_final: 0.8521 (tpp80) REVERT: G 1087 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8699 (tp-100) REVERT: G 1088 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8954 (mm) REVERT: H 1468 GLU cc_start: 0.8811 (tp30) cc_final: 0.8437 (tt0) REVERT: H 1486 ILE cc_start: 0.8880 (mt) cc_final: 0.8617 (mt) REVERT: H 1490 GLU cc_start: 0.9028 (mp0) cc_final: 0.8751 (mp0) outliers start: 29 outliers final: 23 residues processed: 286 average time/residue: 0.1120 time to fit residues: 45.3304 Evaluate side-chains 293 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain G residue 1088 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 30.0000 chunk 50 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.099082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071591 restraints weight = 33206.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073743 restraints weight = 16325.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.075197 restraints weight = 10943.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.076093 restraints weight = 8708.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.076604 restraints weight = 7658.950| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 12230 Z= 0.162 Angle : 0.700 16.638 17678 Z= 0.393 Chirality : 0.045 0.308 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.596 174.614 3803 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.69 % Allowed : 37.54 % Favored : 57.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.96 (0.30), residues: 730 helix: 1.72 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.63 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 845 TYR 0.023 0.002 TYR H1437 PHE 0.029 0.002 PHE B 61 HIS 0.004 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (12230) covalent geometry : angle 0.69979 / 0.39 (17678) hydrogen bonds : bond 0.04217 / 4.78 ( 746) hydrogen bonds : angle 3.23085 / 4.29 ( 1879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.81 seconds wall clock time: 35 minutes 11.53 seconds (2111.53 seconds total)