Starting phenix.real_space_refine on Fri Jul 3 00:49:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m1x_23626/07_2026/7m1x_23626.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m1x_23626/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7m1x_23626/07_2026/7m1x_23626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m1x_23626/07_2026/7m1x_23626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m1x_23626/07_2026/7m1x_23626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m1x_23626/07_2026/7m1x_23626.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.51, per 1000 atoms: 0.22 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: 0.99 Conformation dependent library (CDL) restraints added in 322.8 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: 1.46 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: 3.51 Time building geometry restraints manager: 1.47 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: 15966 1.55 - 3.09: 1545 3.09 - 4.64: 141 4.64 - 6.19: 18 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.200 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- 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 : 0.917 7.733 17678 Z= 0.780 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 0.91723 / 0.78 (17678) hydrogen bonds : bond 0.09819 / 10.83 ( 746) hydrogen bonds : angle 4.08767 / 5.46 ( 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 : 0.300 Fit side-chains revert: symmetry clash 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: 0.8428 (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: 0.8593 (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: 0.8534 (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: 0.9085 (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: 0.8871 (m-80) REVERT: C 821 GLN cc_start: 0.9179 (mp10) cc_final: 0.8943 (mp10) REVERT: C 839 ARG cc_start: 0.8535 (mtt90) cc_final: 0.8278 (mtm-85) REVERT: C 853 TYR cc_start: 0.8956 (t80) cc_final: 0.8400 (t80) REVERT: C 887 GLN cc_start: 0.9200 (tp40) cc_final: 0.8865 (tp-100) REVERT: C 901 LYS cc_start: 0.9030 (pttp) cc_final: 0.8403 (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: 0.8279 (p0) REVERT: D 1265 ASP cc_start: 0.8648 (t70) cc_final: 0.8419 (t0) REVERT: D 1268 GLU cc_start: 0.8987 (tp30) cc_final: 0.8664 (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: 0.8843 (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: 0.8095 (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: 0.7953 (tm-30) REVERT: E 690 MET cc_start: 0.9194 (tpt) cc_final: 0.8972 (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: 0.8986 (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: 0.8487 (ttpt) REVERT: F 243 VAL cc_start: 0.9290 (t) cc_final: 0.9033 (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: 0.8929 (tp40) REVERT: G 1088 LEU cc_start: 0.9347 (mm) cc_final: 0.8950 (mm) REVERT: G 1093 ASP cc_start: 0.8276 (t70) cc_final: 0.8010 (t0) REVERT: H 1433 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8616 (m) REVERT: H 1461 SER cc_start: 0.9526 (t) cc_final: 0.9325 (t) 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: 0.8685 (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: 0.1244 time to fit residues: 58.7999 Evaluate side-chains 287 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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: 1.9990 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: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.095849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.068601 restraints weight = 33009.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.070720 restraints weight = 16225.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.072141 restraints weight = 10923.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.073017 restraints weight = 8749.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073468 restraints weight = 7731.366| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12230 Z= 0.168 Angle : 0.700 7.706 17678 Z= 0.408 Chirality : 0.048 0.249 2019 Planarity : 0.005 0.062 1290 Dihedral : 32.188 176.077 3809 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.50 % Allowed : 22.98 % Favored : 71.52 % 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: -0.02 (0.30), residues: 730 helix: 1.07 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -3.11 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1230 TYR 0.019 0.002 TYR D1318 PHE 0.007 0.001 PHE F 300 HIS 0.007 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.17 (12230) covalent geometry : angle 0.70040 / 0.41 (17678) hydrogen bonds : bond 0.04619 / 5.07 ( 746) hydrogen bonds : angle 3.37781 / 4.46 ( 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: 34 poor density : 316 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8066 (pp20) cc_final: 0.7324 (pp20) REVERT: A 461 LEU cc_start: 0.8823 (mm) cc_final: 0.8612 (mm) REVERT: A 468 GLN cc_start: 0.9073 (tt0) cc_final: 0.8517 (tm-30) REVERT: A 473 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 485 GLN cc_start: 0.8814 (mt0) cc_final: 0.8327 (mt0) REVERT: A 520 MET cc_start: 0.8229 (mtt) cc_final: 0.7788 (mtp) REVERT: B 52 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8502 (tp30) REVERT: B 81 VAL cc_start: 0.9368 (t) cc_final: 0.9017 (p) REVERT: B 92 ARG cc_start: 0.8686 (tmm-80) cc_final: 0.8098 (tmm-80) REVERT: C 826 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7759 (mm110) REVERT: C 839 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7891 (mtm-85) REVERT: C 867 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8559 (tm-30) REVERT: C 887 GLN cc_start: 0.9249 (tp40) cc_final: 0.8885 (tp-100) REVERT: C 901 LYS cc_start: 0.8932 (pttp) cc_final: 0.8374 (tptp) REVERT: C 912 HIS cc_start: 0.8294 (t70) cc_final: 0.7682 (t-90) REVERT: D 1248 ASP cc_start: 0.8279 (p0) cc_final: 0.8071 (p0) REVERT: D 1268 GLU cc_start: 0.8900 (tp30) cc_final: 0.8522 (tp30) REVERT: D 1279 HIS cc_start: 0.8602 (t-90) cc_final: 0.8098 (t70) REVERT: D 1281 ASN cc_start: 0.9354 (t0) cc_final: 0.8918 (t0) REVERT: D 1317 LYS cc_start: 0.9314 (ttmm) cc_final: 0.8997 (ttmt) REVERT: E 699 TYR cc_start: 0.9174 (t80) cc_final: 0.8910 (t80) REVERT: E 705 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8416 (tm-30) REVERT: E 718 THR cc_start: 0.8817 (p) cc_final: 0.8055 (p) REVERT: E 720 MET cc_start: 0.8608 (tpp) cc_final: 0.7445 (mpp) REVERT: E 722 LYS cc_start: 0.9006 (pttt) cc_final: 0.8682 (ptpp) REVERT: E 723 ASP cc_start: 0.8496 (m-30) cc_final: 0.8257 (m-30) REVERT: E 725 GLN cc_start: 0.9191 (mt0) cc_final: 0.8928 (mt0) REVERT: E 733 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7828 (mt-10) REVERT: F 231 LYS cc_start: 0.8891 (tttt) cc_final: 0.8659 (ttpt) REVERT: F 243 VAL cc_start: 0.9404 (t) cc_final: 0.9197 (p) REVERT: F 244 LYS cc_start: 0.9032 (tttt) cc_final: 0.8473 (tttt) REVERT: F 249 LEU cc_start: 0.9257 (mt) cc_final: 0.8982 (mm) REVERT: F 252 GLU cc_start: 0.8747 (mp0) cc_final: 0.8523 (mp0) REVERT: F 274 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8757 (tm-30) REVERT: F 284 MET cc_start: 0.8938 (tpp) cc_final: 0.8466 (mmm) REVERT: F 291 LYS cc_start: 0.9125 (tttp) cc_final: 0.8782 (ttpt) REVERT: G 1034 ARG cc_start: 0.9378 (tmm160) cc_final: 0.8189 (ttm170) REVERT: G 1045 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8909 (ptm160) REVERT: G 1084 ARG cc_start: 0.8905 (tpt170) cc_final: 0.8635 (tpp80) REVERT: G 1087 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8835 (tp40) REVERT: G 1088 LEU cc_start: 0.9353 (mm) cc_final: 0.9048 (mm) REVERT: H 1468 GLU cc_start: 0.8669 (tp30) cc_final: 0.8296 (tt0) REVERT: H 1486 ILE cc_start: 0.9053 (mt) cc_final: 0.8724 (mt) outliers start: 34 outliers final: 24 residues processed: 333 average time/residue: 0.1050 time to fit residues: 48.3288 Evaluate side-chains 306 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 281 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 865 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 1045 ARG Chi-restraints excluded: chain G residue 1049 THR 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: 10.0000 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 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: 4.9990 chunk 23 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 G1033 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.094974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.067446 restraints weight = 33650.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.069594 restraints weight = 16599.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.071024 restraints weight = 11178.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071885 restraints weight = 8948.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072366 restraints weight = 7916.794| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12230 Z= 0.214 Angle : 0.710 7.847 17678 Z= 0.410 Chirality : 0.047 0.259 2019 Planarity : 0.005 0.062 1290 Dihedral : 32.023 175.048 3807 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 6.63 % Allowed : 27.51 % Favored : 65.86 % 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: 0.56 (0.30), residues: 730 helix: 1.52 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -2.98 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1230 TYR 0.024 0.003 TYR D1318 PHE 0.013 0.002 PHE D1267 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 (12230) covalent geometry : angle 0.71031 / 0.41 (17678) hydrogen bonds : bond 0.04795 / 5.32 ( 746) hydrogen bonds : angle 3.37428 / 4.47 ( 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 327 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 286 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8098 (pp20) cc_final: 0.7318 (pp20) REVERT: A 468 GLN cc_start: 0.9099 (tt0) cc_final: 0.8543 (tm-30) REVERT: A 473 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8352 (tm-30) REVERT: A 485 GLN cc_start: 0.8830 (mt0) cc_final: 0.8400 (mt0) REVERT: A 520 MET cc_start: 0.8276 (mtt) cc_final: 0.7844 (mtp) REVERT: A 533 GLU cc_start: 0.8208 (pt0) cc_final: 0.7923 (pt0) REVERT: B 52 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8597 (tp30) REVERT: B 81 VAL cc_start: 0.9373 (t) cc_final: 0.9068 (p) REVERT: B 88 TYR cc_start: 0.8608 (m-10) cc_final: 0.8280 (m-10) REVERT: B 92 ARG cc_start: 0.8817 (tmm-80) cc_final: 0.8134 (tmm-80) REVERT: C 821 GLN cc_start: 0.9107 (mp10) cc_final: 0.8560 (mp10) REVERT: C 822 ARG cc_start: 0.9198 (ttt-90) cc_final: 0.8947 (ttt-90) REVERT: C 839 ARG cc_start: 0.8242 (mtt90) cc_final: 0.7963 (mtm-85) REVERT: C 853 TYR cc_start: 0.8893 (t80) cc_final: 0.8256 (t80) REVERT: C 867 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8639 (tm-30) REVERT: C 887 GLN cc_start: 0.9217 (tp40) cc_final: 0.8145 (tp-100) REVERT: C 901 LYS cc_start: 0.8897 (pttp) cc_final: 0.8444 (tptp) REVERT: C 912 HIS cc_start: 0.8319 (t70) cc_final: 0.7775 (t-90) REVERT: D 1268 GLU cc_start: 0.8984 (tp30) cc_final: 0.8512 (tp30) REVERT: D 1279 HIS cc_start: 0.8634 (t-90) cc_final: 0.8385 (t-90) REVERT: D 1281 ASN cc_start: 0.9349 (t0) cc_final: 0.8935 (t0) REVERT: D 1317 LYS cc_start: 0.9338 (ttmm) cc_final: 0.8976 (ttmt) REVERT: E 668 GLN cc_start: 0.9062 (tt0) cc_final: 0.8133 (tm-30) REVERT: E 690 MET cc_start: 0.8804 (tpp) cc_final: 0.8572 (mmm) REVERT: E 693 GLN cc_start: 0.9163 (tp40) cc_final: 0.8772 (tp40) REVERT: E 705 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8426 (tm-30) REVERT: E 720 MET cc_start: 0.8697 (tpp) cc_final: 0.8140 (mmm) REVERT: E 722 LYS cc_start: 0.9036 (pttt) cc_final: 0.8742 (ptpp) REVERT: E 723 ASP cc_start: 0.8505 (m-30) cc_final: 0.8222 (m-30) REVERT: E 725 GLN cc_start: 0.9283 (mt0) cc_final: 0.8985 (mt0) REVERT: F 244 LYS cc_start: 0.9038 (tttt) cc_final: 0.8490 (tttt) REVERT: F 274 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8679 (tm-30) REVERT: F 284 MET cc_start: 0.8980 (tpp) cc_final: 0.8728 (tpp) REVERT: F 291 LYS cc_start: 0.9156 (tttp) cc_final: 0.8823 (ttpt) REVERT: G 1045 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8871 (ptm160) REVERT: G 1084 ARG cc_start: 0.8932 (tpt170) cc_final: 0.8487 (tpp80) REVERT: G 1087 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8750 (tp-100) REVERT: G 1088 LEU cc_start: 0.9342 (mm) cc_final: 0.9039 (mm) REVERT: H 1486 ILE cc_start: 0.9050 (mt) cc_final: 0.8712 (mt) REVERT: H 1490 GLU cc_start: 0.8956 (mp0) cc_final: 0.8699 (mp0) outliers start: 41 outliers final: 31 residues processed: 306 average time/residue: 0.1083 time to fit residues: 45.9290 Evaluate side-chains 304 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 60 VAL 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 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1253 SER Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS 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 1045 ARG 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 1449 THR 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: 3.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** B 93 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 = 0.3733 r_free = 0.3733 target = 0.096764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.069420 restraints weight = 33420.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.071608 restraints weight = 16192.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.073046 restraints weight = 10819.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.073902 restraints weight = 8627.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074398 restraints weight = 7621.385| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12230 Z= 0.163 Angle : 0.663 6.801 17678 Z= 0.390 Chirality : 0.046 0.254 2019 Planarity : 0.004 0.053 1290 Dihedral : 31.908 175.095 3807 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.83 % Allowed : 28.96 % Favored : 65.21 % 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: 0.88 (0.30), residues: 730 helix: 1.75 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.89 (0.36), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1034 TYR 0.025 0.002 TYR D1318 PHE 0.010 0.002 PHE E 667 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (12230) covalent geometry : angle 0.66332 / 0.39 (17678) hydrogen bonds : bond 0.04332 / 4.82 ( 746) hydrogen bonds : angle 3.18694 / 4.22 ( 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 324 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7988 (pp20) cc_final: 0.7278 (pp20) REVERT: A 468 GLN cc_start: 0.9101 (tt0) cc_final: 0.8493 (tm-30) REVERT: A 473 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 485 GLN cc_start: 0.8786 (mt0) cc_final: 0.8493 (mt0) REVERT: A 520 MET cc_start: 0.8276 (mtt) cc_final: 0.7726 (mtp) REVERT: A 533 GLU cc_start: 0.8280 (pt0) cc_final: 0.8003 (pt0) REVERT: B 52 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8554 (tp30) REVERT: B 92 ARG cc_start: 0.8821 (tmm-80) cc_final: 0.8019 (tmm-80) REVERT: C 821 GLN cc_start: 0.9121 (mp10) cc_final: 0.8885 (mp10) REVERT: C 822 ARG cc_start: 0.9204 (ttt-90) cc_final: 0.8836 (ttt-90) REVERT: C 853 TYR cc_start: 0.8818 (t80) cc_final: 0.8122 (t80) REVERT: C 867 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8647 (tm-30) REVERT: C 875 ASP cc_start: 0.8858 (m-30) cc_final: 0.8340 (p0) REVERT: C 884 ARG cc_start: 0.8874 (tpt170) cc_final: 0.8556 (tpt170) REVERT: C 887 GLN cc_start: 0.9130 (tp40) cc_final: 0.8109 (tp-100) REVERT: C 901 LYS cc_start: 0.8904 (pttp) cc_final: 0.8371 (tptp) REVERT: C 912 HIS cc_start: 0.8423 (t70) cc_final: 0.7730 (t-90) REVERT: D 1268 GLU cc_start: 0.9069 (tp30) cc_final: 0.8717 (tp30) REVERT: D 1281 ASN cc_start: 0.9358 (t0) cc_final: 0.8963 (t0) REVERT: D 1317 LYS cc_start: 0.9312 (ttmm) cc_final: 0.8958 (ttmt) REVERT: E 656 LYS cc_start: 0.9085 (ptpp) cc_final: 0.8792 (ptpp) REVERT: E 693 GLN cc_start: 0.9052 (tp40) cc_final: 0.8590 (tp40) REVERT: E 694 GLU cc_start: 0.8929 (tp30) cc_final: 0.8717 (tp30) REVERT: E 705 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8447 (tm-30) REVERT: E 720 MET cc_start: 0.8842 (tpp) cc_final: 0.8357 (mmm) REVERT: E 722 LYS cc_start: 0.8955 (pttt) cc_final: 0.8683 (ptpp) REVERT: F 225 ASN cc_start: 0.8878 (m-40) cc_final: 0.8614 (m110) REVERT: F 244 LYS cc_start: 0.9084 (tttt) cc_final: 0.8512 (tttt) REVERT: F 247 SER cc_start: 0.9216 (p) cc_final: 0.8966 (t) REVERT: F 274 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8748 (tm-30) REVERT: F 277 LYS cc_start: 0.9538 (mttm) cc_final: 0.9316 (mttm) REVERT: G 1084 ARG cc_start: 0.8923 (tpt170) cc_final: 0.8467 (tpp80) REVERT: G 1087 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8757 (tp-100) REVERT: G 1088 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9004 (mm) REVERT: H 1468 GLU cc_start: 0.8749 (tp30) cc_final: 0.8503 (tt0) REVERT: H 1486 ILE cc_start: 0.8964 (mt) cc_final: 0.8633 (mt) REVERT: H 1490 GLU cc_start: 0.9030 (mp0) cc_final: 0.8742 (mp0) outliers start: 36 outliers final: 23 residues processed: 303 average time/residue: 0.1094 time to fit residues: 45.6309 Evaluate side-chains 297 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 273 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1229 THR 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.0570 chunk 25 optimal weight: 40.0000 chunk 88 optimal weight: 0.4980 chunk 93 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.098169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.070984 restraints weight = 33355.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.073181 restraints weight = 16052.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.074638 restraints weight = 10682.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.075516 restraints weight = 8504.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.075993 restraints weight = 7503.348| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12230 Z= 0.146 Angle : 0.649 8.075 17678 Z= 0.382 Chirality : 0.045 0.259 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.815 175.272 3803 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.69 % Allowed : 30.42 % Favored : 64.89 % 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: 1.78 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.77 (0.36), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 728 TYR 0.025 0.002 TYR D1318 PHE 0.008 0.001 PHE E 704 HIS 0.004 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (12230) covalent geometry : angle 0.64899 / 0.38 (17678) hydrogen bonds : bond 0.04199 / 4.69 ( 746) hydrogen bonds : angle 3.07207 / 4.07 ( 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 327 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8053 (pp20) cc_final: 0.7405 (pp20) REVERT: A 468 GLN cc_start: 0.9027 (tt0) cc_final: 0.8803 (tm-30) REVERT: A 473 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8424 (tm-30) REVERT: A 485 GLN cc_start: 0.8736 (mt0) cc_final: 0.8432 (mt0) REVERT: A 520 MET cc_start: 0.8161 (mtt) cc_final: 0.7702 (mtp) REVERT: B 40 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8597 (tpp80) REVERT: B 52 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8473 (tp30) REVERT: B 88 TYR cc_start: 0.8363 (m-10) cc_final: 0.8052 (m-80) REVERT: B 92 ARG cc_start: 0.8800 (tmm-80) cc_final: 0.8133 (tmm-80) REVERT: C 821 GLN cc_start: 0.9122 (mt0) cc_final: 0.8859 (mp10) REVERT: C 822 ARG cc_start: 0.9174 (ttt-90) cc_final: 0.8752 (ttt-90) REVERT: C 853 TYR cc_start: 0.8739 (t80) cc_final: 0.8102 (t80) REVERT: C 867 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8618 (tm-30) REVERT: C 875 ASP cc_start: 0.8844 (m-30) cc_final: 0.8327 (p0) REVERT: C 884 ARG cc_start: 0.8865 (tpt170) cc_final: 0.8547 (tpt170) REVERT: C 887 GLN cc_start: 0.9145 (tp40) cc_final: 0.8902 (tp-100) REVERT: C 901 LYS cc_start: 0.8800 (pttp) cc_final: 0.8304 (tptp) REVERT: C 912 HIS cc_start: 0.8328 (t70) cc_final: 0.7683 (t-90) REVERT: D 1268 GLU cc_start: 0.9020 (tp30) cc_final: 0.8603 (tp30) REVERT: D 1281 ASN cc_start: 0.9310 (t0) cc_final: 0.8863 (t0) REVERT: D 1317 LYS cc_start: 0.9310 (ttmm) cc_final: 0.8939 (ttmt) REVERT: E 656 LYS cc_start: 0.9036 (ptpp) cc_final: 0.8797 (ptpp) REVERT: E 668 GLN cc_start: 0.9023 (tt0) cc_final: 0.7939 (tm-30) REVERT: E 674 ILE cc_start: 0.9610 (mm) cc_final: 0.9317 (mt) REVERT: E 693 GLN cc_start: 0.9038 (tp40) cc_final: 0.8589 (tp40) REVERT: E 694 GLU cc_start: 0.8916 (tp30) cc_final: 0.8692 (tp30) REVERT: E 705 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8413 (tm-30) REVERT: E 722 LYS cc_start: 0.8886 (pttt) cc_final: 0.8658 (ptpp) REVERT: F 244 LYS cc_start: 0.9201 (tttt) cc_final: 0.8480 (tttt) REVERT: F 247 SER cc_start: 0.8998 (p) cc_final: 0.8692 (t) REVERT: F 274 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8688 (tm-30) REVERT: F 277 LYS cc_start: 0.9530 (mttm) cc_final: 0.9309 (mttm) REVERT: F 298 TYR cc_start: 0.9095 (m-80) cc_final: 0.8878 (m-80) REVERT: G 1045 ARG cc_start: 0.9267 (ptm160) cc_final: 0.8914 (ptm-80) REVERT: G 1084 ARG cc_start: 0.8923 (tpt170) cc_final: 0.8467 (tpp80) REVERT: G 1087 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8786 (tp-100) REVERT: G 1088 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8991 (mm) REVERT: H 1468 GLU cc_start: 0.8698 (tp30) cc_final: 0.8464 (tt0) REVERT: H 1486 ILE cc_start: 0.8887 (mt) cc_final: 0.8568 (mt) outliers start: 29 outliers final: 20 residues processed: 306 average time/residue: 0.1033 time to fit residues: 43.8083 Evaluate side-chains 307 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 40 ARG 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 886 LEU 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 724 ILE Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 291 LYS 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: 7.9990 chunk 51 optimal weight: 0.0070 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 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 = 0.3734 r_free = 0.3734 target = 0.096987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.069590 restraints weight = 33625.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.071732 restraints weight = 16437.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.073176 restraints weight = 11018.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.074040 restraints weight = 8789.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074501 restraints weight = 7763.149| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 12230 Z= 0.186 Angle : 0.681 15.166 17678 Z= 0.391 Chirality : 0.045 0.257 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.846 174.874 3803 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 6.15 % Allowed : 31.55 % Favored : 62.30 % 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: 1.01 (0.31), residues: 730 helix: 1.81 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.78 (0.36), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 683 TYR 0.022 0.002 TYR D1237 PHE 0.029 0.002 PHE A 467 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (12230) covalent geometry : angle 0.68148 / 0.39 (17678) hydrogen bonds : bond 0.04373 / 4.87 ( 746) hydrogen bonds : angle 3.23017 / 4.26 ( 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 328 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 290 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8015 (pp20) cc_final: 0.7434 (pp20) REVERT: A 468 GLN cc_start: 0.9086 (tt0) cc_final: 0.8834 (tm-30) REVERT: A 473 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8402 (tm-30) REVERT: A 485 GLN cc_start: 0.8783 (mt0) cc_final: 0.8436 (mt0) REVERT: A 490 MET cc_start: 0.8285 (mmm) cc_final: 0.8069 (mmm) REVERT: A 520 MET cc_start: 0.8224 (mtt) cc_final: 0.7719 (mtp) REVERT: B 52 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8546 (tp30) REVERT: B 88 TYR cc_start: 0.8510 (m-10) cc_final: 0.8090 (m-80) REVERT: C 821 GLN cc_start: 0.9120 (mt0) cc_final: 0.8845 (mp10) REVERT: C 822 ARG cc_start: 0.9204 (ttt-90) cc_final: 0.8699 (ttt-90) REVERT: C 853 TYR cc_start: 0.8835 (t80) cc_final: 0.8192 (t80) REVERT: C 867 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8789 (tm-30) REVERT: C 875 ASP cc_start: 0.8875 (m-30) cc_final: 0.8351 (p0) REVERT: C 884 ARG cc_start: 0.8880 (tpt170) cc_final: 0.8565 (tpt170) REVERT: C 887 GLN cc_start: 0.9166 (tp40) cc_final: 0.8884 (tp-100) REVERT: C 901 LYS cc_start: 0.8813 (pttp) cc_final: 0.8337 (tptp) REVERT: C 912 HIS cc_start: 0.8324 (t70) cc_final: 0.7729 (t-90) REVERT: D 1265 ASP cc_start: 0.8507 (t0) cc_final: 0.8276 (t0) REVERT: D 1268 GLU cc_start: 0.9070 (tp30) cc_final: 0.8634 (tp30) REVERT: D 1281 ASN cc_start: 0.9310 (t0) cc_final: 0.8879 (t0) REVERT: D 1317 LYS cc_start: 0.9350 (ttmm) cc_final: 0.9003 (ttmt) REVERT: E 656 LYS cc_start: 0.9068 (ptpp) cc_final: 0.8823 (ptpp) REVERT: E 693 GLN cc_start: 0.9074 (tp40) cc_final: 0.8566 (tp40) REVERT: E 705 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8448 (tm-30) REVERT: E 722 LYS cc_start: 0.8857 (pttt) cc_final: 0.8641 (ptpp) REVERT: F 244 LYS cc_start: 0.9191 (tttt) cc_final: 0.8641 (tttt) REVERT: F 274 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8670 (tm-30) REVERT: F 279 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8431 (mtpt) REVERT: F 284 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8472 (tpp) REVERT: F 298 TYR cc_start: 0.9126 (m-80) cc_final: 0.8921 (m-80) REVERT: G 1045 ARG cc_start: 0.9278 (ptm160) cc_final: 0.8885 (ptm-80) REVERT: G 1084 ARG cc_start: 0.8939 (tpt170) cc_final: 0.8493 (tpp80) REVERT: G 1087 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8739 (tp-100) REVERT: G 1088 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9009 (mm) REVERT: H 1490 GLU cc_start: 0.9127 (mp0) cc_final: 0.8878 (pm20) outliers start: 38 outliers final: 31 residues processed: 301 average time/residue: 0.1089 time to fit residues: 45.3216 Evaluate side-chains 308 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 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 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 B residue 97 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 1241 VAL 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 E residue 724 ILE Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1021 GLN Chi-restraints excluded: chain G residue 1046 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 16 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 13 optimal weight: 50.0000 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.097449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070061 restraints weight = 33489.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.072231 restraints weight = 16363.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073684 restraints weight = 10950.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.074539 restraints weight = 8723.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.075034 restraints weight = 7711.387| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 12230 Z= 0.169 Angle : 0.664 10.143 17678 Z= 0.385 Chirality : 0.045 0.258 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.812 175.122 3803 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.47 % Allowed : 31.88 % 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: 0.99 (0.31), residues: 730 helix: 1.78 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.78 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 40 TYR 0.046 0.002 TYR D1237 PHE 0.026 0.002 PHE B 61 HIS 0.004 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (12230) covalent geometry : angle 0.66373 / 0.38 (17678) hydrogen bonds : bond 0.04281 / 4.79 ( 746) hydrogen bonds : angle 3.20982 / 4.24 ( 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 324 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 284 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8073 (pp20) cc_final: 0.7397 (pp20) REVERT: A 460 LEU cc_start: 0.8698 (mm) cc_final: 0.7769 (mt) REVERT: A 468 GLN cc_start: 0.9081 (tt0) cc_final: 0.8837 (tm-30) REVERT: A 473 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 520 MET cc_start: 0.8214 (mtt) cc_final: 0.7704 (mtp) REVERT: B 52 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8524 (tp30) REVERT: B 61 PHE cc_start: 0.9364 (t80) cc_final: 0.9117 (t80) REVERT: B 88 TYR cc_start: 0.8406 (m-10) cc_final: 0.7903 (m-80) REVERT: C 821 GLN cc_start: 0.9122 (mt0) cc_final: 0.8841 (mp10) REVERT: C 822 ARG cc_start: 0.9153 (ttt-90) cc_final: 0.8862 (ttt90) REVERT: C 853 TYR cc_start: 0.8653 (t80) cc_final: 0.8046 (t80) REVERT: C 867 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8782 (tm-30) REVERT: C 875 ASP cc_start: 0.8855 (m-30) cc_final: 0.8339 (p0) REVERT: C 887 GLN cc_start: 0.9169 (tp40) cc_final: 0.8884 (tp-100) REVERT: C 901 LYS cc_start: 0.8813 (pttp) cc_final: 0.8345 (tptp) REVERT: C 912 HIS cc_start: 0.8316 (t70) cc_final: 0.7727 (t-90) REVERT: D 1265 ASP cc_start: 0.8536 (t0) cc_final: 0.8260 (t0) REVERT: D 1268 GLU cc_start: 0.9073 (tp30) cc_final: 0.8636 (tp30) REVERT: D 1281 ASN cc_start: 0.9294 (t0) cc_final: 0.8876 (t0) REVERT: D 1317 LYS cc_start: 0.9326 (ttmm) cc_final: 0.8984 (ttmt) REVERT: E 656 LYS cc_start: 0.9081 (ptpp) cc_final: 0.8859 (ptpp) REVERT: E 668 GLN cc_start: 0.9053 (tt0) cc_final: 0.7996 (tm-30) REVERT: E 693 GLN cc_start: 0.9076 (tp40) cc_final: 0.8596 (tp40) REVERT: E 694 GLU cc_start: 0.8886 (tp30) cc_final: 0.8680 (tp30) REVERT: E 705 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8443 (tm-30) REVERT: F 244 LYS cc_start: 0.9180 (tttt) cc_final: 0.8635 (tttt) REVERT: F 274 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8764 (tm-30) REVERT: F 279 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8252 (mtmt) REVERT: F 284 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (tpp) REVERT: G 1026 GLN cc_start: 0.8666 (mm110) cc_final: 0.8055 (mp10) REVERT: G 1031 ARG cc_start: 0.8806 (ttm-80) cc_final: 0.8576 (ttm170) REVERT: G 1045 ARG cc_start: 0.9307 (ptm160) cc_final: 0.8912 (ptm-80) REVERT: G 1084 ARG cc_start: 0.8947 (tpt170) cc_final: 0.8495 (tpp80) REVERT: G 1087 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8772 (tp-100) REVERT: G 1088 LEU cc_start: 0.9323 (mm) cc_final: 0.9008 (mm) REVERT: H 1490 GLU cc_start: 0.9132 (mp0) cc_final: 0.8930 (mp0) outliers start: 40 outliers final: 31 residues processed: 297 average time/residue: 0.1079 time to fit residues: 44.7688 Evaluate side-chains 310 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 B residue 97 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 1241 VAL Chi-restraints excluded: chain D residue 1263 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 E residue 724 ILE Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 284 MET 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 1087 GLN Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1488 SER 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: 1.9990 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 53 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.098324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.071032 restraints weight = 33590.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.073253 restraints weight = 16320.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.074732 restraints weight = 10879.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.075602 restraints weight = 8638.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076063 restraints weight = 7628.653| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 12230 Z= 0.153 Angle : 0.665 15.973 17678 Z= 0.382 Chirality : 0.044 0.259 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.749 175.135 3803 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.02 % Allowed : 34.30 % 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: 1.00 (0.31), residues: 730 helix: 1.77 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.69 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 40 TYR 0.040 0.002 TYR D1237 PHE 0.025 0.002 PHE A 467 HIS 0.004 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (12230) covalent geometry : angle 0.66542 / 0.38 (17678) hydrogen bonds : bond 0.04200 / 4.72 ( 746) hydrogen bonds : angle 3.10823 / 4.12 ( 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 317 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 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: 0.8048 (pp20) cc_final: 0.7377 (pp20) REVERT: A 460 LEU cc_start: 0.8711 (mm) cc_final: 0.7768 (mt) REVERT: A 468 GLN cc_start: 0.9069 (tt0) cc_final: 0.8836 (tm-30) REVERT: A 473 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8391 (tm-30) REVERT: A 490 MET cc_start: 0.8219 (mmm) cc_final: 0.7995 (mmm) REVERT: A 520 MET cc_start: 0.8163 (mtt) cc_final: 0.7633 (mtp) REVERT: B 61 PHE cc_start: 0.9354 (t80) cc_final: 0.9101 (t80) REVERT: B 88 TYR cc_start: 0.8387 (m-10) cc_final: 0.7904 (m-80) REVERT: C 821 GLN cc_start: 0.9102 (mt0) cc_final: 0.8827 (mp10) REVERT: C 822 ARG cc_start: 0.9173 (ttt-90) cc_final: 0.8810 (ttt90) REVERT: C 853 TYR cc_start: 0.8586 (t80) cc_final: 0.7986 (t80) REVERT: C 867 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8753 (tm-30) REVERT: C 875 ASP cc_start: 0.8816 (m-30) cc_final: 0.8341 (p0) REVERT: C 887 GLN cc_start: 0.9164 (tp40) cc_final: 0.8886 (tp-100) REVERT: C 901 LYS cc_start: 0.8737 (pttp) cc_final: 0.8242 (tptp) REVERT: C 912 HIS cc_start: 0.8280 (t70) cc_final: 0.7737 (t-90) REVERT: D 1232 GLU cc_start: 0.7716 (tp30) cc_final: 0.7301 (tp30) REVERT: D 1268 GLU cc_start: 0.9068 (tp30) cc_final: 0.8614 (tp30) REVERT: D 1281 ASN cc_start: 0.9261 (t0) cc_final: 0.8842 (t0) REVERT: D 1317 LYS cc_start: 0.9312 (ttmm) cc_final: 0.8971 (ttmt) REVERT: E 674 ILE cc_start: 0.9608 (mm) cc_final: 0.9335 (mt) REVERT: E 690 MET cc_start: 0.8971 (tpp) cc_final: 0.8733 (tpp) REVERT: E 693 GLN cc_start: 0.9098 (tp40) cc_final: 0.8645 (tp40) REVERT: E 705 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8445 (tm-30) REVERT: E 720 MET cc_start: 0.8944 (mmm) cc_final: 0.8551 (mmt) REVERT: F 244 LYS cc_start: 0.9201 (tttt) cc_final: 0.8611 (tttt) REVERT: F 274 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8588 (tm-30) REVERT: F 279 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8232 (mtmt) REVERT: F 284 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8484 (tpp) REVERT: G 1026 GLN cc_start: 0.8664 (mm110) cc_final: 0.8056 (mp10) REVERT: G 1045 ARG cc_start: 0.9304 (ptm160) cc_final: 0.8916 (ptm-80) REVERT: G 1084 ARG cc_start: 0.8943 (tpt170) cc_final: 0.8481 (tpp80) REVERT: G 1087 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8768 (tp-100) REVERT: G 1088 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8988 (mm) outliers start: 31 outliers final: 25 residues processed: 295 average time/residue: 0.1097 time to fit residues: 45.3243 Evaluate side-chains 302 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 886 LEU 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 E residue 719 ILE Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 284 MET 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 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 1488 SER 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: 10.0000 chunk 27 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 87 optimal weight: 0.0170 chunk 91 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.097539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.070253 restraints weight = 33230.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.072455 restraints weight = 16283.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.073888 restraints weight = 10908.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.074770 restraints weight = 8702.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075276 restraints weight = 7671.952| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12230 Z= 0.168 Angle : 0.673 15.137 17678 Z= 0.385 Chirality : 0.044 0.257 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.746 174.994 3803 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.69 % Allowed : 34.95 % Favored : 60.36 % 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: 1.07 (0.31), residues: 730 helix: 1.82 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.69 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 40 TYR 0.040 0.002 TYR D1237 PHE 0.022 0.002 PHE B 61 HIS 0.004 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (12230) covalent geometry : angle 0.67320 / 0.39 (17678) hydrogen bonds : bond 0.04266 / 4.79 ( 746) hydrogen bonds : angle 3.16640 / 4.19 ( 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 304 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8030 (pp20) cc_final: 0.7365 (pp20) REVERT: A 460 LEU cc_start: 0.8583 (mm) cc_final: 0.7700 (mt) REVERT: A 468 GLN cc_start: 0.9108 (tt0) cc_final: 0.8835 (tm-30) REVERT: A 473 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8383 (tm-30) REVERT: A 490 MET cc_start: 0.8259 (mmm) cc_final: 0.8006 (mmm) REVERT: A 520 MET cc_start: 0.8188 (mtt) cc_final: 0.7640 (mtp) REVERT: B 88 TYR cc_start: 0.8419 (m-10) cc_final: 0.8013 (m-80) REVERT: C 821 GLN cc_start: 0.9125 (mt0) cc_final: 0.8843 (mp10) REVERT: C 822 ARG cc_start: 0.9182 (ttt-90) cc_final: 0.8809 (ttt90) REVERT: C 853 TYR cc_start: 0.8617 (t80) cc_final: 0.8047 (t80) REVERT: C 867 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8807 (tm-30) REVERT: C 875 ASP cc_start: 0.8823 (m-30) cc_final: 0.8329 (p0) REVERT: C 887 GLN cc_start: 0.9128 (tp40) cc_final: 0.8851 (tp-100) REVERT: C 901 LYS cc_start: 0.8757 (pttp) cc_final: 0.8226 (tptp) REVERT: C 912 HIS cc_start: 0.8315 (t70) cc_final: 0.7736 (t-90) REVERT: D 1232 GLU cc_start: 0.7721 (tp30) cc_final: 0.7391 (tp30) REVERT: D 1268 GLU cc_start: 0.9103 (tp30) cc_final: 0.8608 (tp30) REVERT: D 1281 ASN cc_start: 0.9255 (t0) cc_final: 0.8856 (t0) REVERT: D 1317 LYS cc_start: 0.9296 (ttmm) cc_final: 0.8961 (ttmt) REVERT: E 668 GLN cc_start: 0.9068 (tt0) cc_final: 0.7997 (tm-30) REVERT: E 674 ILE cc_start: 0.9610 (mm) cc_final: 0.9345 (mt) REVERT: E 693 GLN cc_start: 0.9099 (tp40) cc_final: 0.8559 (tp40) REVERT: E 694 GLU cc_start: 0.8997 (tp30) cc_final: 0.8773 (tp30) REVERT: E 705 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8473 (tm-30) REVERT: F 244 LYS cc_start: 0.9183 (tttt) cc_final: 0.8765 (tttt) REVERT: F 274 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8762 (tm-30) REVERT: F 279 LYS cc_start: 0.8667 (mtmt) cc_final: 0.8233 (mtmt) REVERT: G 1045 ARG cc_start: 0.9318 (ptm160) cc_final: 0.8904 (ptm-80) REVERT: G 1084 ARG cc_start: 0.8950 (tpt170) cc_final: 0.8480 (tpp80) REVERT: G 1087 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8742 (tp-100) REVERT: G 1088 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8983 (mm) REVERT: H 1490 GLU cc_start: 0.9034 (mp0) cc_final: 0.8778 (pm20) outliers start: 29 outliers final: 26 residues processed: 284 average time/residue: 0.0978 time to fit residues: 38.9927 Evaluate side-chains 301 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 B residue 97 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1282 LYS 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 E residue 724 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 94 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 30.0000 chunk 13 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 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 = 0.3722 r_free = 0.3722 target = 0.096123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068603 restraints weight = 33816.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.070737 restraints weight = 16753.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.072132 restraints weight = 11308.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.072993 restraints weight = 9063.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.073465 restraints weight = 8016.044| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 12230 Z= 0.226 Angle : 0.695 9.884 17678 Z= 0.397 Chirality : 0.045 0.265 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.795 174.616 3803 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.18 % Allowed : 34.14 % 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: 1.03 (0.31), residues: 730 helix: 1.81 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.76 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 40 TYR 0.042 0.003 TYR D1237 PHE 0.022 0.002 PHE B 61 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (12230) covalent geometry : angle 0.69486 / 0.40 (17678) hydrogen bonds : bond 0.04637 / 5.21 ( 746) hydrogen bonds : angle 3.33252 / 4.39 ( 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: 32 poor density : 273 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8037 (pp20) cc_final: 0.7374 (pp20) REVERT: A 460 LEU cc_start: 0.8613 (mm) cc_final: 0.7750 (mt) REVERT: A 468 GLN cc_start: 0.9164 (tt0) cc_final: 0.8606 (tm-30) REVERT: A 473 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8275 (tm-30) REVERT: A 520 MET cc_start: 0.8226 (mtt) cc_final: 0.7622 (mtp) REVERT: B 88 TYR cc_start: 0.8428 (m-10) cc_final: 0.8001 (m-80) REVERT: C 821 GLN cc_start: 0.9135 (mt0) cc_final: 0.8584 (mp10) REVERT: C 822 ARG cc_start: 0.9194 (ttt-90) cc_final: 0.8630 (ttt-90) REVERT: C 853 TYR cc_start: 0.8603 (t80) cc_final: 0.8015 (t80) REVERT: C 867 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8817 (tm-30) REVERT: C 875 ASP cc_start: 0.8846 (m-30) cc_final: 0.8347 (p0) REVERT: C 887 GLN cc_start: 0.9148 (tp40) cc_final: 0.8869 (tp-100) REVERT: C 901 LYS cc_start: 0.8781 (pttp) cc_final: 0.8247 (tptp) REVERT: C 912 HIS cc_start: 0.8338 (t70) cc_final: 0.7801 (t-90) REVERT: D 1231 LYS cc_start: 0.9058 (tppt) cc_final: 0.8471 (ptpt) REVERT: D 1268 GLU cc_start: 0.9111 (tp30) cc_final: 0.8602 (tp30) REVERT: D 1281 ASN cc_start: 0.9283 (t0) cc_final: 0.8870 (t0) REVERT: D 1317 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8958 (ttmt) REVERT: E 693 GLN cc_start: 0.9187 (tp40) cc_final: 0.8566 (tp40) REVERT: E 694 GLU cc_start: 0.9014 (tp30) cc_final: 0.8781 (tp30) REVERT: E 705 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8457 (tm-30) REVERT: F 244 LYS cc_start: 0.9161 (tttt) cc_final: 0.8823 (tttt) REVERT: F 274 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8778 (tm-30) REVERT: F 279 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8265 (mtmt) REVERT: G 1026 GLN cc_start: 0.8714 (mm110) cc_final: 0.8148 (mp10) REVERT: G 1084 ARG cc_start: 0.8952 (tpt170) cc_final: 0.8496 (tpp80) REVERT: G 1087 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8751 (tp-100) REVERT: G 1088 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9020 (mm) REVERT: H 1490 GLU cc_start: 0.8980 (mp0) cc_final: 0.8718 (pm20) outliers start: 32 outliers final: 26 residues processed: 285 average time/residue: 0.1014 time to fit residues: 40.4646 Evaluate side-chains 295 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 842 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS 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 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 1087 GLN Chi-restraints excluded: chain G residue 1088 LEU Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1509 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 30.0000 chunk 50 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 GLN E 668 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.098942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071652 restraints weight = 33183.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.073813 restraints weight = 16292.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.075272 restraints weight = 10934.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.076183 restraints weight = 8698.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.076688 restraints weight = 7640.692| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12230 Z= 0.147 Angle : 0.680 19.179 17678 Z= 0.386 Chirality : 0.044 0.265 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.676 175.240 3803 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 4.37 % Allowed : 35.76 % Favored : 59.87 % 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: 1.81 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.66 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1296 TYR 0.037 0.002 TYR D1237 PHE 0.023 0.002 PHE B 61 HIS 0.002 0.001 HIS G1033 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (12230) covalent geometry : angle 0.67972 / 0.39 (17678) hydrogen bonds : bond 0.04246 / 4.80 ( 746) hydrogen bonds : angle 3.11349 / 4.14 ( 1879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1786.80 seconds wall clock time: 31 minutes 34.88 seconds (1894.88 seconds total)