Starting phenix.real_space_refine on Thu Jul 2 13:11:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkv_48339/07_2026/9mkv_48339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkv_48339/07_2026/9mkv_48339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mkv_48339/07_2026/9mkv_48339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkv_48339/07_2026/9mkv_48339.map" model { file = "/net/cci-nas-00/data/ceres_data/9mkv_48339/07_2026/9mkv_48339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkv_48339/07_2026/9mkv_48339.cif" } resolution = 3.68 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= 0.015 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 52 5.49 5 S 16 5.16 5 C 5273 2.51 5 N 1402 2.21 5 O 1738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 8481 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 7394 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 18, 'TRANS': 875} Chain breaks: 12 Chain: "B" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 636 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 8, 'rna3p': 21} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 1.48, per 1000 atoms: 0.17 Number of scatterers: 8481 At special positions: 0 Unit cell: (82.56, 103.2, 135.02, 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 16 16.00 P 52 15.00 O 1738 8.00 N 1402 7.00 C 5273 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: 0.63 Conformation dependent library (CDL) restraints added in 162.2 milliseconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1702 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 47.3% alpha, 10.9% beta 17 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 39 through 69 removed outlier: 3.839A pdb=" N LYS A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 83 through 89 Processing helix chain 'A' and resid 94 through 115 removed outlier: 3.874A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.166A pdb=" N LYS A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 121' Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.709A pdb=" N ALA A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 190 removed outlier: 3.559A pdb=" N TYR A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.930A pdb=" N LYS A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 removed outlier: 5.007A pdb=" N ASN A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.591A pdb=" N LYS A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 removed outlier: 3.571A pdb=" N VAL A 672 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 681 removed outlier: 4.181A pdb=" N LYS A 680 " --> pdb=" O LYS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 692 removed outlier: 3.834A pdb=" N LEU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 731 Processing helix chain 'A' and resid 734 through 738 removed outlier: 3.869A pdb=" N PHE A 737 " --> pdb=" O TRP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 759 removed outlier: 4.215A pdb=" N PHE A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 757 " --> pdb=" O PHE A 753 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 759 " --> pdb=" O ARG A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 781 Processing helix chain 'A' and resid 790 through 794 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 813 through 819 removed outlier: 3.587A pdb=" N ASP A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 908 removed outlier: 3.783A pdb=" N GLU A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 978 through 994 removed outlier: 3.960A pdb=" N GLU A 982 " --> pdb=" O LYS A 978 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 983 " --> pdb=" O GLU A 979 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1022 through 1036 Processing helix chain 'A' and resid 1102 through 1111 removed outlier: 3.996A pdb=" N LYS A1111 " --> pdb=" O GLU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1181 Processing helix chain 'A' and resid 1191 through 1198 removed outlier: 3.855A pdb=" N GLU A1198 " --> pdb=" O ALA A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1216 Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 4.053A pdb=" N ALA A1246 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1275 removed outlier: 3.673A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1298 Processing sheet with id=AA1, first strand: chain 'A' and resid 595 through 596 removed outlier: 4.342A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 15 " --> pdb=" O ILE A 884 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 595 through 596 Processing sheet with id=AA3, first strand: chain 'A' and resid 935 through 940 removed outlier: 7.095A pdb=" N LEU A 928 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLN A 938 " --> pdb=" O TYR A 926 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR A 926 " --> pdb=" O GLN A 938 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N THR A 940 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA A 924 " --> pdb=" O THR A 940 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 916 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU A1006 " --> pdb=" O ILE A 916 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ARG A 918 " --> pdb=" O GLU A1006 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1115 through 1116 removed outlier: 3.783A pdb=" N PHE A1126 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A1144 " --> pdb=" O PHE A1126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1150 through 1151 312 hydrogen bonds defined for protein. 867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2305 1.34 - 1.45: 1777 1.45 - 1.57: 4544 1.57 - 1.69: 101 1.69 - 1.81: 25 Bond restraints: 8752 Sorted by residual: bond pdb=" C3' DT C -3 " pdb=" C2' DT C -3 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" N ILE A 37 " pdb=" CA ILE A 37 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.04e+00 bond pdb=" N LEU A 38 " pdb=" CA LEU A 38 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.21e-02 6.83e+03 6.75e+00 bond pdb=" C1' DT C -1 " pdb=" N1 DT C -1 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.59e+00 bond pdb=" C3' DC C -5 " pdb=" C2' DC C -5 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.37e+00 ... (remaining 8747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 11671 1.47 - 2.95: 272 2.95 - 4.42: 30 4.42 - 5.90: 8 5.90 - 7.37: 3 Bond angle restraints: 11984 Sorted by residual: angle pdb=" N3 DT C -1 " pdb=" C4 DT C -1 " pdb=" O4 DT C -1 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" O4' DT C 1 " pdb=" C4' DT C 1 " pdb=" C3' DT C 1 " ideal model delta sigma weight residual 106.00 103.45 2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" C LYS A 217 " pdb=" N TYR A 218 " pdb=" CA TYR A 218 " ideal model delta sigma weight residual 121.66 114.29 7.37 1.76e+00 3.23e-01 1.75e+01 angle pdb=" N3 DT D -3 " pdb=" C4 DT D -3 " pdb=" O4 DT D -3 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 11979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 4447 16.73 - 33.45: 566 33.45 - 50.18: 152 50.18 - 66.91: 70 66.91 - 83.63: 13 Dihedral angle restraints: 5248 sinusoidal: 2614 harmonic: 2634 Sorted by residual: dihedral pdb=" CA SER A 80 " pdb=" C SER A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta harmonic sigma weight residual 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ASN A 148 " pdb=" C ASN A 148 " pdb=" N GLY A 149 " pdb=" CA GLY A 149 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA GLY A 149 " pdb=" C GLY A 149 " pdb=" N ILE A 150 " pdb=" CA ILE A 150 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 943 0.038 - 0.076: 284 0.076 - 0.114: 69 0.114 - 0.151: 14 0.151 - 0.189: 2 Chirality restraints: 1312 Sorted by residual: chirality pdb=" CB ILE A 71 " pdb=" CA ILE A 71 " pdb=" CG1 ILE A 71 " pdb=" CG2 ILE A 71 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA ILE A1002 " pdb=" N ILE A1002 " pdb=" C ILE A1002 " pdb=" CB ILE A1002 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1309 not shown) Planarity restraints: 1341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 30 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C ASN A 30 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN A 30 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 31 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 724 " -0.024 2.00e-02 2.50e+03 1.52e-02 4.59e+00 pdb=" CG TYR A 724 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 724 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 724 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 724 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 724 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 724 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 724 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 2 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C SER A 2 " 0.026 2.00e-02 2.50e+03 pdb=" O SER A 2 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE A 3 " -0.009 2.00e-02 2.50e+03 ... (remaining 1338 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1664 2.77 - 3.31: 8279 3.31 - 3.84: 13897 3.84 - 4.37: 15624 4.37 - 4.90: 25658 Nonbonded interactions: 65122 Sorted by model distance: nonbonded pdb=" O TYR A 79 " pdb=" OG SER A 80 " model vdw 2.243 3.040 nonbonded pdb=" NZ LYS A 102 " pdb=" O VAL A 204 " model vdw 2.263 3.120 nonbonded pdb=" O TYR A 11 " pdb=" ND2 ASN A 887 " model vdw 2.275 3.120 nonbonded pdb=" OH TYR A 11 " pdb=" OD1 ASN A1036 " model vdw 2.279 3.040 nonbonded pdb=" O LYS A 937 " pdb=" NE2 GLN A 938 " model vdw 2.295 3.120 ... (remaining 65117 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.280 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.003 0.036 8752 Z= 0.210 Angle : 0.519 7.372 11984 Z= 0.383 Chirality : 0.039 0.189 1312 Planarity : 0.003 0.029 1341 Dihedral : 16.753 83.634 3546 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.69 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.29), residues: 868 helix: 1.14 (0.28), residues: 370 sheet: -0.32 (0.55), residues: 103 loop : -1.25 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 690 TYR 0.034 0.001 TYR A 724 PHE 0.014 0.001 PHE A 720 TRP 0.002 0.001 TRP A1142 HIS 0.001 0.000 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.21 ( 8752) covalent geometry : angle 0.51941 / 0.38 (11984) hydrogen bonds : bond 0.14839 / 10.32 ( 344) hydrogen bonds : angle 6.17306 / 4.37 ( 943) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8921 (m110) cc_final: 0.8715 (m-40) REVERT: A 321 MET cc_start: 0.8960 (mmm) cc_final: 0.8564 (mmm) REVERT: A 328 ILE cc_start: 0.8946 (mm) cc_final: 0.8736 (mm) REVERT: A 329 LEU cc_start: 0.8733 (mm) cc_final: 0.8495 (mm) REVERT: A 1217 MET cc_start: 0.7933 (mtp) cc_final: 0.7298 (mtp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0713 time to fit residues: 10.8548 Evaluate side-chains 56 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.079448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.064151 restraints weight = 45440.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.065904 restraints weight = 24640.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.066934 restraints weight = 16506.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.067698 restraints weight = 12778.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.068125 restraints weight = 10711.306| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8752 Z= 0.183 Angle : 0.573 7.696 11984 Z= 0.330 Chirality : 0.040 0.169 1312 Planarity : 0.004 0.036 1341 Dihedral : 16.253 73.515 1656 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.80 % Favored : 96.08 % Rotamer: Outliers : 1.47 % Allowed : 9.57 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.29), residues: 868 helix: 1.13 (0.28), residues: 368 sheet: -0.45 (0.55), residues: 103 loop : -1.31 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1272 TYR 0.034 0.002 TYR A 218 PHE 0.023 0.001 PHE A1064 TRP 0.005 0.001 TRP A 609 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 ( 8752) covalent geometry : angle 0.57272 / 0.33 (11984) hydrogen bonds : bond 0.05311 / 3.48 ( 344) hydrogen bonds : angle 5.48884 / 3.92 ( 943) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.6947 (t80) REVERT: A 321 MET cc_start: 0.8913 (mmm) cc_final: 0.8494 (mmm) REVERT: A 328 ILE cc_start: 0.8880 (mm) cc_final: 0.8656 (mm) REVERT: A 329 LEU cc_start: 0.8791 (mm) cc_final: 0.8525 (mm) REVERT: A 752 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: A 1217 MET cc_start: 0.7966 (mtp) cc_final: 0.7489 (mtp) REVERT: A 1267 LEU cc_start: 0.9467 (tt) cc_final: 0.9139 (mt) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.0552 time to fit residues: 5.7878 Evaluate side-chains 61 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1269 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 74 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.079810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.064579 restraints weight = 45349.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.066357 restraints weight = 24508.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.067477 restraints weight = 16330.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.068136 restraints weight = 12482.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.068622 restraints weight = 10577.484| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8752 Z= 0.134 Angle : 0.511 7.490 11984 Z= 0.298 Chirality : 0.038 0.135 1312 Planarity : 0.003 0.038 1341 Dihedral : 16.264 73.418 1656 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 1.10 % Allowed : 12.27 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.29), residues: 868 helix: 1.19 (0.28), residues: 364 sheet: -0.46 (0.54), residues: 103 loop : -1.33 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1272 TYR 0.030 0.001 TYR A 218 PHE 0.014 0.001 PHE A1147 TRP 0.005 0.001 TRP A 175 HIS 0.002 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 8752) covalent geometry : angle 0.51096 / 0.30 (11984) hydrogen bonds : bond 0.04749 / 3.13 ( 344) hydrogen bonds : angle 5.22218 / 3.73 ( 943) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6857 (t80) REVERT: A 321 MET cc_start: 0.8856 (mmm) cc_final: 0.8469 (mmm) REVERT: A 328 ILE cc_start: 0.8864 (mm) cc_final: 0.8616 (mm) REVERT: A 329 LEU cc_start: 0.8797 (mm) cc_final: 0.8529 (mm) REVERT: A 752 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7867 (pt0) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.0626 time to fit residues: 5.8889 Evaluate side-chains 58 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.079399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.064215 restraints weight = 46508.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.065977 restraints weight = 25016.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.067085 restraints weight = 16682.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.067830 restraints weight = 12737.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.068286 restraints weight = 10641.758| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8752 Z= 0.148 Angle : 0.536 9.131 11984 Z= 0.305 Chirality : 0.038 0.175 1312 Planarity : 0.003 0.040 1341 Dihedral : 16.276 73.408 1656 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.85 % Rotamer: Outliers : 1.35 % Allowed : 13.01 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.29), residues: 868 helix: 1.18 (0.28), residues: 364 sheet: -0.43 (0.54), residues: 103 loop : -1.33 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.028 0.001 TYR A 218 PHE 0.039 0.002 PHE A1064 TRP 0.004 0.001 TRP A 175 HIS 0.002 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 8752) covalent geometry : angle 0.53604 / 0.30 (11984) hydrogen bonds : bond 0.04642 / 3.07 ( 344) hydrogen bonds : angle 5.15582 / 3.69 ( 943) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6944 (t80) REVERT: A 321 MET cc_start: 0.8742 (mmm) cc_final: 0.8378 (mmm) REVERT: A 328 ILE cc_start: 0.8862 (mm) cc_final: 0.8610 (mm) REVERT: A 329 LEU cc_start: 0.8820 (mm) cc_final: 0.8515 (mm) REVERT: A 752 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: A 1267 LEU cc_start: 0.9455 (tt) cc_final: 0.9121 (mt) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.0512 time to fit residues: 5.1675 Evaluate side-chains 59 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1296 GLN A1299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.077425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.062332 restraints weight = 46420.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.064009 restraints weight = 25083.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.065066 restraints weight = 16814.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.065715 restraints weight = 12935.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.066181 restraints weight = 10975.776| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8752 Z= 0.214 Angle : 0.597 8.343 11984 Z= 0.337 Chirality : 0.040 0.136 1312 Planarity : 0.004 0.043 1341 Dihedral : 16.373 73.369 1656 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 2.45 % Allowed : 14.36 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.29), residues: 868 helix: 1.02 (0.28), residues: 368 sheet: -0.48 (0.55), residues: 103 loop : -1.43 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 186 TYR 0.028 0.002 TYR A 218 PHE 0.030 0.002 PHE A1147 TRP 0.007 0.001 TRP A 609 HIS 0.004 0.001 HIS A 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 ( 8752) covalent geometry : angle 0.59674 / 0.34 (11984) hydrogen bonds : bond 0.05184 / 3.42 ( 344) hydrogen bonds : angle 5.31214 / 3.78 ( 943) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.8833 (mm) cc_final: 0.8604 (mm) REVERT: A 329 LEU cc_start: 0.8813 (mm) cc_final: 0.8473 (mm) REVERT: A 752 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: A 1035 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8634 (tp) REVERT: A 1064 PHE cc_start: 0.8199 (m-80) cc_final: 0.7908 (m-80) outliers start: 20 outliers final: 11 residues processed: 68 average time/residue: 0.0502 time to fit residues: 5.5636 Evaluate side-chains 62 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1025 GLN ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.078427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063326 restraints weight = 45848.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.065043 restraints weight = 24401.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.066134 restraints weight = 16256.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.066829 restraints weight = 12450.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.067225 restraints weight = 10498.419| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8752 Z= 0.135 Angle : 0.528 8.408 11984 Z= 0.302 Chirality : 0.038 0.170 1312 Planarity : 0.003 0.042 1341 Dihedral : 16.352 73.243 1656 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 1.84 % Allowed : 15.95 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.29), residues: 868 helix: 1.18 (0.28), residues: 361 sheet: -0.44 (0.55), residues: 104 loop : -1.36 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 921 TYR 0.023 0.001 TYR A 201 PHE 0.018 0.001 PHE A1147 TRP 0.005 0.001 TRP A 175 HIS 0.003 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8752) covalent geometry : angle 0.52833 / 0.30 (11984) hydrogen bonds : bond 0.04696 / 3.12 ( 344) hydrogen bonds : angle 5.08358 / 3.64 ( 943) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.8604 (mmm) cc_final: 0.8263 (mmm) REVERT: A 328 ILE cc_start: 0.8872 (mm) cc_final: 0.8632 (mm) REVERT: A 329 LEU cc_start: 0.8811 (mm) cc_final: 0.8527 (mm) REVERT: A 752 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: A 1217 MET cc_start: 0.8017 (mtp) cc_final: 0.7595 (mtp) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.0548 time to fit residues: 5.7843 Evaluate side-chains 60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1269 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 58 optimal weight: 10.0000 chunk 83 optimal weight: 0.0970 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.078654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.063581 restraints weight = 46154.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.065325 restraints weight = 24546.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.066431 restraints weight = 16205.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.067078 restraints weight = 12371.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.067561 restraints weight = 10478.867| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8752 Z= 0.127 Angle : 0.524 8.315 11984 Z= 0.298 Chirality : 0.039 0.169 1312 Planarity : 0.003 0.040 1341 Dihedral : 16.354 73.260 1656 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.80 % Favored : 96.08 % Rotamer: Outliers : 1.84 % Allowed : 16.32 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.29), residues: 868 helix: 1.19 (0.28), residues: 368 sheet: -0.30 (0.54), residues: 103 loop : -1.30 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.022 0.001 TYR A 201 PHE 0.031 0.001 PHE A 831 TRP 0.005 0.001 TRP A 808 HIS 0.002 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 8752) covalent geometry : angle 0.52390 / 0.30 (11984) hydrogen bonds : bond 0.04506 / 2.99 ( 344) hydrogen bonds : angle 4.99027 / 3.58 ( 943) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.8863 (mm) cc_final: 0.8620 (mm) REVERT: A 329 LEU cc_start: 0.8807 (mm) cc_final: 0.8508 (mm) REVERT: A 752 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: A 1066 LYS cc_start: 0.8996 (pttt) cc_final: 0.8738 (pttm) REVERT: A 1217 MET cc_start: 0.8000 (mtp) cc_final: 0.7542 (mtp) outliers start: 15 outliers final: 11 residues processed: 66 average time/residue: 0.0556 time to fit residues: 5.9427 Evaluate side-chains 64 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 61 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1025 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.078159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.063116 restraints weight = 45627.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.064833 restraints weight = 24298.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065924 restraints weight = 16141.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.066582 restraints weight = 12354.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.067084 restraints weight = 10433.244| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8752 Z= 0.149 Angle : 0.541 8.165 11984 Z= 0.307 Chirality : 0.039 0.148 1312 Planarity : 0.003 0.042 1341 Dihedral : 16.364 73.255 1656 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.15 % Favored : 95.74 % Rotamer: Outliers : 2.21 % Allowed : 16.07 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.29), residues: 868 helix: 1.13 (0.28), residues: 369 sheet: -0.35 (0.54), residues: 103 loop : -1.33 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 692 TYR 0.028 0.002 TYR A 83 PHE 0.015 0.001 PHE A 831 TRP 0.005 0.001 TRP A 175 HIS 0.003 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 8752) covalent geometry : angle 0.54086 / 0.31 (11984) hydrogen bonds : bond 0.04605 / 3.04 ( 344) hydrogen bonds : angle 5.01839 / 3.59 ( 943) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.8877 (mm) cc_final: 0.8621 (mm) REVERT: A 329 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 752 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: A 1035 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8594 (tp) REVERT: A 1217 MET cc_start: 0.8004 (mtp) cc_final: 0.7526 (mtp) outliers start: 18 outliers final: 11 residues processed: 66 average time/residue: 0.0502 time to fit residues: 5.3847 Evaluate side-chains 62 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.076550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.061529 restraints weight = 46413.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.063189 restraints weight = 24870.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.064215 restraints weight = 16602.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.064913 restraints weight = 12798.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.065293 restraints weight = 10771.026| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8752 Z= 0.238 Angle : 0.651 8.332 11984 Z= 0.363 Chirality : 0.042 0.237 1312 Planarity : 0.004 0.045 1341 Dihedral : 16.419 73.272 1656 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.53 % Favored : 94.35 % Rotamer: Outliers : 1.96 % Allowed : 17.18 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.29), residues: 868 helix: 0.81 (0.27), residues: 371 sheet: -0.63 (0.55), residues: 100 loop : -1.50 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 692 TYR 0.031 0.002 TYR A 83 PHE 0.014 0.002 PHE A 753 TRP 0.008 0.001 TRP A 609 HIS 0.005 0.001 HIS A 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 ( 8752) covalent geometry : angle 0.65054 / 0.36 (11984) hydrogen bonds : bond 0.05352 / 3.51 ( 344) hydrogen bonds : angle 5.32891 / 3.79 ( 943) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.8849 (mm) cc_final: 0.8619 (mm) REVERT: A 329 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8389 (mm) REVERT: A 752 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: A 1035 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8463 (tp) outliers start: 16 outliers final: 12 residues processed: 63 average time/residue: 0.0546 time to fit residues: 5.5824 Evaluate side-chains 64 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.077397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.062355 restraints weight = 45765.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.064038 restraints weight = 24504.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.065073 restraints weight = 16375.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.065759 restraints weight = 12631.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.066208 restraints weight = 10665.266| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8752 Z= 0.164 Angle : 0.585 8.589 11984 Z= 0.329 Chirality : 0.040 0.209 1312 Planarity : 0.003 0.046 1341 Dihedral : 16.401 73.160 1656 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 1.84 % Allowed : 17.67 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.29), residues: 868 helix: 0.92 (0.28), residues: 371 sheet: -0.61 (0.55), residues: 100 loop : -1.48 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 692 TYR 0.033 0.002 TYR A 83 PHE 0.013 0.001 PHE A 880 TRP 0.005 0.001 TRP A 141 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 8752) covalent geometry : angle 0.58453 / 0.33 (11984) hydrogen bonds : bond 0.04933 / 3.26 ( 344) hydrogen bonds : angle 5.16115 / 3.68 ( 943) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.8870 (mm) cc_final: 0.8622 (mm) REVERT: A 329 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8384 (mm) REVERT: A 752 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7988 (pt0) outliers start: 15 outliers final: 11 residues processed: 61 average time/residue: 0.0531 time to fit residues: 5.2932 Evaluate side-chains 61 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 6 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.076233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.061272 restraints weight = 46367.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.062925 restraints weight = 24812.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.063952 restraints weight = 16581.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.064630 restraints weight = 12798.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.065024 restraints weight = 10797.802| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8752 Z= 0.240 Angle : 0.646 8.250 11984 Z= 0.362 Chirality : 0.042 0.243 1312 Planarity : 0.004 0.047 1341 Dihedral : 16.448 73.213 1656 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.76 % Favored : 94.12 % Rotamer: Outliers : 1.96 % Allowed : 17.55 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.28), residues: 868 helix: 0.74 (0.27), residues: 370 sheet: -0.74 (0.54), residues: 100 loop : -1.62 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 692 TYR 0.031 0.002 TYR A 201 PHE 0.013 0.002 PHE A1064 TRP 0.009 0.002 TRP A 609 HIS 0.005 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 ( 8752) covalent geometry : angle 0.64618 / 0.36 (11984) hydrogen bonds : bond 0.05413 / 3.54 ( 344) hydrogen bonds : angle 5.36132 / 3.81 ( 943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.84 seconds wall clock time: 22 minutes 11.70 seconds (1331.70 seconds total)