Starting phenix.real_space_refine on Wed Aug 5 06:02:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkv_48339/08_2026/9mkv_48339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkv_48339/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mkv_48339/08_2026/9mkv_48339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkv_48339/08_2026/9mkv_48339.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mkv_48339/08_2026/9mkv_48339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkv_48339/08_2026/9mkv_48339.map" } 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-2.2rc3-6140/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: 1.45, 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: 0.62 Conformation dependent library (CDL) restraints added in 217.6 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: 1.00 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: 1.23 Time building geometry restraints manager: 0.86 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: 11601 1.47 - 2.95: 342 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: 909 0.038 - 0.076: 289 0.076 - 0.114: 77 0.114 - 0.151: 35 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=" C2' A B 3 " pdb=" C3' A B 3 " pdb=" O2' A B 3 " pdb=" C1' A B 3 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.88e-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: 1.320 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.450 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.220 ------------------------------------------------------------------------------- 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= 0.212 Angle : 0.554 7.372 11984 Z= 0.414 Chirality : 0.043 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 0.00273 / 0.21 ( 8752) covalent geometry : angle 0.55403 / 0.41 (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 : 0.208 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: 0.7297 (mtp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0647 time to fit residues: 9.9106 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 : 0.266 ------------------------------------------------------------------------------- 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: 0.7980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.080211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.064899 restraints weight = 45271.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.066698 restraints weight = 24554.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.067795 restraints weight = 16357.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.068551 restraints weight = 12554.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.068978 restraints weight = 10534.328| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8752 Z= 0.153 Angle : 0.553 7.411 11984 Z= 0.318 Chirality : 0.039 0.167 1312 Planarity : 0.004 0.035 1341 Dihedral : 16.243 73.515 1656 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 1.35 % Allowed : 8.22 % Favored : 90.43 % 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: -0.18 (0.29), residues: 868 helix: 1.14 (0.28), residues: 369 sheet: -0.43 (0.54), residues: 103 loop : -1.25 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1272 TYR 0.034 0.002 TYR A 218 PHE 0.018 0.001 PHE A1064 TRP 0.004 0.001 TRP A 141 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 8752) covalent geometry : angle 0.55321 / 0.32 (11984) hydrogen bonds : bond 0.05249 / 3.45 ( 344) hydrogen bonds : angle 5.42238 / 3.88 ( 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 71 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.9161 (mmt-90) cc_final: 0.8814 (mmt90) REVERT: A 319 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6938 (t80) REVERT: A 321 MET cc_start: 0.8934 (mmm) cc_final: 0.8518 (mmm) REVERT: A 328 ILE cc_start: 0.8876 (mm) cc_final: 0.8636 (mm) REVERT: A 329 LEU cc_start: 0.8778 (mm) cc_final: 0.8527 (mm) REVERT: A 752 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: A 1217 MET cc_start: 0.7930 (mtp) cc_final: 0.7327 (mtp) REVERT: A 1267 LEU cc_start: 0.9462 (tt) cc_final: 0.9130 (mt) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.0624 time to fit residues: 6.5159 Evaluate side-chains 60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 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: 0.9990 chunk 18 optimal weight: 0.6980 chunk 83 optimal weight: 0.0070 chunk 64 optimal weight: 3.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.080131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.064888 restraints weight = 45267.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.066659 restraints weight = 24431.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.067790 restraints weight = 16319.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.068517 restraints weight = 12436.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.068934 restraints weight = 10426.447| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1475 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= 0.130 Angle : 0.508 7.372 11984 Z= 0.295 Chirality : 0.038 0.136 1312 Planarity : 0.003 0.038 1341 Dihedral : 16.237 73.598 1656 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 1.10 % Allowed : 12.15 % Favored : 86.75 % 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: -0.15 (0.29), residues: 868 helix: 1.20 (0.28), residues: 371 sheet: -0.45 (0.53), residues: 103 loop : -1.27 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1272 TYR 0.030 0.002 TYR A 218 PHE 0.015 0.001 PHE A1147 TRP 0.004 0.001 TRP A 175 HIS 0.002 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 8752) covalent geometry : angle 0.50753 / 0.29 (11984) hydrogen bonds : bond 0.04684 / 3.08 ( 344) hydrogen bonds : angle 5.18465 / 3.71 ( 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 : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.6899 (t80) REVERT: A 321 MET cc_start: 0.8856 (mmm) cc_final: 0.8448 (mmm) REVERT: A 328 ILE cc_start: 0.8862 (mm) cc_final: 0.8615 (mm) REVERT: A 329 LEU cc_start: 0.8804 (mm) cc_final: 0.8526 (mm) REVERT: A 752 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7847 (pt0) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.0654 time to fit residues: 6.1875 Evaluate side-chains 59 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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: 2.9990 chunk 82 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.080830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.065566 restraints weight = 45837.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.067366 restraints weight = 24458.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.068515 restraints weight = 16281.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.069232 restraints weight = 12388.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.069742 restraints weight = 10385.944| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8752 Z= 0.110 Angle : 0.514 10.248 11984 Z= 0.290 Chirality : 0.038 0.176 1312 Planarity : 0.003 0.037 1341 Dihedral : 16.240 73.564 1656 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 1.23 % Allowed : 13.50 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.29), residues: 868 helix: 1.26 (0.28), residues: 359 sheet: -0.42 (0.53), residues: 104 loop : -1.30 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1272 TYR 0.026 0.001 TYR A 218 PHE 0.043 0.001 PHE A1064 TRP 0.004 0.001 TRP A 808 HIS 0.002 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 8752) covalent geometry : angle 0.51394 / 0.29 (11984) hydrogen bonds : bond 0.04267 / 2.84 ( 344) hydrogen bonds : angle 4.96826 / 3.57 ( 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 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.6904 (t80) REVERT: A 321 MET cc_start: 0.8832 (mmm) cc_final: 0.8482 (mmm) REVERT: A 328 ILE cc_start: 0.8856 (mm) cc_final: 0.8606 (mm) REVERT: A 329 LEU cc_start: 0.8779 (mm) cc_final: 0.8512 (mm) REVERT: A 752 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: A 1217 MET cc_start: 0.7969 (mtp) cc_final: 0.7671 (mtp) REVERT: A 1267 LEU cc_start: 0.9430 (tt) cc_final: 0.9090 (mt) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.0564 time to fit residues: 5.5320 Evaluate side-chains 61 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.077964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.062819 restraints weight = 46397.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.064558 restraints weight = 25013.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.065621 restraints weight = 16687.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.066341 restraints weight = 12804.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.066777 restraints weight = 10740.274| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8752 Z= 0.213 Angle : 0.590 8.113 11984 Z= 0.331 Chirality : 0.040 0.153 1312 Planarity : 0.004 0.041 1341 Dihedral : 16.301 73.582 1656 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 1.84 % Allowed : 13.62 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.29), residues: 868 helix: 1.08 (0.28), residues: 370 sheet: -0.43 (0.54), residues: 103 loop : -1.41 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 186 TYR 0.028 0.002 TYR A 218 PHE 0.027 0.002 PHE A1064 TRP 0.007 0.001 TRP A 609 HIS 0.005 0.001 HIS A 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 ( 8752) covalent geometry : angle 0.58984 / 0.33 (11984) hydrogen bonds : bond 0.04993 / 3.27 ( 344) hydrogen bonds : angle 5.19717 / 3.71 ( 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 71 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.8829 (mm) cc_final: 0.8588 (mm) REVERT: A 329 LEU cc_start: 0.8816 (mm) cc_final: 0.8483 (mm) REVERT: A 752 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8002 (pt0) outliers start: 15 outliers final: 9 residues processed: 67 average time/residue: 0.0547 time to fit residues: 5.9523 Evaluate side-chains 59 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.079806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.064740 restraints weight = 45400.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.066487 restraints weight = 24222.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.067604 restraints weight = 16072.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.068315 restraints weight = 12252.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.068787 restraints weight = 10295.381| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8752 Z= 0.110 Angle : 0.507 8.224 11984 Z= 0.290 Chirality : 0.038 0.169 1312 Planarity : 0.003 0.038 1341 Dihedral : 16.269 73.432 1656 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 1.60 % Allowed : 14.36 % Favored : 84.05 % 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: -0.13 (0.29), residues: 868 helix: 1.21 (0.28), residues: 370 sheet: -0.37 (0.53), residues: 103 loop : -1.27 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 921 TYR 0.021 0.001 TYR A 201 PHE 0.034 0.001 PHE A1064 TRP 0.005 0.001 TRP A 808 HIS 0.003 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 8752) covalent geometry : angle 0.50713 / 0.29 (11984) hydrogen bonds : bond 0.04255 / 2.86 ( 344) hydrogen bonds : angle 4.89564 / 3.52 ( 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 68 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.8606 (mmm) cc_final: 0.8226 (mmm) REVERT: A 328 ILE cc_start: 0.8848 (mm) cc_final: 0.8608 (mm) REVERT: A 329 LEU cc_start: 0.8805 (mm) cc_final: 0.8538 (mm) REVERT: A 752 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7928 (pt0) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.0480 time to fit residues: 4.9648 Evaluate side-chains 60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.076748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.061611 restraints weight = 46857.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.063304 restraints weight = 25093.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.064355 restraints weight = 16729.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.065048 restraints weight = 12857.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.065481 restraints weight = 10797.024| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8752 Z= 0.255 Angle : 0.637 8.258 11984 Z= 0.354 Chirality : 0.042 0.138 1312 Planarity : 0.004 0.044 1341 Dihedral : 16.350 73.522 1656 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.49 % Favored : 95.39 % Rotamer: Outliers : 2.21 % Allowed : 15.09 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.29), residues: 868 helix: 0.94 (0.27), residues: 372 sheet: -0.45 (0.54), residues: 103 loop : -1.48 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 186 TYR 0.026 0.002 TYR A 218 PHE 0.029 0.002 PHE A 831 TRP 0.009 0.002 TRP A 609 HIS 0.006 0.001 HIS A 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.26 ( 8752) covalent geometry : angle 0.63677 / 0.35 (11984) hydrogen bonds : bond 0.05206 / 3.39 ( 344) hydrogen bonds : angle 5.28213 / 3.77 ( 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 70 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.8517 (mmm) cc_final: 0.8297 (mmm) REVERT: A 328 ILE cc_start: 0.8841 (mm) cc_final: 0.8626 (mm) REVERT: A 329 LEU cc_start: 0.8796 (mm) cc_final: 0.8476 (mm) REVERT: A 1035 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8649 (tp) REVERT: A 1147 PHE cc_start: 0.8947 (t80) cc_final: 0.8680 (t80) REVERT: A 1217 MET cc_start: 0.8084 (mtp) cc_final: 0.7702 (mtp) outliers start: 18 outliers final: 14 residues processed: 63 average time/residue: 0.0491 time to fit residues: 5.1349 Evaluate side-chains 63 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 720 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 61 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.078018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.062948 restraints weight = 45742.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.064682 restraints weight = 24251.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.065754 restraints weight = 16051.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.066449 restraints weight = 12263.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.066875 restraints weight = 10317.545| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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= 0.140 Angle : 0.538 8.031 11984 Z= 0.305 Chirality : 0.039 0.132 1312 Planarity : 0.003 0.043 1341 Dihedral : 16.323 73.387 1656 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.26 % Favored : 95.62 % Rotamer: Outliers : 1.72 % Allowed : 15.71 % Favored : 82.58 % 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: -0.24 (0.29), residues: 868 helix: 1.13 (0.28), residues: 369 sheet: -0.36 (0.55), residues: 103 loop : -1.36 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 692 TYR 0.026 0.002 TYR A 83 PHE 0.016 0.001 PHE A1064 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 0.00294 / 0.14 ( 8752) covalent geometry : angle 0.53781 / 0.30 (11984) hydrogen bonds : bond 0.04645 / 3.09 ( 344) hydrogen bonds : angle 5.04434 / 3.61 ( 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 66 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.8864 (mm) cc_final: 0.8613 (mm) REVERT: A 329 LEU cc_start: 0.8813 (mm) cc_final: 0.8489 (mm) REVERT: A 1035 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8655 (tp) outliers start: 14 outliers final: 12 residues processed: 61 average time/residue: 0.0495 time to fit residues: 5.1091 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 : 0.205 ------------------------------------------------------------------------------- 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 891 SER Chi-restraints excluded: chain A residue 980 MET 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: 6.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.077731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.062677 restraints weight = 46068.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.064414 restraints weight = 24507.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.065492 restraints weight = 16181.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.066190 restraints weight = 12361.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.066623 restraints weight = 10358.863| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8752 Z= 0.158 Angle : 0.549 8.385 11984 Z= 0.309 Chirality : 0.039 0.132 1312 Planarity : 0.003 0.042 1341 Dihedral : 16.333 73.381 1656 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 1.72 % Allowed : 16.56 % 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: -0.25 (0.29), residues: 868 helix: 1.12 (0.28), residues: 370 sheet: -0.40 (0.55), residues: 103 loop : -1.36 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 692 TYR 0.032 0.002 TYR A 83 PHE 0.015 0.001 PHE A1064 TRP 0.004 0.001 TRP A 141 HIS 0.003 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 8752) covalent geometry : angle 0.54948 / 0.31 (11984) hydrogen bonds : bond 0.04675 / 3.09 ( 344) hydrogen bonds : angle 5.03249 / 3.60 ( 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 66 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.8857 (mm) cc_final: 0.8616 (mm) REVERT: A 329 LEU cc_start: 0.8753 (mm) cc_final: 0.8440 (mm) REVERT: A 1035 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8610 (tp) REVERT: A 1217 MET cc_start: 0.8012 (mtp) cc_final: 0.7558 (mtp) outliers start: 14 outliers final: 12 residues processed: 62 average time/residue: 0.0466 time to fit residues: 4.9122 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 : 0.220 ------------------------------------------------------------------------------- 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 891 SER Chi-restraints excluded: chain A residue 980 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.076957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.061951 restraints weight = 46031.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.063641 restraints weight = 24604.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.064691 restraints weight = 16359.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.065377 restraints weight = 12511.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.065778 restraints weight = 10539.530| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2451 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= 0.195 Angle : 0.588 8.223 11984 Z= 0.330 Chirality : 0.040 0.153 1312 Planarity : 0.003 0.043 1341 Dihedral : 16.358 73.359 1656 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.70 % Rotamer: Outliers : 1.47 % Allowed : 17.06 % Favored : 81.47 % 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: -0.40 (0.29), residues: 868 helix: 1.00 (0.28), residues: 371 sheet: -0.50 (0.55), residues: 103 loop : -1.45 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 692 TYR 0.032 0.002 TYR A 83 PHE 0.016 0.002 PHE A1064 TRP 0.006 0.001 TRP A 609 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 ( 8752) covalent geometry : angle 0.58804 / 0.33 (11984) hydrogen bonds : bond 0.04985 / 3.28 ( 344) hydrogen bonds : angle 5.15127 / 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 62 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.8841 (mm) cc_final: 0.8606 (mm) REVERT: A 329 LEU cc_start: 0.8722 (mm) cc_final: 0.8374 (mm) REVERT: A 1035 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8603 (tp) REVERT: A 1217 MET cc_start: 0.8027 (mtp) cc_final: 0.7559 (mtp) outliers start: 12 outliers final: 10 residues processed: 58 average time/residue: 0.0535 time to fit residues: 5.1841 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 : 0.312 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 6 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.076896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.061919 restraints weight = 45997.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.063617 restraints weight = 24424.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.064671 restraints weight = 16163.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.065340 restraints weight = 12378.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.065763 restraints weight = 10438.561| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8752 Z= 0.188 Angle : 0.587 8.475 11984 Z= 0.329 Chirality : 0.040 0.165 1312 Planarity : 0.003 0.044 1341 Dihedral : 16.378 73.292 1656 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.07 % Favored : 94.82 % Rotamer: Outliers : 1.72 % Allowed : 17.06 % Favored : 81.23 % 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: -0.48 (0.29), residues: 868 helix: 0.96 (0.28), 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 0.002 0.000 ARG A 918 TYR 0.030 0.002 TYR A 83 PHE 0.016 0.002 PHE A1064 TRP 0.006 0.001 TRP A 609 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 ( 8752) covalent geometry : angle 0.58718 / 0.33 (11984) hydrogen bonds : bond 0.05009 / 3.30 ( 344) hydrogen bonds : angle 5.17683 / 3.69 ( 943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1327.14 seconds wall clock time: 23 minutes 39.20 seconds (1419.20 seconds total)