Starting phenix.real_space_refine on Tue Mar 3 21:31:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkv_48339/03_2026/9mkv_48339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkv_48339/03_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_48339/03_2026/9mkv_48339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkv_48339/03_2026/9mkv_48339.map" model { file = "/net/cci-nas-00/data/ceres_data/9mkv_48339/03_2026/9mkv_48339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkv_48339/03_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-5986/lib/python3.9/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: 1.99, per 1000 atoms: 0.23 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: 0.80 Conformation dependent library (CDL) restraints added in 262.2 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: 1.10 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: 1.66 Time building geometry restraints manager: 1.01 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=" 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=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta sigma weight residual 1.461 1.489 -0.027 1.17e-02 7.31e+03 5.44e+00 bond pdb=" CA ALA A 33 " pdb=" CB ALA A 33 " ideal model delta sigma weight residual 1.530 1.495 0.035 1.58e-02 4.01e+03 4.95e+00 bond pdb=" N ASP A 39 " pdb=" CA ASP A 39 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.17e-02 7.31e+03 4.33e+00 ... (remaining 8747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 11732 1.47 - 2.95: 209 2.95 - 4.42: 32 4.42 - 5.90: 8 5.90 - 7.37: 3 Bond angle restraints: 11984 Sorted by residual: 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=" C SER A 2 " pdb=" N ILE A 3 " pdb=" CA ILE A 3 " ideal model delta sigma weight residual 121.97 128.24 -6.27 1.80e+00 3.09e-01 1.21e+01 angle pdb=" C LEU A 36 " pdb=" N ILE A 37 " pdb=" CA ILE A 37 " ideal model delta sigma weight residual 122.66 119.47 3.19 9.70e-01 1.06e+00 1.08e+01 angle pdb=" CA TYR A 218 " pdb=" CB TYR A 218 " pdb=" CG TYR A 218 " ideal model delta sigma weight residual 113.90 119.64 -5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" N ILE A 37 " pdb=" CA ILE A 37 " pdb=" C ILE A 37 " ideal model delta sigma weight residual 111.90 109.36 2.54 8.10e-01 1.52e+00 9.84e+00 ... (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: 976 0.038 - 0.076: 257 0.076 - 0.114: 64 0.114 - 0.151: 13 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: 1.620 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: 0.030 Set scattering table: 0.030 Process input model: 9.860 Find NCS groups from input model: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.002 0.035 8752 Z= 0.124 Angle : 0.493 7.372 11984 Z= 0.291 Chirality : 0.038 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 covalent geometry : bond 0.00223 ( 8752) covalent geometry : angle 0.49338 (11984) hydrogen bonds : bond 0.14839 ( 344) hydrogen bonds : angle 6.17306 ( 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 : 0.429 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: 0.0858 time to fit residues: 12.9826 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 : 0.312 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 938 GLN ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.078424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.063258 restraints weight = 45622.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.064971 restraints weight = 24778.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.066049 restraints weight = 16520.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.066719 restraints weight = 12680.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.067193 restraints weight = 10741.975| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8752 Z= 0.184 Angle : 0.583 7.914 11984 Z= 0.321 Chirality : 0.039 0.151 1312 Planarity : 0.004 0.037 1341 Dihedral : 16.295 73.483 1656 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 2.21 % Allowed : 8.83 % 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: -0.21 (0.29), residues: 868 helix: 1.23 (0.28), residues: 365 sheet: -0.47 (0.56), residues: 104 loop : -1.36 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1272 TYR 0.032 0.002 TYR A 218 PHE 0.021 0.002 PHE A1064 TRP 0.004 0.001 TRP A 609 HIS 0.003 0.001 HIS A 694 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8752) covalent geometry : angle 0.58275 (11984) hydrogen bonds : bond 0.04807 ( 344) hydrogen bonds : angle 5.37128 ( 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 80 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.8716 (mmm) cc_final: 0.8491 (mmm) REVERT: A 328 ILE cc_start: 0.8858 (mm) cc_final: 0.8620 (mm) REVERT: A 329 LEU cc_start: 0.8798 (mm) cc_final: 0.8476 (mm) REVERT: A 752 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: A 897 ASN cc_start: 0.8899 (p0) cc_final: 0.8688 (p0) REVERT: A 1217 MET cc_start: 0.7984 (mtp) cc_final: 0.7383 (mtp) outliers start: 18 outliers final: 13 residues processed: 74 average time/residue: 0.0634 time to fit residues: 7.4069 Evaluate side-chains 60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 633 MET 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 1074 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.077689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.062650 restraints weight = 45766.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.064321 restraints weight = 24590.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.065395 restraints weight = 16492.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.066062 restraints weight = 12685.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.066521 restraints weight = 10735.860| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8752 Z= 0.184 Angle : 0.578 9.962 11984 Z= 0.319 Chirality : 0.039 0.173 1312 Planarity : 0.003 0.041 1341 Dihedral : 16.380 73.255 1656 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.84 % Favored : 95.05 % Rotamer: Outliers : 2.33 % Allowed : 12.15 % Favored : 85.52 % 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: -0.29 (0.29), residues: 868 helix: 1.12 (0.28), residues: 368 sheet: -0.46 (0.56), residues: 103 loop : -1.39 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 186 TYR 0.028 0.002 TYR A 218 PHE 0.015 0.002 PHE A1124 TRP 0.005 0.001 TRP A 609 HIS 0.003 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8752) covalent geometry : angle 0.57845 (11984) hydrogen bonds : bond 0.04755 ( 344) hydrogen bonds : angle 5.26599 ( 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 74 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.8835 (mm) cc_final: 0.8625 (mm) REVERT: A 329 LEU cc_start: 0.8785 (mm) cc_final: 0.8440 (mm) REVERT: A 752 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: A 897 ASN cc_start: 0.8965 (p0) cc_final: 0.8714 (p0) outliers start: 19 outliers final: 13 residues processed: 68 average time/residue: 0.0603 time to fit residues: 6.6053 Evaluate side-chains 63 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL 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 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 1199 SER Chi-restraints excluded: chain A residue 1255 ASP 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: 8.9990 chunk 82 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3722 r_free = 0.3722 target = 0.076605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.061521 restraints weight = 46992.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.063215 restraints weight = 25032.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.064269 restraints weight = 16645.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.064963 restraints weight = 12791.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.065346 restraints weight = 10765.133| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8752 Z= 0.205 Angle : 0.599 7.960 11984 Z= 0.329 Chirality : 0.040 0.133 1312 Planarity : 0.004 0.045 1341 Dihedral : 16.427 73.213 1656 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 2.82 % Allowed : 15.46 % 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: -0.51 (0.29), residues: 868 helix: 0.88 (0.27), residues: 371 sheet: -0.50 (0.56), residues: 103 loop : -1.49 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 186 TYR 0.021 0.002 TYR A 218 PHE 0.036 0.002 PHE A1147 TRP 0.007 0.001 TRP A 609 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 8752) covalent geometry : angle 0.59911 (11984) hydrogen bonds : bond 0.04958 ( 344) hydrogen bonds : angle 5.31801 ( 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 77 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9143 (pt) REVERT: A 328 ILE cc_start: 0.8859 (mm) cc_final: 0.8626 (mm) REVERT: A 329 LEU cc_start: 0.8768 (mm) cc_final: 0.8390 (mm) REVERT: A 897 ASN cc_start: 0.8989 (p0) cc_final: 0.8716 (p0) outliers start: 23 outliers final: 16 residues processed: 71 average time/residue: 0.0509 time to fit residues: 5.9350 Evaluate side-chains 65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 264 PHE 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 915 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 1199 SER 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: 2.9990 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.076340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.061403 restraints weight = 46514.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.063082 restraints weight = 24452.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.064145 restraints weight = 16241.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.064778 restraints weight = 12441.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.065225 restraints weight = 10542.114| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8752 Z= 0.200 Angle : 0.593 7.886 11984 Z= 0.325 Chirality : 0.039 0.136 1312 Planarity : 0.003 0.045 1341 Dihedral : 16.462 73.186 1656 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 3.07 % Allowed : 17.79 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.53 (0.29), residues: 868 helix: 0.85 (0.27), residues: 371 sheet: -0.50 (0.57), 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 0.022 0.002 TYR A 201 PHE 0.029 0.002 PHE A1147 TRP 0.007 0.001 TRP A 609 HIS 0.007 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8752) covalent geometry : angle 0.59292 (11984) hydrogen bonds : bond 0.04923 ( 344) hydrogen bonds : angle 5.26438 ( 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 74 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9159 (pt) REVERT: A 218 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.4339 (p90) REVERT: A 328 ILE cc_start: 0.8856 (mm) cc_final: 0.8632 (mm) REVERT: A 329 LEU cc_start: 0.8680 (mm) cc_final: 0.8296 (mm) REVERT: A 897 ASN cc_start: 0.8983 (p0) cc_final: 0.8703 (p0) REVERT: A 941 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7834 (t80) REVERT: A 1147 PHE cc_start: 0.8996 (t80) cc_final: 0.8729 (t80) outliers start: 25 outliers final: 16 residues processed: 67 average time/residue: 0.0565 time to fit residues: 6.2736 Evaluate side-chains 66 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 264 PHE 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 915 SER Chi-restraints excluded: chain A residue 941 PHE 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: 8.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 25 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.077017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.061951 restraints weight = 46038.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.063723 restraints weight = 23893.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.064833 restraints weight = 15638.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.065536 restraints weight = 11896.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.065930 restraints weight = 9948.648| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2801 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= 0.154 Angle : 0.548 7.739 11984 Z= 0.300 Chirality : 0.038 0.135 1312 Planarity : 0.003 0.045 1341 Dihedral : 16.404 73.151 1656 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 2.58 % Allowed : 19.51 % Favored : 77.91 % 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: -0.28 (0.29), residues: 868 helix: 1.08 (0.28), residues: 372 sheet: 0.22 (0.60), residues: 90 loop : -1.52 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 690 TYR 0.022 0.001 TYR A 201 PHE 0.020 0.001 PHE A1147 TRP 0.005 0.001 TRP A 175 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8752) covalent geometry : angle 0.54765 (11984) hydrogen bonds : bond 0.04484 ( 344) hydrogen bonds : angle 5.03520 ( 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 71 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9150 (pt) REVERT: A 328 ILE cc_start: 0.8861 (mm) cc_final: 0.8616 (mm) REVERT: A 329 LEU cc_start: 0.8692 (mm) cc_final: 0.8310 (mm) REVERT: A 897 ASN cc_start: 0.8990 (p0) cc_final: 0.8714 (p0) outliers start: 21 outliers final: 13 residues processed: 67 average time/residue: 0.0638 time to fit residues: 6.7365 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 : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 264 PHE 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 915 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 1199 SER 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: 6.9990 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.076067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.061098 restraints weight = 47159.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.062785 restraints weight = 25120.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.063873 restraints weight = 16769.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.064527 restraints weight = 12823.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.064964 restraints weight = 10855.533| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8752 Z= 0.197 Angle : 0.597 7.789 11984 Z= 0.326 Chirality : 0.039 0.147 1312 Planarity : 0.003 0.046 1341 Dihedral : 16.454 73.146 1656 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 2.45 % Allowed : 19.88 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.29), residues: 868 helix: 1.00 (0.28), residues: 367 sheet: -0.51 (0.56), residues: 102 loop : -1.52 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 692 TYR 0.026 0.002 TYR A 201 PHE 0.020 0.002 PHE A1091 TRP 0.007 0.001 TRP A 609 HIS 0.005 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8752) covalent geometry : angle 0.59681 (11984) hydrogen bonds : bond 0.04863 ( 344) hydrogen bonds : angle 5.13067 ( 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 65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9151 (pt) REVERT: A 328 ILE cc_start: 0.8855 (mm) cc_final: 0.8634 (mm) REVERT: A 329 LEU cc_start: 0.8670 (mm) cc_final: 0.8277 (mm) REVERT: A 897 ASN cc_start: 0.8986 (p0) cc_final: 0.8707 (p0) REVERT: A 941 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7706 (t80) outliers start: 20 outliers final: 15 residues processed: 60 average time/residue: 0.0596 time to fit residues: 5.9640 Evaluate side-chains 62 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 941 PHE 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: 5.9990 chunk 3 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.076041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.061062 restraints weight = 45924.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.062792 restraints weight = 23983.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.063900 restraints weight = 15808.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.064579 restraints weight = 12044.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.064992 restraints weight = 10103.144| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8752 Z= 0.187 Angle : 0.585 7.634 11984 Z= 0.319 Chirality : 0.039 0.135 1312 Planarity : 0.003 0.048 1341 Dihedral : 16.485 73.140 1656 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.07 % Favored : 94.82 % Rotamer: Outliers : 2.70 % Allowed : 20.25 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.46 (0.29), residues: 868 helix: 1.01 (0.28), residues: 367 sheet: -0.56 (0.56), residues: 102 loop : -1.51 (0.30), residues: 399 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 0.018 0.002 PHE A 264 TRP 0.007 0.001 TRP A 609 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8752) covalent geometry : angle 0.58546 (11984) hydrogen bonds : bond 0.04758 ( 344) hydrogen bonds : angle 5.13908 ( 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 68 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9155 (pt) REVERT: A 186 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8526 (mmt90) REVERT: A 328 ILE cc_start: 0.8862 (mm) cc_final: 0.8641 (mm) REVERT: A 329 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8286 (mm) REVERT: A 686 GLU cc_start: 0.9279 (tt0) cc_final: 0.9057 (tp30) REVERT: A 897 ASN cc_start: 0.8987 (p0) cc_final: 0.8725 (p0) REVERT: A 941 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7578 (t80) outliers start: 22 outliers final: 16 residues processed: 60 average time/residue: 0.0608 time to fit residues: 5.9524 Evaluate side-chains 64 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 300 ILE 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 769 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 941 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.076044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.061088 restraints weight = 46086.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.062815 restraints weight = 24004.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.063922 restraints weight = 15805.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.064614 restraints weight = 12017.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.065043 restraints weight = 10043.191| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8752 Z= 0.178 Angle : 0.577 7.525 11984 Z= 0.316 Chirality : 0.039 0.133 1312 Planarity : 0.003 0.048 1341 Dihedral : 16.492 73.133 1656 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.70 % Rotamer: Outliers : 2.94 % Allowed : 20.49 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.44 (0.29), residues: 868 helix: 1.02 (0.28), residues: 367 sheet: -0.59 (0.55), residues: 102 loop : -1.48 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 43 TYR 0.028 0.002 TYR A 201 PHE 0.017 0.001 PHE A 264 TRP 0.006 0.001 TRP A 141 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8752) covalent geometry : angle 0.57728 (11984) hydrogen bonds : bond 0.04705 ( 344) hydrogen bonds : angle 5.12011 ( 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 69 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8523 (mmt90) REVERT: A 328 ILE cc_start: 0.8843 (mm) cc_final: 0.8631 (mm) REVERT: A 329 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 686 GLU cc_start: 0.9298 (tt0) cc_final: 0.9013 (tp30) REVERT: A 897 ASN cc_start: 0.8985 (p0) cc_final: 0.8709 (p0) REVERT: A 941 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7370 (t80) REVERT: A 988 VAL cc_start: 0.9281 (t) cc_final: 0.9017 (t) outliers start: 24 outliers final: 19 residues processed: 62 average time/residue: 0.0679 time to fit residues: 6.6291 Evaluate side-chains 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 1006 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 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: 8.9990 chunk 68 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 overall best weight: 4.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.075012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.060258 restraints weight = 46469.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.061902 restraints weight = 24900.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.062952 restraints weight = 16642.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.063604 restraints weight = 12787.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.064042 restraints weight = 10801.085| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3382 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= 0.230 Angle : 0.633 7.983 11984 Z= 0.346 Chirality : 0.041 0.149 1312 Planarity : 0.004 0.050 1341 Dihedral : 16.611 73.197 1656 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.88 % Favored : 94.01 % Rotamer: Outliers : 2.94 % Allowed : 20.74 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.28), residues: 868 helix: 0.76 (0.27), residues: 371 sheet: -0.67 (0.56), residues: 97 loop : -1.62 (0.29), residues: 400 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 0.019 0.002 PHE A 264 TRP 0.009 0.002 TRP A 609 HIS 0.005 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 8752) covalent geometry : angle 0.63344 (11984) hydrogen bonds : bond 0.05220 ( 344) hydrogen bonds : angle 5.36419 ( 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 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8552 (mmt90) REVERT: A 329 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8315 (mm) REVERT: A 897 ASN cc_start: 0.8984 (p0) cc_final: 0.8711 (p0) REVERT: A 941 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7572 (t80) outliers start: 24 outliers final: 19 residues processed: 59 average time/residue: 0.0614 time to fit residues: 5.8738 Evaluate side-chains 64 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 1006 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 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 6 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 938 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.074744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.060038 restraints weight = 46710.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.061644 restraints weight = 24868.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.062683 restraints weight = 16741.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.063356 restraints weight = 12880.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.063729 restraints weight = 10818.639| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3523 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= 0.241 Angle : 0.652 8.714 11984 Z= 0.356 Chirality : 0.041 0.154 1312 Planarity : 0.004 0.051 1341 Dihedral : 16.721 74.014 1656 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.88 % Favored : 94.01 % Rotamer: Outliers : 2.94 % Allowed : 21.23 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.93 (0.28), residues: 868 helix: 0.56 (0.27), residues: 371 sheet: -0.70 (0.55), residues: 99 loop : -1.75 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 692 TYR 0.032 0.002 TYR A 201 PHE 0.019 0.002 PHE A 264 TRP 0.010 0.002 TRP A 609 HIS 0.006 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 8752) covalent geometry : angle 0.65237 (11984) hydrogen bonds : bond 0.05325 ( 344) hydrogen bonds : angle 5.46725 ( 943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1512.12 seconds wall clock time: 26 minutes 52.31 seconds (1612.31 seconds total)