Starting phenix.real_space_refine on Sat Aug 23 08:53:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jft_36217/08_2025/8jft_36217_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jft_36217/08_2025/8jft_36217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jft_36217/08_2025/8jft_36217_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jft_36217/08_2025/8jft_36217_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jft_36217/08_2025/8jft_36217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jft_36217/08_2025/8jft_36217.map" } resolution = 3.31 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= 0.011 sd= 0.105 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 86 5.49 5 S 15 5.16 5 C 6760 2.51 5 N 1930 2.21 5 O 2385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11176 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8443 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 25, 'TRANS': 1015} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 15, 'ASN:plan1': 3, 'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1820 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 39, 'rna3p_pyr': 38} Link IDs: {'rna2p': 8, 'rna3p': 77} Chain breaks: 1 Chain: "C" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 913 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 2.52, per 1000 atoms: 0.23 Number of scatterers: 11176 At special positions: 0 Unit cell: (122.72, 96.72, 117.52, 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 15 16.00 P 86 15.00 O 2385 8.00 N 1930 7.00 C 6760 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: 0.76 Conformation dependent library (CDL) restraints added in 408.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 52.0% alpha, 10.3% beta 19 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 40 through 74 removed outlier: 4.413A pdb=" N ASN A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 120 through 124 removed outlier: 4.015A pdb=" N VAL A 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 172 through 188 removed outlier: 3.621A pdb=" N TYR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.741A pdb=" N ILE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.683A pdb=" N ILE A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.523A pdb=" N GLU A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 438 through 444 removed outlier: 4.188A pdb=" N ASP A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 444' Processing helix chain 'A' and resid 447 through 469 Processing helix chain 'A' and resid 483 through 513 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 520 through 530 removed outlier: 3.685A pdb=" N ASP A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 549 removed outlier: 3.764A pdb=" N LEU A 546 " --> pdb=" O PRO A 542 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 600 through 614 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.562A pdb=" N GLU A 624 " --> pdb=" O LYS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 646 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.767A pdb=" N THR A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 714 removed outlier: 3.637A pdb=" N ALA A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 705 " --> pdb=" O HIS A 701 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.900A pdb=" N LYS A 764 " --> pdb=" O ILE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 827 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.920A pdb=" N TYR A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 1000 through 1007 Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 148 through 155 Processing sheet with id=AA1, first strand: chain 'A' and resid 672 through 675 removed outlier: 4.025A pdb=" N ASP A 473 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 31 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N SER A 772 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 33 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 553 through 557 Processing sheet with id=AA4, first strand: chain 'A' and resid 791 through 793 Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 805 Processing sheet with id=AA6, first strand: chain 'A' and resid 891 through 892 Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 929 removed outlier: 3.694A pdb=" N ALA A 964 " --> pdb=" O VAL A 916 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 918 " --> pdb=" O PHE A 962 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE A 962 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 933 through 936 Processing sheet with id=AA9, first strand: chain 'A' and resid 1017 through 1019 removed outlier: 7.507A pdb=" N ARG A 991 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 984 " --> pdb=" O ARG A 991 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 993 " --> pdb=" O ILE A 982 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 81 448 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1696 1.31 - 1.43: 3472 1.43 - 1.56: 6190 1.56 - 1.68: 170 1.68 - 1.81: 27 Bond restraints: 11555 Sorted by residual: bond pdb=" C ARG A 47 " pdb=" O ARG A 47 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.17e-02 7.31e+03 2.39e+01 bond pdb=" O3' U B 71 " pdb=" P U B 72 " ideal model delta sigma weight residual 1.607 1.679 -0.072 1.50e-02 4.44e+03 2.29e+01 bond pdb=" CA SER A 49 " pdb=" CB SER A 49 " ideal model delta sigma weight residual 1.528 1.456 0.072 1.59e-02 3.96e+03 2.07e+01 bond pdb=" CA SER A 106 " pdb=" CB SER A 106 " ideal model delta sigma weight residual 1.528 1.466 0.063 1.56e-02 4.11e+03 1.62e+01 bond pdb=" CA SER C 76 " pdb=" CB SER C 76 " ideal model delta sigma weight residual 1.532 1.459 0.072 1.82e-02 3.02e+03 1.58e+01 ... (remaining 11550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 14134 2.03 - 4.05: 1629 4.05 - 6.08: 198 6.08 - 8.10: 29 8.10 - 10.13: 5 Bond angle restraints: 15995 Sorted by residual: angle pdb=" N ARG A 51 " pdb=" CA ARG A 51 " pdb=" C ARG A 51 " ideal model delta sigma weight residual 111.28 102.89 8.39 1.09e+00 8.42e-01 5.92e+01 angle pdb=" N LEU A 110 " pdb=" CA LEU A 110 " pdb=" C LEU A 110 " ideal model delta sigma weight residual 111.28 103.47 7.81 1.09e+00 8.42e-01 5.13e+01 angle pdb=" N GLU A 45 " pdb=" CA GLU A 45 " pdb=" C GLU A 45 " ideal model delta sigma weight residual 111.82 103.58 8.24 1.16e+00 7.43e-01 5.05e+01 angle pdb=" N PRO A1014 " pdb=" CA PRO A1014 " pdb=" C PRO A1014 " ideal model delta sigma weight residual 114.03 122.59 -8.56 1.23e+00 6.61e-01 4.84e+01 angle pdb=" N TYR C 147 " pdb=" CA TYR C 147 " pdb=" C TYR C 147 " ideal model delta sigma weight residual 114.12 104.50 9.62 1.39e+00 5.18e-01 4.79e+01 ... (remaining 15990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 6780 35.58 - 71.16: 315 71.16 - 106.73: 30 106.73 - 142.31: 2 142.31 - 177.89: 2 Dihedral angle restraints: 7129 sinusoidal: 3701 harmonic: 3428 Sorted by residual: dihedral pdb=" C4' U B 73 " pdb=" C3' U B 73 " pdb=" C2' U B 73 " pdb=" C1' U B 73 " ideal model delta sinusoidal sigma weight residual -35.00 33.95 -68.95 1 8.00e+00 1.56e-02 9.61e+01 dihedral pdb=" O4' U B 73 " pdb=" C2' U B 73 " pdb=" C1' U B 73 " pdb=" C3' U B 73 " ideal model delta sinusoidal sigma weight residual -35.00 31.37 -66.37 1 8.00e+00 1.56e-02 8.99e+01 dihedral pdb=" O4' U B 11 " pdb=" C1' U B 11 " pdb=" N1 U B 11 " pdb=" C2 U B 11 " ideal model delta sinusoidal sigma weight residual -128.00 49.89 -177.89 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1229 0.070 - 0.140: 350 0.140 - 0.211: 196 0.211 - 0.281: 51 0.281 - 0.351: 11 Chirality restraints: 1837 Sorted by residual: chirality pdb=" CA PRO A1014 " pdb=" N PRO A1014 " pdb=" C PRO A1014 " pdb=" CB PRO A1014 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA TYR C 77 " pdb=" N TYR C 77 " pdb=" C TYR C 77 " pdb=" CB TYR C 77 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ILE A 880 " pdb=" N ILE A 880 " pdb=" C ILE A 880 " pdb=" CB ILE A 880 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1834 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 973 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C LYS A 973 " -0.063 2.00e-02 2.50e+03 pdb=" O LYS A 973 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 974 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1006 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLU A1006 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU A1006 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A1007 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1020 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ILE A1020 " 0.054 2.00e-02 2.50e+03 pdb=" O ILE A1020 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA A1021 " -0.019 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2683 2.79 - 3.32: 10879 3.32 - 3.85: 18832 3.85 - 4.37: 22503 4.37 - 4.90: 34978 Nonbonded interactions: 89875 Sorted by model distance: nonbonded pdb=" O ARG A 209 " pdb=" O2' U B 16 " model vdw 2.264 3.040 nonbonded pdb=" OG SER A 957 " pdb=" OE1 GLN A 959 " model vdw 2.271 3.040 nonbonded pdb=" OD2 ASP A 545 " pdb=" OH TYR A 553 " model vdw 2.287 3.040 nonbonded pdb=" O2' G B 87 " pdb=" OP1 U B 88 " model vdw 2.297 3.040 nonbonded pdb=" ND2 ASN A 413 " pdb=" N GLN A 414 " model vdw 2.298 3.200 ... (remaining 89870 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.710 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 11555 Z= 0.613 Angle : 1.270 10.126 15995 Z= 0.943 Chirality : 0.089 0.351 1837 Planarity : 0.005 0.041 1740 Dihedral : 18.180 177.886 4923 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.90 % Allowed : 5.48 % Favored : 93.62 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -0.00 (0.24), residues: 1145 helix: 0.78 (0.23), residues: 527 sheet: 0.09 (0.51), residues: 101 loop : -0.78 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 685 TYR 0.026 0.002 TYR A 256 PHE 0.019 0.002 PHE C 165 TRP 0.011 0.002 TRP A 408 HIS 0.006 0.001 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00834 (11555) covalent geometry : angle 1.27048 (15995) hydrogen bonds : bond 0.18676 ( 492) hydrogen bonds : angle 8.14781 ( 1380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8177 (p90) cc_final: 0.7961 (p90) REVERT: A 232 MET cc_start: 0.8264 (mmt) cc_final: 0.7096 (ttt) REVERT: A 243 GLU cc_start: 0.7998 (tp30) cc_final: 0.7785 (tp30) REVERT: A 331 ASP cc_start: 0.8019 (m-30) cc_final: 0.7797 (m-30) REVERT: A 366 GLU cc_start: 0.8507 (tt0) cc_final: 0.8217 (tt0) REVERT: A 386 LEU cc_start: 0.8671 (mt) cc_final: 0.8233 (mt) REVERT: A 440 LEU cc_start: 0.8906 (mm) cc_final: 0.8393 (mm) REVERT: A 534 CYS cc_start: 0.7587 (t) cc_final: 0.6827 (t) REVERT: A 605 LYS cc_start: 0.9398 (tmtt) cc_final: 0.9179 (tptt) REVERT: A 696 LYS cc_start: 0.8625 (mmtm) cc_final: 0.7926 (pttt) REVERT: A 769 TYR cc_start: 0.8358 (m-80) cc_final: 0.7915 (m-80) REVERT: A 813 ASN cc_start: 0.8398 (t0) cc_final: 0.7839 (t0) REVERT: A 833 ASP cc_start: 0.7947 (t70) cc_final: 0.7053 (t70) REVERT: A 987 ASP cc_start: 0.8219 (p0) cc_final: 0.7818 (p0) REVERT: A 996 MET cc_start: 0.7650 (mtm) cc_final: 0.6912 (mtm) REVERT: A 1024 THR cc_start: 0.9254 (m) cc_final: 0.8983 (p) REVERT: C 78 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8349 (mt) REVERT: C 93 ASP cc_start: 0.8801 (t0) cc_final: 0.8519 (t0) REVERT: C 95 TYR cc_start: 0.7786 (m-80) cc_final: 0.7432 (m-80) REVERT: C 106 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C 129 ASN cc_start: 0.7823 (t0) cc_final: 0.7173 (t0) outliers start: 9 outliers final: 2 residues processed: 221 average time/residue: 0.0868 time to fit residues: 27.9176 Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 120 ASN A 154 GLN A 252 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN A 413 ASN A 414 GLN A 472 ASN A 570 ASN A 580 ASN A 695 ASN A 785 ASN A 968 ASN A 990 ASN C 163 HIS C 169 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101783 restraints weight = 17501.637| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.68 r_work: 0.3116 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11555 Z= 0.153 Angle : 0.606 8.617 15995 Z= 0.313 Chirality : 0.040 0.143 1837 Planarity : 0.003 0.027 1740 Dihedral : 18.783 178.317 2582 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.09 % Allowed : 10.77 % Favored : 87.14 % 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 aren not related in a simple way. whole: 0.34 (0.24), residues: 1145 helix: 1.20 (0.22), residues: 541 sheet: -0.28 (0.46), residues: 119 loop : -0.69 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 47 TYR 0.019 0.001 TYR A 256 PHE 0.015 0.002 PHE A 683 TRP 0.010 0.001 TRP A 408 HIS 0.009 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00326 (11555) covalent geometry : angle 0.60636 (15995) hydrogen bonds : bond 0.04790 ( 492) hydrogen bonds : angle 4.86385 ( 1380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 232 MET cc_start: 0.8273 (mmt) cc_final: 0.7231 (ttt) REVERT: A 362 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6587 (tm-30) REVERT: A 366 GLU cc_start: 0.8176 (tt0) cc_final: 0.7818 (mm-30) REVERT: A 386 LEU cc_start: 0.8436 (mt) cc_final: 0.7964 (mt) REVERT: A 394 ASN cc_start: 0.6657 (t0) cc_final: 0.6431 (t0) REVERT: A 406 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6876 (tp30) REVERT: A 442 ASP cc_start: 0.7932 (m-30) cc_final: 0.7729 (t0) REVERT: A 478 LEU cc_start: 0.8510 (tp) cc_final: 0.8268 (tt) REVERT: A 534 CYS cc_start: 0.7092 (t) cc_final: 0.6739 (t) REVERT: A 605 LYS cc_start: 0.9313 (tmtt) cc_final: 0.9055 (tptt) REVERT: A 657 MET cc_start: 0.8204 (mmm) cc_final: 0.7954 (mmt) REVERT: A 677 ASN cc_start: 0.7531 (t0) cc_final: 0.6245 (m-40) REVERT: A 696 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7384 (pttp) REVERT: A 813 ASN cc_start: 0.8582 (t0) cc_final: 0.7811 (t0) REVERT: A 833 ASP cc_start: 0.7515 (t70) cc_final: 0.6509 (t70) REVERT: A 987 ASP cc_start: 0.8626 (p0) cc_final: 0.8276 (p0) REVERT: A 989 LEU cc_start: 0.8590 (mt) cc_final: 0.8388 (mp) REVERT: A 996 MET cc_start: 0.7594 (mtm) cc_final: 0.6984 (mtm) REVERT: A 1024 THR cc_start: 0.9299 (m) cc_final: 0.8971 (p) REVERT: C 93 ASP cc_start: 0.9070 (t0) cc_final: 0.8856 (t0) REVERT: C 95 TYR cc_start: 0.8085 (m-80) cc_final: 0.7690 (m-80) REVERT: C 97 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.8252 (t80) REVERT: C 135 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8760 (tm-30) outliers start: 21 outliers final: 11 residues processed: 182 average time/residue: 0.0840 time to fit residues: 22.3306 Evaluate side-chains 162 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 35 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 overall best weight: 2.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 863 ASN C 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.152585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099625 restraints weight = 17644.399| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.70 r_work: 0.3078 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11555 Z= 0.162 Angle : 0.546 6.411 15995 Z= 0.285 Chirality : 0.039 0.162 1837 Planarity : 0.003 0.029 1740 Dihedral : 18.512 177.568 2579 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.59 % Allowed : 11.57 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.25), residues: 1145 helix: 1.36 (0.22), residues: 544 sheet: -0.29 (0.46), residues: 119 loop : -0.66 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 685 TYR 0.020 0.001 TYR A 18 PHE 0.015 0.002 PHE A 569 TRP 0.008 0.001 TRP A 408 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00349 (11555) covalent geometry : angle 0.54561 (15995) hydrogen bonds : bond 0.04370 ( 492) hydrogen bonds : angle 4.48303 ( 1380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 THR cc_start: 0.8412 (p) cc_final: 0.8074 (t) REVERT: A 45 GLU cc_start: 0.8233 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 120 ASN cc_start: 0.7621 (t0) cc_final: 0.7392 (t0) REVERT: A 232 MET cc_start: 0.8286 (mmt) cc_final: 0.7155 (ttp) REVERT: A 239 TYR cc_start: 0.7393 (m-80) cc_final: 0.7188 (m-80) REVERT: A 362 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6606 (tm-30) REVERT: A 366 GLU cc_start: 0.8113 (tt0) cc_final: 0.7739 (mm-30) REVERT: A 386 LEU cc_start: 0.8404 (mt) cc_final: 0.7916 (mt) REVERT: A 406 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6751 (tp30) REVERT: A 432 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8316 (pt0) REVERT: A 478 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8289 (tt) REVERT: A 605 LYS cc_start: 0.9365 (tmtt) cc_final: 0.9082 (tptt) REVERT: A 677 ASN cc_start: 0.7475 (t0) cc_final: 0.6305 (m110) REVERT: A 687 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7698 (ttpp) REVERT: A 696 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7448 (pttp) REVERT: A 813 ASN cc_start: 0.8720 (t0) cc_final: 0.8368 (t0) REVERT: A 829 MET cc_start: 0.8076 (mtp) cc_final: 0.7235 (mtp) REVERT: A 833 ASP cc_start: 0.7622 (t70) cc_final: 0.5975 (p0) REVERT: A 860 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8498 (mp0) REVERT: A 987 ASP cc_start: 0.8616 (p0) cc_final: 0.8292 (p0) REVERT: A 996 MET cc_start: 0.7562 (mtm) cc_final: 0.7146 (mtm) REVERT: A 1024 THR cc_start: 0.9304 (m) cc_final: 0.8971 (p) REVERT: C 74 ASN cc_start: 0.8873 (m-40) cc_final: 0.8569 (m110) REVERT: C 86 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8089 (mm-30) REVERT: C 95 TYR cc_start: 0.8309 (m-80) cc_final: 0.7749 (m-80) REVERT: C 97 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8383 (t80) REVERT: C 135 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8807 (tm-30) outliers start: 26 outliers final: 14 residues processed: 168 average time/residue: 0.0834 time to fit residues: 20.4089 Evaluate side-chains 159 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 40.0000 chunk 56 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 74 optimal weight: 0.0870 chunk 120 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 0.2980 overall best weight: 2.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 141 ASN ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN C 108 GLN C 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.151573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098200 restraints weight = 17620.918| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.69 r_work: 0.3062 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11555 Z= 0.176 Angle : 0.535 6.318 15995 Z= 0.281 Chirality : 0.039 0.149 1837 Planarity : 0.003 0.032 1740 Dihedral : 18.365 177.531 2579 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.19 % Allowed : 13.56 % Favored : 84.25 % 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 aren not related in a simple way. whole: 0.60 (0.25), residues: 1145 helix: 1.46 (0.23), residues: 543 sheet: -0.32 (0.47), residues: 114 loop : -0.60 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 208 TYR 0.018 0.001 TYR A 939 PHE 0.014 0.001 PHE A 925 TRP 0.010 0.001 TRP A 408 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd covalent geometry : bond 0.00383 (11555) covalent geometry : angle 0.53515 (15995) hydrogen bonds : bond 0.04060 ( 492) hydrogen bonds : angle 4.35557 ( 1380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 14 THR cc_start: 0.8517 (p) cc_final: 0.8199 (t) REVERT: A 45 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7999 (tm-30) REVERT: A 120 ASN cc_start: 0.7580 (t0) cc_final: 0.7315 (t0) REVERT: A 229 TRP cc_start: 0.7495 (t60) cc_final: 0.7194 (t60) REVERT: A 232 MET cc_start: 0.8365 (mmt) cc_final: 0.7961 (mmp) REVERT: A 234 MET cc_start: 0.7935 (mmt) cc_final: 0.7709 (mmm) REVERT: A 239 TYR cc_start: 0.7438 (m-80) cc_final: 0.7226 (m-80) REVERT: A 362 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6697 (tm-30) REVERT: A 366 GLU cc_start: 0.8119 (tt0) cc_final: 0.7758 (mm-30) REVERT: A 386 LEU cc_start: 0.8385 (mt) cc_final: 0.7826 (mt) REVERT: A 406 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6688 (tp30) REVERT: A 432 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8308 (pt0) REVERT: A 478 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8281 (tt) REVERT: A 605 LYS cc_start: 0.9365 (tmtt) cc_final: 0.9067 (tptt) REVERT: A 657 MET cc_start: 0.8060 (mmt) cc_final: 0.7823 (mmm) REVERT: A 677 ASN cc_start: 0.7423 (t0) cc_final: 0.6299 (m-40) REVERT: A 687 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7711 (ttpp) REVERT: A 696 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7506 (pttp) REVERT: A 813 ASN cc_start: 0.8674 (t0) cc_final: 0.8286 (t0) REVERT: A 829 MET cc_start: 0.8108 (mtp) cc_final: 0.7114 (mtp) REVERT: A 833 ASP cc_start: 0.7791 (t70) cc_final: 0.6350 (p0) REVERT: A 860 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8506 (mp0) REVERT: A 987 ASP cc_start: 0.8592 (p0) cc_final: 0.8281 (p0) REVERT: A 996 MET cc_start: 0.7581 (mtm) cc_final: 0.7135 (mtm) REVERT: A 1024 THR cc_start: 0.9315 (m) cc_final: 0.8947 (p) REVERT: C 86 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8136 (mm-30) REVERT: C 95 TYR cc_start: 0.8364 (m-80) cc_final: 0.7709 (m-80) REVERT: C 97 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8414 (t80) REVERT: C 135 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8848 (tm-30) outliers start: 22 outliers final: 16 residues processed: 161 average time/residue: 0.0913 time to fit residues: 21.6677 Evaluate side-chains 161 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 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 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094579 restraints weight = 17607.745| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.67 r_work: 0.3040 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11555 Z= 0.270 Angle : 0.618 8.430 15995 Z= 0.321 Chirality : 0.041 0.196 1837 Planarity : 0.004 0.037 1740 Dihedral : 18.289 177.320 2579 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.29 % Allowed : 13.46 % Favored : 83.25 % 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 aren not related in a simple way. whole: 0.39 (0.25), residues: 1145 helix: 1.28 (0.22), residues: 551 sheet: -0.64 (0.45), residues: 119 loop : -0.65 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 338 TYR 0.028 0.002 TYR A 18 PHE 0.021 0.002 PHE A 925 TRP 0.012 0.002 TRP A 408 HIS 0.005 0.001 HIS A 700 Details of bonding type rmsd covalent geometry : bond 0.00588 (11555) covalent geometry : angle 0.61755 (15995) hydrogen bonds : bond 0.04543 ( 492) hydrogen bonds : angle 4.53273 ( 1380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8707 (mp) cc_final: 0.8389 (mp) REVERT: A 45 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 120 ASN cc_start: 0.7597 (t0) cc_final: 0.7324 (t0) REVERT: A 229 TRP cc_start: 0.7610 (t60) cc_final: 0.7299 (t60) REVERT: A 239 TYR cc_start: 0.7805 (m-80) cc_final: 0.7541 (m-80) REVERT: A 362 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6913 (tm-30) REVERT: A 366 GLU cc_start: 0.8007 (tt0) cc_final: 0.7629 (mm-30) REVERT: A 386 LEU cc_start: 0.8386 (mt) cc_final: 0.7779 (mt) REVERT: A 406 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6710 (tp30) REVERT: A 429 ASP cc_start: 0.7709 (t0) cc_final: 0.6943 (p0) REVERT: A 478 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 605 LYS cc_start: 0.9374 (tmtt) cc_final: 0.9066 (tptt) REVERT: A 657 MET cc_start: 0.8319 (mmt) cc_final: 0.7859 (mmm) REVERT: A 677 ASN cc_start: 0.7588 (t0) cc_final: 0.6406 (m110) REVERT: A 687 LYS cc_start: 0.8410 (mmmt) cc_final: 0.7827 (ttpp) REVERT: A 696 LYS cc_start: 0.8292 (mmtm) cc_final: 0.7545 (pttp) REVERT: A 829 MET cc_start: 0.8308 (mtp) cc_final: 0.7317 (mtp) REVERT: A 833 ASP cc_start: 0.7771 (t70) cc_final: 0.6431 (p0) REVERT: A 860 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8525 (mp0) REVERT: A 987 ASP cc_start: 0.8647 (p0) cc_final: 0.8337 (p0) REVERT: A 1024 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8878 (p) REVERT: C 86 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8188 (mm-30) REVERT: C 95 TYR cc_start: 0.8355 (m-80) cc_final: 0.7598 (m-10) REVERT: C 97 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8448 (t80) REVERT: C 135 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8890 (tm-30) outliers start: 33 outliers final: 18 residues processed: 168 average time/residue: 0.0921 time to fit residues: 22.9040 Evaluate side-chains 159 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 30.0000 chunk 32 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS C 74 ASN C 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.148684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095169 restraints weight = 17786.948| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.70 r_work: 0.3031 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11555 Z= 0.240 Angle : 0.600 8.020 15995 Z= 0.312 Chirality : 0.040 0.210 1837 Planarity : 0.004 0.046 1740 Dihedral : 18.294 177.456 2579 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.99 % Allowed : 14.66 % Favored : 82.35 % 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 aren not related in a simple way. whole: 0.36 (0.25), residues: 1145 helix: 1.30 (0.22), residues: 551 sheet: -0.75 (0.45), residues: 119 loop : -0.71 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 685 TYR 0.027 0.002 TYR A 18 PHE 0.018 0.002 PHE A 925 TRP 0.011 0.001 TRP A 408 HIS 0.004 0.001 HIS A 700 Details of bonding type rmsd covalent geometry : bond 0.00523 (11555) covalent geometry : angle 0.60003 (15995) hydrogen bonds : bond 0.04366 ( 492) hydrogen bonds : angle 4.48892 ( 1380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8675 (mp) cc_final: 0.8357 (mp) REVERT: A 45 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 76 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6159 (mp) REVERT: A 229 TRP cc_start: 0.7577 (t60) cc_final: 0.7295 (t60) REVERT: A 232 MET cc_start: 0.8158 (mmt) cc_final: 0.7795 (mmp) REVERT: A 362 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6870 (tm-30) REVERT: A 366 GLU cc_start: 0.8119 (tt0) cc_final: 0.7760 (mm-30) REVERT: A 386 LEU cc_start: 0.8320 (mt) cc_final: 0.7701 (mt) REVERT: A 406 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6696 (tp30) REVERT: A 429 ASP cc_start: 0.7844 (t0) cc_final: 0.7055 (p0) REVERT: A 478 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8216 (tt) REVERT: A 605 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9069 (tptt) REVERT: A 657 MET cc_start: 0.8401 (mmt) cc_final: 0.7899 (mmm) REVERT: A 677 ASN cc_start: 0.7553 (t0) cc_final: 0.6382 (m110) REVERT: A 687 LYS cc_start: 0.8389 (mmmt) cc_final: 0.7807 (ttpp) REVERT: A 696 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7532 (pttp) REVERT: A 769 TYR cc_start: 0.8676 (m-80) cc_final: 0.8395 (m-80) REVERT: A 829 MET cc_start: 0.8212 (mtp) cc_final: 0.7167 (mtp) REVERT: A 833 ASP cc_start: 0.7762 (t70) cc_final: 0.6366 (p0) REVERT: A 860 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8534 (mp0) REVERT: A 987 ASP cc_start: 0.8646 (p0) cc_final: 0.8336 (p0) REVERT: A 1024 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.8882 (p) REVERT: C 86 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8162 (mm-30) REVERT: C 95 TYR cc_start: 0.8377 (m-80) cc_final: 0.7552 (m-10) REVERT: C 97 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8428 (t80) REVERT: C 135 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8872 (tm-30) outliers start: 30 outliers final: 23 residues processed: 164 average time/residue: 0.0843 time to fit residues: 20.2596 Evaluate side-chains 175 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102562 restraints weight = 17369.193| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.67 r_work: 0.3142 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11555 Z= 0.111 Angle : 0.523 9.232 15995 Z= 0.274 Chirality : 0.038 0.222 1837 Planarity : 0.003 0.034 1740 Dihedral : 18.242 178.011 2579 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.09 % Allowed : 16.25 % Favored : 81.66 % 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 aren not related in a simple way. whole: 0.64 (0.25), residues: 1145 helix: 1.58 (0.23), residues: 542 sheet: -0.57 (0.45), residues: 114 loop : -0.60 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 685 TYR 0.021 0.001 TYR A 18 PHE 0.022 0.001 PHE A 635 TRP 0.009 0.001 TRP A 408 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00237 (11555) covalent geometry : angle 0.52271 (15995) hydrogen bonds : bond 0.03637 ( 492) hydrogen bonds : angle 4.26514 ( 1380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7982 (tpp80) cc_final: 0.7603 (tpp80) REVERT: A 14 THR cc_start: 0.8229 (p) cc_final: 0.7919 (t) REVERT: A 45 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 76 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6049 (mp) REVERT: A 120 ASN cc_start: 0.7553 (t0) cc_final: 0.7349 (t0) REVERT: A 229 TRP cc_start: 0.7426 (t60) cc_final: 0.7180 (t60) REVERT: A 232 MET cc_start: 0.8215 (mmt) cc_final: 0.7770 (mmt) REVERT: A 362 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6835 (tm-30) REVERT: A 366 GLU cc_start: 0.8088 (tt0) cc_final: 0.7736 (mm-30) REVERT: A 386 LEU cc_start: 0.8317 (mt) cc_final: 0.7766 (mt) REVERT: A 406 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6640 (tp30) REVERT: A 429 ASP cc_start: 0.7791 (t0) cc_final: 0.6927 (p0) REVERT: A 605 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9080 (tptt) REVERT: A 657 MET cc_start: 0.8257 (mmm) cc_final: 0.7905 (mmm) REVERT: A 677 ASN cc_start: 0.7412 (t0) cc_final: 0.6209 (m-40) REVERT: A 687 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7783 (ttpp) REVERT: A 696 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7430 (pttp) REVERT: A 829 MET cc_start: 0.7935 (mtp) cc_final: 0.6814 (mtp) REVERT: A 833 ASP cc_start: 0.7755 (t70) cc_final: 0.6231 (p0) REVERT: A 856 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7857 (tppt) REVERT: A 987 ASP cc_start: 0.8625 (p0) cc_final: 0.8352 (p0) REVERT: A 1024 THR cc_start: 0.9352 (m) cc_final: 0.8974 (p) REVERT: C 95 TYR cc_start: 0.8254 (m-80) cc_final: 0.7391 (m-10) REVERT: C 125 ASP cc_start: 0.8394 (t70) cc_final: 0.7882 (t0) REVERT: C 135 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8822 (tm-30) outliers start: 21 outliers final: 16 residues processed: 174 average time/residue: 0.0826 time to fit residues: 21.0929 Evaluate side-chains 177 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.151757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098759 restraints weight = 17536.447| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.67 r_work: 0.3085 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11555 Z= 0.222 Angle : 0.590 9.011 15995 Z= 0.306 Chirality : 0.040 0.230 1837 Planarity : 0.004 0.046 1740 Dihedral : 18.204 177.736 2579 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.49 % Allowed : 17.15 % Favored : 80.36 % 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 aren not related in a simple way. whole: 0.55 (0.25), residues: 1145 helix: 1.51 (0.23), residues: 544 sheet: -0.72 (0.45), residues: 119 loop : -0.62 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 685 TYR 0.022 0.002 TYR A 855 PHE 0.018 0.002 PHE A 925 TRP 0.012 0.001 TRP A 408 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd covalent geometry : bond 0.00492 (11555) covalent geometry : angle 0.58960 (15995) hydrogen bonds : bond 0.04129 ( 492) hydrogen bonds : angle 4.38722 ( 1380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7968 (tpp80) cc_final: 0.7510 (tpp80) REVERT: A 45 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 76 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6109 (mp) REVERT: A 120 ASN cc_start: 0.7554 (t0) cc_final: 0.7334 (t0) REVERT: A 229 TRP cc_start: 0.7440 (t60) cc_final: 0.7169 (t60) REVERT: A 232 MET cc_start: 0.8133 (mmt) cc_final: 0.7647 (mmt) REVERT: A 291 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7531 (ttmm) REVERT: A 362 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6894 (tm-30) REVERT: A 366 GLU cc_start: 0.8102 (tt0) cc_final: 0.7743 (mm-30) REVERT: A 386 LEU cc_start: 0.8269 (mt) cc_final: 0.7710 (mt) REVERT: A 406 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6652 (tp30) REVERT: A 429 ASP cc_start: 0.7828 (t0) cc_final: 0.6994 (p0) REVERT: A 605 LYS cc_start: 0.9372 (tmtt) cc_final: 0.9073 (tptt) REVERT: A 677 ASN cc_start: 0.7487 (t0) cc_final: 0.6287 (m110) REVERT: A 696 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7463 (pttp) REVERT: A 769 TYR cc_start: 0.8797 (m-80) cc_final: 0.8395 (m-80) REVERT: A 829 MET cc_start: 0.8079 (mtp) cc_final: 0.7081 (mtp) REVERT: A 833 ASP cc_start: 0.7699 (t70) cc_final: 0.6479 (p0) REVERT: A 860 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8359 (mp0) REVERT: A 987 ASP cc_start: 0.8659 (p0) cc_final: 0.8384 (p0) REVERT: C 95 TYR cc_start: 0.8363 (m-80) cc_final: 0.7469 (m-10) REVERT: C 125 ASP cc_start: 0.8427 (t70) cc_final: 0.7921 (t0) REVERT: C 135 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8801 (tm-30) outliers start: 25 outliers final: 20 residues processed: 173 average time/residue: 0.0835 time to fit residues: 21.2774 Evaluate side-chains 175 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 715 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.154685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102247 restraints weight = 17280.674| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.67 r_work: 0.3137 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11555 Z= 0.137 Angle : 0.539 8.329 15995 Z= 0.283 Chirality : 0.038 0.231 1837 Planarity : 0.003 0.037 1740 Dihedral : 18.153 178.013 2579 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.29 % Allowed : 17.45 % Favored : 80.26 % 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 aren not related in a simple way. whole: 0.65 (0.25), residues: 1145 helix: 1.60 (0.23), residues: 542 sheet: -0.64 (0.45), residues: 114 loop : -0.59 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 685 TYR 0.025 0.001 TYR A 855 PHE 0.014 0.001 PHE A 914 TRP 0.006 0.001 TRP C 63 HIS 0.002 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00302 (11555) covalent geometry : angle 0.53905 (15995) hydrogen bonds : bond 0.03703 ( 492) hydrogen bonds : angle 4.27212 ( 1380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.8000 (tpp80) cc_final: 0.7603 (tpp80) REVERT: A 45 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 76 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6086 (mp) REVERT: A 120 ASN cc_start: 0.7528 (t0) cc_final: 0.7302 (t0) REVERT: A 229 TRP cc_start: 0.7403 (t60) cc_final: 0.7158 (t60) REVERT: A 232 MET cc_start: 0.8172 (mmt) cc_final: 0.7735 (mmt) REVERT: A 291 LYS cc_start: 0.7886 (ttmm) cc_final: 0.7660 (ttmm) REVERT: A 362 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 366 GLU cc_start: 0.8111 (tt0) cc_final: 0.7750 (mm-30) REVERT: A 386 LEU cc_start: 0.8329 (mt) cc_final: 0.7714 (mt) REVERT: A 406 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6654 (tp30) REVERT: A 429 ASP cc_start: 0.7785 (t0) cc_final: 0.6801 (p0) REVERT: A 605 LYS cc_start: 0.9370 (tmtt) cc_final: 0.9077 (tptt) REVERT: A 657 MET cc_start: 0.7963 (mmt) cc_final: 0.7693 (mmm) REVERT: A 677 ASN cc_start: 0.7468 (t0) cc_final: 0.6236 (m-40) REVERT: A 687 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7800 (ttpp) REVERT: A 696 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7424 (pttp) REVERT: A 769 TYR cc_start: 0.8806 (m-80) cc_final: 0.8449 (m-80) REVERT: A 829 MET cc_start: 0.7968 (mtp) cc_final: 0.6907 (mtp) REVERT: A 833 ASP cc_start: 0.7601 (t70) cc_final: 0.6271 (p0) REVERT: A 856 LYS cc_start: 0.8129 (tmtt) cc_final: 0.7207 (tptp) REVERT: A 860 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8143 (mp0) REVERT: A 987 ASP cc_start: 0.8640 (p0) cc_final: 0.8374 (p0) REVERT: C 95 TYR cc_start: 0.8321 (m-80) cc_final: 0.7453 (m-10) REVERT: C 125 ASP cc_start: 0.8428 (t70) cc_final: 0.7942 (t0) REVERT: C 135 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8797 (tm-30) outliers start: 23 outliers final: 18 residues processed: 173 average time/residue: 0.0892 time to fit residues: 22.6049 Evaluate side-chains 178 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 715 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 93 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.155513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102825 restraints weight = 17550.395| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.71 r_work: 0.3145 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11555 Z= 0.131 Angle : 0.536 8.581 15995 Z= 0.281 Chirality : 0.038 0.225 1837 Planarity : 0.003 0.040 1740 Dihedral : 18.048 177.959 2577 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.19 % Allowed : 17.85 % Favored : 79.96 % 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 aren not related in a simple way. whole: 0.71 (0.25), residues: 1145 helix: 1.65 (0.23), residues: 539 sheet: -0.53 (0.46), residues: 104 loop : -0.56 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 685 TYR 0.017 0.001 TYR A 837 PHE 0.027 0.002 PHE A 635 TRP 0.008 0.001 TRP A 408 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00288 (11555) covalent geometry : angle 0.53560 (15995) hydrogen bonds : bond 0.03614 ( 492) hydrogen bonds : angle 4.19558 ( 1380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7968 (tpp80) cc_final: 0.7573 (tpp80) REVERT: A 45 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7975 (tm-30) REVERT: A 76 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6113 (mp) REVERT: A 120 ASN cc_start: 0.7505 (t0) cc_final: 0.7275 (t0) REVERT: A 229 TRP cc_start: 0.7344 (t60) cc_final: 0.7110 (t60) REVERT: A 232 MET cc_start: 0.8167 (mmt) cc_final: 0.7734 (mmt) REVERT: A 291 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7673 (ttmm) REVERT: A 362 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6845 (tm-30) REVERT: A 366 GLU cc_start: 0.8107 (tt0) cc_final: 0.7747 (mm-30) REVERT: A 386 LEU cc_start: 0.8305 (mt) cc_final: 0.7779 (mt) REVERT: A 406 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6600 (tp30) REVERT: A 429 ASP cc_start: 0.7700 (t0) cc_final: 0.6784 (p0) REVERT: A 605 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9083 (tptt) REVERT: A 641 PHE cc_start: 0.7344 (m-80) cc_final: 0.6778 (m-80) REVERT: A 644 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7988 (tpt170) REVERT: A 657 MET cc_start: 0.7956 (mmt) cc_final: 0.7737 (mmm) REVERT: A 677 ASN cc_start: 0.7313 (t0) cc_final: 0.6159 (m110) REVERT: A 696 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7410 (pttp) REVERT: A 769 TYR cc_start: 0.8812 (m-80) cc_final: 0.8492 (m-80) REVERT: A 829 MET cc_start: 0.7975 (mtp) cc_final: 0.6992 (mtp) REVERT: A 833 ASP cc_start: 0.7769 (t70) cc_final: 0.6491 (p0) REVERT: A 856 LYS cc_start: 0.8263 (tmtt) cc_final: 0.7297 (tptp) REVERT: A 860 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8196 (mp0) REVERT: A 987 ASP cc_start: 0.8641 (p0) cc_final: 0.8376 (p0) REVERT: C 95 TYR cc_start: 0.8307 (m-80) cc_final: 0.7416 (m-10) REVERT: C 125 ASP cc_start: 0.8433 (t70) cc_final: 0.7917 (t0) REVERT: C 128 ASN cc_start: 0.8476 (t0) cc_final: 0.7831 (m-40) outliers start: 22 outliers final: 17 residues processed: 174 average time/residue: 0.0848 time to fit residues: 21.6364 Evaluate side-chains 178 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 715 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 147 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 73 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.156161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103505 restraints weight = 17450.738| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.70 r_work: 0.3159 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11555 Z= 0.124 Angle : 0.530 8.631 15995 Z= 0.275 Chirality : 0.038 0.217 1837 Planarity : 0.003 0.038 1740 Dihedral : 17.980 177.564 2577 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.89 % Allowed : 18.34 % Favored : 79.76 % 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 aren not related in a simple way. whole: 0.82 (0.25), residues: 1145 helix: 1.72 (0.23), residues: 539 sheet: -0.47 (0.46), residues: 104 loop : -0.49 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 685 TYR 0.016 0.001 TYR A 837 PHE 0.013 0.001 PHE A 914 TRP 0.006 0.001 TRP C 63 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00275 (11555) covalent geometry : angle 0.53015 (15995) hydrogen bonds : bond 0.03482 ( 492) hydrogen bonds : angle 4.14262 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2634.64 seconds wall clock time: 45 minutes 45.61 seconds (2745.61 seconds total)