Starting phenix.real_space_refine on Thu Jul 2 23:52:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jft_36217/07_2026/8jft_36217_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jft_36217/07_2026/8jft_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jft_36217/07_2026/8jft_36217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jft_36217/07_2026/8jft_36217.map" model { file = "/net/cci-nas-00/data/ceres_data/8jft_36217/07_2026/8jft_36217_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jft_36217/07_2026/8jft_36217_neut.cif" } 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-dev-6108/lib/python3.11/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: 0.82 Conformation dependent library (CDL) restraints added in 304.1 milliseconds 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: 1.05 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: 2.31 Time building geometry restraints manager: 1.05 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 0.030 Set scattering table: 0.030 Process input model: 11.600 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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= 0.617 Angle : 1.270 10.126 15995 Z= 0.947 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 are 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/Z covalent geometry : bond 0.00834 / 0.62 (11555) covalent geometry : angle 1.27048 / 0.95 (15995) hydrogen bonds : bond 0.18676 / 12.24 ( 492) hydrogen bonds : angle 8.14781 / 5.78 ( 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 : 0.406 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: 0.8232 (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: 0.8397 (t0) cc_final: 0.7838 (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: 0.0845 time to fit residues: 27.4249 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 : 0.290 ------------------------------------------------------------------------------- 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: 10.0000 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: 1.9990 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: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 863 ASN A 968 ASN A 990 ASN C 163 HIS C 169 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102117 restraints weight = 17257.900| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.62 r_work: 0.3112 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11555 Z= 0.168 Angle : 0.606 10.033 15995 Z= 0.343 Chirality : 0.042 0.171 1837 Planarity : 0.004 0.037 1740 Dihedral : 18.974 178.053 2582 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.09 % Allowed : 10.67 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.24), residues: 1145 helix: 1.08 (0.22), residues: 539 sheet: -0.11 (0.48), residues: 119 loop : -0.70 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 685 TYR 0.018 0.002 TYR A 256 PHE 0.015 0.002 PHE A 635 TRP 0.011 0.001 TRP A 408 HIS 0.013 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (11555) covalent geometry : angle 0.60639 / 0.34 (15995) hydrogen bonds : bond 0.06070 / 4.11 ( 492) hydrogen bonds : angle 5.18577 / 3.76 ( 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 186 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.267 Fit side-chains REVERT: A 232 MET cc_start: 0.8128 (mmt) cc_final: 0.6965 (ttt) REVERT: A 362 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6834 (tm-30) REVERT: A 366 GLU cc_start: 0.8177 (tt0) cc_final: 0.7885 (tt0) REVERT: A 386 LEU cc_start: 0.8423 (mt) cc_final: 0.7976 (mt) REVERT: A 406 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6792 (tp30) REVERT: A 478 LEU cc_start: 0.8510 (tp) cc_final: 0.8279 (tt) REVERT: A 534 CYS cc_start: 0.6971 (t) cc_final: 0.6632 (t) REVERT: A 605 LYS cc_start: 0.9325 (tmtt) cc_final: 0.9029 (tptt) REVERT: A 657 MET cc_start: 0.8508 (mmm) cc_final: 0.8214 (mmt) REVERT: A 677 ASN cc_start: 0.7505 (t0) cc_final: 0.6233 (m-40) REVERT: A 696 LYS cc_start: 0.8331 (mmtm) cc_final: 0.7507 (pttp) REVERT: A 829 MET cc_start: 0.8117 (mtp) cc_final: 0.7894 (mtp) REVERT: A 833 ASP cc_start: 0.7659 (t70) cc_final: 0.6750 (t70) REVERT: A 987 ASP cc_start: 0.8585 (p0) cc_final: 0.8243 (p0) REVERT: A 996 MET cc_start: 0.7664 (mtm) cc_final: 0.7020 (mtm) REVERT: A 1008 MET cc_start: 0.9089 (mtm) cc_final: 0.8864 (mtm) REVERT: A 1024 THR cc_start: 0.9295 (m) cc_final: 0.8949 (p) REVERT: C 93 ASP cc_start: 0.9094 (t0) cc_final: 0.8857 (t0) REVERT: C 95 TYR cc_start: 0.8133 (m-80) cc_final: 0.7686 (m-80) REVERT: C 97 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.8147 (t80) outliers start: 21 outliers final: 13 residues processed: 177 average time/residue: 0.0861 time to fit residues: 22.7977 Evaluate side-chains 161 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 439 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 144 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: 7.9990 chunk 50 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 141 ASN A 264 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 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 = 0.3941 r_free = 0.3941 target = 0.149144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097173 restraints weight = 17539.208| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.63 r_work: 0.3037 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11555 Z= 0.243 Angle : 0.603 9.251 15995 Z= 0.336 Chirality : 0.042 0.168 1837 Planarity : 0.004 0.032 1740 Dihedral : 18.712 178.228 2579 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.89 % Allowed : 12.36 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1145 helix: 1.01 (0.22), residues: 551 sheet: -0.59 (0.45), residues: 124 loop : -0.83 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 685 TYR 0.028 0.002 TYR A 855 PHE 0.026 0.002 PHE A 281 TRP 0.010 0.002 TRP A 408 HIS 0.010 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 (11555) covalent geometry : angle 0.60251 / 0.34 (15995) hydrogen bonds : bond 0.05925 / 4.03 ( 492) hydrogen bonds : angle 4.92883 / 3.57 ( 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 174 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7883 (t70) cc_final: 0.7583 (t70) REVERT: A 35 LEU cc_start: 0.8688 (mp) cc_final: 0.8416 (mp) REVERT: A 232 MET cc_start: 0.8291 (mmt) cc_final: 0.7256 (ttp) REVERT: A 243 GLU cc_start: 0.7444 (tp30) cc_final: 0.7211 (tp30) REVERT: A 362 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6635 (tm-30) REVERT: A 366 GLU cc_start: 0.8196 (tt0) cc_final: 0.7856 (tt0) REVERT: A 386 LEU cc_start: 0.8451 (mt) cc_final: 0.7981 (mt) REVERT: A 406 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6816 (tp30) REVERT: A 478 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8235 (tt) REVERT: A 534 CYS cc_start: 0.7084 (t) cc_final: 0.6733 (t) REVERT: A 605 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9052 (tptt) REVERT: A 677 ASN cc_start: 0.7630 (t0) cc_final: 0.6385 (m110) REVERT: A 696 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7428 (pttp) REVERT: A 833 ASP cc_start: 0.7736 (t70) cc_final: 0.6656 (t70) REVERT: A 860 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8557 (mp0) REVERT: A 987 ASP cc_start: 0.8558 (p0) cc_final: 0.8193 (p0) REVERT: A 1024 THR cc_start: 0.9310 (m) cc_final: 0.8958 (p) REVERT: C 93 ASP cc_start: 0.9064 (t0) cc_final: 0.8845 (t0) REVERT: C 95 TYR cc_start: 0.8226 (m-80) cc_final: 0.7741 (m-80) REVERT: C 97 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8373 (t80) REVERT: C 166 GLU cc_start: 0.8489 (tp30) cc_final: 0.8269 (tp30) outliers start: 29 outliers final: 18 residues processed: 164 average time/residue: 0.0908 time to fit residues: 22.1056 Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 175 ASP 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 384 SER 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 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 83 THR 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 147 TYR Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 122 optimal weight: 0.1980 chunk 74 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN C 108 GLN C 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.152624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100043 restraints weight = 17509.103| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.66 r_work: 0.3088 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11555 Z= 0.131 Angle : 0.497 6.821 15995 Z= 0.281 Chirality : 0.038 0.139 1837 Planarity : 0.003 0.037 1740 Dihedral : 18.638 177.917 2579 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.09 % Allowed : 13.36 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1145 helix: 1.30 (0.22), residues: 545 sheet: -0.49 (0.45), residues: 119 loop : -0.77 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 685 TYR 0.024 0.001 TYR A 855 PHE 0.027 0.002 PHE A 281 TRP 0.011 0.001 TRP A 408 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (11555) covalent geometry : angle 0.49688 / 0.28 (15995) hydrogen bonds : bond 0.04844 / 3.31 ( 492) hydrogen bonds : angle 4.55454 / 3.29 ( 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 175 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 168 ILE cc_start: 0.8477 (tt) cc_final: 0.8264 (pt) REVERT: A 232 MET cc_start: 0.8330 (mmt) cc_final: 0.7257 (ttt) REVERT: A 234 MET cc_start: 0.7408 (mmt) cc_final: 0.7165 (mmm) REVERT: A 243 GLU cc_start: 0.7479 (tp30) cc_final: 0.7200 (tp30) REVERT: A 362 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6562 (tm-30) REVERT: A 366 GLU cc_start: 0.8159 (tt0) cc_final: 0.7769 (mm-30) REVERT: A 386 LEU cc_start: 0.8406 (mt) cc_final: 0.7930 (mt) REVERT: A 406 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6681 (tp30) REVERT: A 432 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8347 (pt0) REVERT: A 478 LEU cc_start: 0.8489 (tp) cc_final: 0.8259 (tt) REVERT: A 534 CYS cc_start: 0.7032 (t) cc_final: 0.6689 (t) REVERT: A 605 LYS cc_start: 0.9356 (tmtt) cc_final: 0.9046 (tptt) REVERT: A 677 ASN cc_start: 0.7498 (t0) cc_final: 0.6291 (m-40) REVERT: A 696 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7415 (pttp) REVERT: A 813 ASN cc_start: 0.8738 (t0) cc_final: 0.8007 (t0) REVERT: A 833 ASP cc_start: 0.7630 (t70) cc_final: 0.6595 (t70) REVERT: A 860 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8511 (mp0) REVERT: A 987 ASP cc_start: 0.8666 (p0) cc_final: 0.8374 (p0) REVERT: A 1024 THR cc_start: 0.9315 (m) cc_final: 0.8965 (p) REVERT: C 74 ASN cc_start: 0.8863 (m-40) cc_final: 0.8605 (m110) REVERT: C 93 ASP cc_start: 0.9079 (t0) cc_final: 0.8877 (t0) REVERT: C 95 TYR cc_start: 0.8178 (m-80) cc_final: 0.7730 (m-80) REVERT: C 97 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8365 (t80) outliers start: 21 outliers final: 13 residues processed: 165 average time/residue: 0.0983 time to fit residues: 23.9538 Evaluate side-chains 160 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 183 LEU 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 441 VAL 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 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: 9.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 43 optimal weight: 0.0040 chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 985 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 = 0.3987 r_free = 0.3987 target = 0.153199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100735 restraints weight = 17370.779| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.66 r_work: 0.3099 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11555 Z= 0.118 Angle : 0.477 9.013 15995 Z= 0.268 Chirality : 0.038 0.137 1837 Planarity : 0.003 0.032 1740 Dihedral : 18.550 178.161 2579 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.79 % Allowed : 14.36 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.24), residues: 1145 helix: 1.39 (0.22), residues: 545 sheet: -0.49 (0.46), residues: 114 loop : -0.64 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 137 TYR 0.027 0.001 TYR A 939 PHE 0.030 0.001 PHE A 281 TRP 0.010 0.001 TRP A 408 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (11555) covalent geometry : angle 0.47708 / 0.27 (15995) hydrogen bonds : bond 0.04475 / 3.05 ( 492) hydrogen bonds : angle 4.43552 / 3.22 ( 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 173 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8442 (mttt) cc_final: 0.8143 (mtmt) REVERT: A 168 ILE cc_start: 0.8502 (tt) cc_final: 0.8278 (pt) REVERT: A 229 TRP cc_start: 0.7453 (t60) cc_final: 0.7170 (t60) REVERT: A 232 MET cc_start: 0.8341 (mmt) cc_final: 0.7253 (ttp) REVERT: A 234 MET cc_start: 0.7491 (mmt) cc_final: 0.7249 (mmm) REVERT: A 243 GLU cc_start: 0.7538 (tp30) cc_final: 0.7227 (tp30) REVERT: A 362 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6603 (tm-30) REVERT: A 366 GLU cc_start: 0.8153 (tt0) cc_final: 0.7761 (mm-30) REVERT: A 386 LEU cc_start: 0.8413 (mt) cc_final: 0.7929 (mt) REVERT: A 406 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6689 (tp30) REVERT: A 432 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8333 (pt0) REVERT: A 478 LEU cc_start: 0.8536 (tp) cc_final: 0.8322 (tt) REVERT: A 605 LYS cc_start: 0.9355 (tmtt) cc_final: 0.9039 (tptt) REVERT: A 657 MET cc_start: 0.8330 (mmt) cc_final: 0.7864 (mmm) REVERT: A 677 ASN cc_start: 0.7468 (t0) cc_final: 0.6281 (m-40) REVERT: A 696 LYS cc_start: 0.8223 (mmtm) cc_final: 0.7417 (pttp) REVERT: A 813 ASN cc_start: 0.8771 (t0) cc_final: 0.8024 (t0) REVERT: A 833 ASP cc_start: 0.7635 (t70) cc_final: 0.6603 (t70) REVERT: A 860 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8536 (mp0) REVERT: A 987 ASP cc_start: 0.8661 (p0) cc_final: 0.8376 (p0) REVERT: A 996 MET cc_start: 0.7576 (mtp) cc_final: 0.6875 (mtm) REVERT: A 1024 THR cc_start: 0.9313 (m) cc_final: 0.8959 (p) REVERT: C 95 TYR cc_start: 0.8175 (m-80) cc_final: 0.7814 (m-80) REVERT: C 97 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8387 (t80) outliers start: 18 outliers final: 14 residues processed: 164 average time/residue: 0.0876 time to fit residues: 20.9284 Evaluate side-chains 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 97 TYR 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 Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 39 optimal weight: 0.0060 overall best weight: 3.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.150138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097186 restraints weight = 17589.734| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.66 r_work: 0.3051 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11555 Z= 0.202 Angle : 0.538 11.269 15995 Z= 0.295 Chirality : 0.039 0.151 1837 Planarity : 0.003 0.033 1740 Dihedral : 18.429 178.706 2579 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.29 % Allowed : 15.05 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1145 helix: 1.39 (0.22), residues: 546 sheet: -0.63 (0.46), residues: 114 loop : -0.69 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.022 0.002 TYR A 855 PHE 0.030 0.002 PHE A 281 TRP 0.010 0.001 TRP A 408 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (11555) covalent geometry : angle 0.53806 / 0.30 (15995) hydrogen bonds : bond 0.04645 / 3.17 ( 492) hydrogen bonds : angle 4.47456 / 3.26 ( 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 169 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 232 MET cc_start: 0.8382 (mmt) cc_final: 0.7258 (ttp) REVERT: A 234 MET cc_start: 0.7700 (mmt) cc_final: 0.7446 (mmm) REVERT: A 243 GLU cc_start: 0.7582 (tp30) cc_final: 0.7261 (tp30) REVERT: A 362 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6685 (tm-30) REVERT: A 366 GLU cc_start: 0.8168 (tt0) cc_final: 0.7770 (mm-30) REVERT: A 386 LEU cc_start: 0.8419 (mt) cc_final: 0.7887 (mt) REVERT: A 406 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6656 (tp30) REVERT: A 432 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8319 (pt0) REVERT: A 478 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8333 (tt) REVERT: A 605 LYS cc_start: 0.9376 (tmtt) cc_final: 0.9052 (tptt) REVERT: A 657 MET cc_start: 0.8411 (mmt) cc_final: 0.7931 (mmm) REVERT: A 677 ASN cc_start: 0.7474 (t0) cc_final: 0.6278 (m-40) REVERT: A 696 LYS cc_start: 0.8257 (mmtm) cc_final: 0.7496 (pttp) REVERT: A 810 ASP cc_start: 0.7739 (t70) cc_final: 0.7524 (t70) REVERT: A 813 ASN cc_start: 0.8773 (t0) cc_final: 0.8065 (t0) REVERT: A 829 MET cc_start: 0.8202 (mtp) cc_final: 0.7307 (mtp) REVERT: A 833 ASP cc_start: 0.7715 (t70) cc_final: 0.6163 (p0) REVERT: A 860 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8539 (mp0) REVERT: A 987 ASP cc_start: 0.8664 (p0) cc_final: 0.8370 (p0) REVERT: A 1024 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.8941 (p) REVERT: C 89 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7857 (t0) REVERT: C 95 TYR cc_start: 0.8292 (m-80) cc_final: 0.7844 (m-80) REVERT: C 97 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8392 (t80) REVERT: C 135 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8763 (tm-30) outliers start: 23 outliers final: 17 residues processed: 158 average time/residue: 0.0799 time to fit residues: 18.6966 Evaluate side-chains 161 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 202 ILE 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 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 887 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 87 VAL 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 124 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 ASN C 74 ASN C 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.152240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099596 restraints weight = 17439.137| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.67 r_work: 0.3088 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11555 Z= 0.134 Angle : 0.491 9.051 15995 Z= 0.272 Chirality : 0.038 0.176 1837 Planarity : 0.003 0.031 1740 Dihedral : 18.372 178.776 2579 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.60 % Allowed : 16.55 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1145 helix: 1.56 (0.23), residues: 539 sheet: -0.66 (0.45), residues: 114 loop : -0.62 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 685 TYR 0.018 0.001 TYR A 939 PHE 0.029 0.002 PHE A 281 TRP 0.008 0.001 TRP A 408 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11555) covalent geometry : angle 0.49100 / 0.27 (15995) hydrogen bonds : bond 0.04177 / 2.85 ( 492) hydrogen bonds : angle 4.37230 / 3.18 ( 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 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 229 TRP cc_start: 0.7435 (t60) cc_final: 0.7170 (t60) REVERT: A 232 MET cc_start: 0.8367 (mmt) cc_final: 0.7237 (ttp) REVERT: A 234 MET cc_start: 0.7635 (mmt) cc_final: 0.7378 (mmm) REVERT: A 243 GLU cc_start: 0.7593 (tp30) cc_final: 0.7268 (tp30) REVERT: A 291 LYS cc_start: 0.7392 (mtmm) cc_final: 0.7080 (ttmm) REVERT: A 362 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6669 (tm-30) REVERT: A 366 GLU cc_start: 0.8129 (tt0) cc_final: 0.7724 (mm-30) REVERT: A 386 LEU cc_start: 0.8395 (mt) cc_final: 0.7869 (mt) REVERT: A 432 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8321 (pt0) REVERT: A 478 LEU cc_start: 0.8500 (tp) cc_final: 0.8284 (tt) REVERT: A 605 LYS cc_start: 0.9378 (tmtt) cc_final: 0.9061 (tptt) REVERT: A 657 MET cc_start: 0.8434 (mmt) cc_final: 0.8090 (mmm) REVERT: A 677 ASN cc_start: 0.7450 (t0) cc_final: 0.6307 (m110) REVERT: A 696 LYS cc_start: 0.8276 (mmtm) cc_final: 0.7521 (pttp) REVERT: A 810 ASP cc_start: 0.7696 (t70) cc_final: 0.7472 (t70) REVERT: A 813 ASN cc_start: 0.8764 (t0) cc_final: 0.8114 (t0) REVERT: A 829 MET cc_start: 0.8106 (mtp) cc_final: 0.7099 (mtp) REVERT: A 833 ASP cc_start: 0.7762 (t70) cc_final: 0.6339 (p0) REVERT: A 860 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8509 (mp0) REVERT: A 987 ASP cc_start: 0.8657 (p0) cc_final: 0.8370 (p0) REVERT: A 1024 THR cc_start: 0.9335 (m) cc_final: 0.8946 (p) REVERT: C 95 TYR cc_start: 0.8291 (m-80) cc_final: 0.7821 (m-80) REVERT: C 97 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8387 (t80) REVERT: C 135 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8734 (tm-30) outliers start: 16 outliers final: 14 residues processed: 158 average time/residue: 0.0845 time to fit residues: 19.7758 Evaluate side-chains 170 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 124 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 overall best weight: 2.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 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 = 0.3969 r_free = 0.3969 target = 0.151787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099152 restraints weight = 17483.355| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.66 r_work: 0.3082 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3045 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= 0.156 Angle : 0.509 9.170 15995 Z= 0.281 Chirality : 0.039 0.156 1837 Planarity : 0.003 0.037 1740 Dihedral : 18.303 178.649 2579 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.89 % Allowed : 17.05 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1145 helix: 1.61 (0.23), residues: 539 sheet: -0.70 (0.46), residues: 114 loop : -0.61 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 338 TYR 0.026 0.001 TYR A 855 PHE 0.020 0.002 PHE A 281 TRP 0.009 0.001 TRP A 408 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (11555) covalent geometry : angle 0.50909 / 0.28 (15995) hydrogen bonds : bond 0.04229 / 2.87 ( 492) hydrogen bonds : angle 4.37805 / 3.18 ( 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 167 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 232 MET cc_start: 0.8377 (mmt) cc_final: 0.7268 (ttp) REVERT: A 234 MET cc_start: 0.7831 (mmt) cc_final: 0.7583 (mmm) REVERT: A 243 GLU cc_start: 0.7557 (tp30) cc_final: 0.7229 (tp30) REVERT: A 291 LYS cc_start: 0.7433 (mtmm) cc_final: 0.7111 (ttmm) REVERT: A 329 TYR cc_start: 0.8279 (t80) cc_final: 0.8078 (t80) REVERT: A 362 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6738 (tm-30) REVERT: A 366 GLU cc_start: 0.8126 (tt0) cc_final: 0.7762 (mm-30) REVERT: A 386 LEU cc_start: 0.8399 (mt) cc_final: 0.7872 (mt) REVERT: A 432 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8323 (pt0) REVERT: A 478 LEU cc_start: 0.8528 (tp) cc_final: 0.8305 (tt) REVERT: A 605 LYS cc_start: 0.9388 (tmtt) cc_final: 0.9071 (tptt) REVERT: A 657 MET cc_start: 0.8439 (mmt) cc_final: 0.8188 (mmm) REVERT: A 677 ASN cc_start: 0.7439 (t0) cc_final: 0.6308 (m110) REVERT: A 696 LYS cc_start: 0.8278 (mmtm) cc_final: 0.7523 (pttp) REVERT: A 810 ASP cc_start: 0.7707 (t70) cc_final: 0.7488 (t70) REVERT: A 813 ASN cc_start: 0.8752 (t0) cc_final: 0.8442 (t0) REVERT: A 829 MET cc_start: 0.8170 (mtp) cc_final: 0.7244 (mtp) REVERT: A 833 ASP cc_start: 0.7783 (t70) cc_final: 0.6456 (p0) REVERT: A 860 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8578 (mp0) REVERT: A 987 ASP cc_start: 0.8650 (p0) cc_final: 0.8378 (p0) REVERT: A 1024 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.8953 (p) REVERT: C 95 TYR cc_start: 0.8304 (m-80) cc_final: 0.7848 (m-80) REVERT: C 97 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8409 (t80) REVERT: C 135 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8718 (tm-30) outliers start: 19 outliers final: 16 residues processed: 158 average time/residue: 0.0808 time to fit residues: 19.0005 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 : 0.368 ------------------------------------------------------------------------------- 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 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 714 ILE 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 76 SER Chi-restraints excluded: chain C residue 97 TYR 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 Chi-restraints excluded: chain C residue 167 ILE 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: 6.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100622 restraints weight = 17415.499| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.67 r_work: 0.3127 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11555 Z= 0.169 Angle : 0.510 8.600 15995 Z= 0.284 Chirality : 0.039 0.180 1837 Planarity : 0.003 0.043 1740 Dihedral : 18.240 178.189 2579 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.29 % Allowed : 17.05 % Favored : 80.66 % 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 are not related in a simple way. whole: 0.62 (0.25), residues: 1145 helix: 1.60 (0.23), residues: 539 sheet: -0.72 (0.46), residues: 114 loop : -0.60 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 685 TYR 0.024 0.002 TYR A 18 PHE 0.025 0.002 PHE A 635 TRP 0.009 0.001 TRP A 408 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (11555) covalent geometry : angle 0.51002 / 0.28 (15995) hydrogen bonds : bond 0.04207 / 2.86 ( 492) hydrogen bonds : angle 4.38207 / 3.18 ( 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 168 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7946 (tpp80) cc_final: 0.7578 (tpp80) REVERT: A 232 MET cc_start: 0.8369 (mmt) cc_final: 0.7899 (mmt) REVERT: A 234 MET cc_start: 0.7799 (mmt) cc_final: 0.7545 (mmm) REVERT: A 243 GLU cc_start: 0.7545 (tp30) cc_final: 0.7219 (tp30) REVERT: A 362 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6753 (tm-30) REVERT: A 366 GLU cc_start: 0.8119 (tt0) cc_final: 0.7763 (mm-30) REVERT: A 386 LEU cc_start: 0.8388 (mt) cc_final: 0.7867 (mt) REVERT: A 432 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8311 (pt0) REVERT: A 478 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8282 (tt) REVERT: A 494 MET cc_start: 0.4828 (ttm) cc_final: 0.4457 (ttm) REVERT: A 605 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9068 (tptt) REVERT: A 657 MET cc_start: 0.8379 (mmt) cc_final: 0.8145 (mmm) REVERT: A 677 ASN cc_start: 0.7487 (t0) cc_final: 0.6288 (m110) REVERT: A 696 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7397 (mtmt) REVERT: A 810 ASP cc_start: 0.7699 (t70) cc_final: 0.7479 (t70) REVERT: A 813 ASN cc_start: 0.8770 (t0) cc_final: 0.8478 (t0) REVERT: A 829 MET cc_start: 0.8070 (mtp) cc_final: 0.7118 (mtp) REVERT: A 833 ASP cc_start: 0.7749 (t70) cc_final: 0.6401 (p0) REVERT: A 860 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8542 (mp0) REVERT: A 987 ASP cc_start: 0.8638 (p0) cc_final: 0.8357 (p0) REVERT: C 95 TYR cc_start: 0.8259 (m-80) cc_final: 0.7783 (m-80) REVERT: C 97 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8378 (t80) REVERT: C 135 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8763 (tm-30) outliers start: 23 outliers final: 18 residues processed: 155 average time/residue: 0.0866 time to fit residues: 20.0589 Evaluate side-chains 174 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 341 ILE Chi-restraints excluded: chain A residue 368 LEU 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 605 LYS Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 714 ILE 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 76 SER Chi-restraints excluded: chain C residue 97 TYR 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 Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 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 = 0.4005 r_free = 0.4005 target = 0.154823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.102201 restraints weight = 17585.764| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.71 r_work: 0.3134 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11555 Z= 0.131 Angle : 0.494 8.238 15995 Z= 0.275 Chirality : 0.038 0.178 1837 Planarity : 0.003 0.039 1740 Dihedral : 18.172 178.010 2579 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.69 % Allowed : 17.75 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1145 helix: 1.69 (0.23), residues: 539 sheet: -0.69 (0.46), residues: 114 loop : -0.56 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 685 TYR 0.022 0.001 TYR A 855 PHE 0.030 0.002 PHE A 281 TRP 0.008 0.001 TRP A 408 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11555) covalent geometry : angle 0.49376 / 0.27 (15995) hydrogen bonds : bond 0.03962 / 2.70 ( 492) hydrogen bonds : angle 4.30581 / 3.12 ( 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 180 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7615 (tpp80) REVERT: A 45 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 229 TRP cc_start: 0.7243 (t60) cc_final: 0.7019 (t60) REVERT: A 232 MET cc_start: 0.8344 (mmt) cc_final: 0.7887 (mmt) REVERT: A 234 MET cc_start: 0.7741 (mmt) cc_final: 0.7490 (mmm) REVERT: A 243 GLU cc_start: 0.7453 (tp30) cc_final: 0.7121 (tp30) REVERT: A 291 LYS cc_start: 0.7480 (mtmm) cc_final: 0.7237 (ttmm) REVERT: A 362 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6792 (tm-30) REVERT: A 366 GLU cc_start: 0.8102 (tt0) cc_final: 0.7744 (mm-30) REVERT: A 386 LEU cc_start: 0.8380 (mt) cc_final: 0.7851 (mt) REVERT: A 432 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8280 (pt0) REVERT: A 443 ASP cc_start: 0.8697 (t70) cc_final: 0.8477 (p0) REVERT: A 478 LEU cc_start: 0.8442 (tp) cc_final: 0.8230 (tt) REVERT: A 605 LYS cc_start: 0.9381 (tmtt) cc_final: 0.9067 (tptt) REVERT: A 677 ASN cc_start: 0.7448 (t0) cc_final: 0.6254 (m110) REVERT: A 696 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7451 (pttp) REVERT: A 810 ASP cc_start: 0.7633 (t70) cc_final: 0.7419 (t70) REVERT: A 813 ASN cc_start: 0.8769 (t0) cc_final: 0.8469 (t0) REVERT: A 829 MET cc_start: 0.7905 (mtp) cc_final: 0.6952 (mtp) REVERT: A 833 ASP cc_start: 0.7671 (t70) cc_final: 0.6361 (p0) REVERT: A 860 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8352 (mp0) REVERT: A 987 ASP cc_start: 0.8629 (p0) cc_final: 0.8353 (p0) REVERT: C 95 TYR cc_start: 0.8208 (m-80) cc_final: 0.7733 (m-80) REVERT: C 125 ASP cc_start: 0.8360 (t70) cc_final: 0.7872 (t0) REVERT: C 135 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8744 (tm-30) outliers start: 17 outliers final: 16 residues processed: 171 average time/residue: 0.0925 time to fit residues: 23.4242 Evaluate side-chains 171 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 690 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 76 SER 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 Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3972 r_free = 0.3972 target = 0.151909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099017 restraints weight = 17677.720| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.69 r_work: 0.3086 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11555 Z= 0.219 Angle : 0.561 9.864 15995 Z= 0.307 Chirality : 0.040 0.194 1837 Planarity : 0.004 0.046 1740 Dihedral : 18.129 177.895 2579 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.29 % Allowed : 17.55 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1145 helix: 1.52 (0.23), residues: 539 sheet: -0.74 (0.46), residues: 114 loop : -0.60 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 685 TYR 0.031 0.002 TYR A 18 PHE 0.026 0.002 PHE A 281 TRP 0.016 0.001 TRP A 408 HIS 0.003 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (11555) covalent geometry : angle 0.56133 / 0.31 (15995) hydrogen bonds : bond 0.04403 / 3.02 ( 492) hydrogen bonds : angle 4.43717 / 3.23 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.33 seconds wall clock time: 45 minutes 37.84 seconds (2737.84 seconds total)