Starting phenix.real_space_refine on Wed Aug 5 17:39:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jft_36217/08_2026/8jft_36217_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jft_36217/08_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_36217/08_2026/8jft_36217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jft_36217/08_2026/8jft_36217.map" model { file = "/net/cci-nas-00/data/ceres_data/8jft_36217/08_2026/8jft_36217_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jft_36217/08_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-2.2rc3-6140/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: 2.18, per 1000 atoms: 0.20 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: 0.79 Conformation dependent library (CDL) restraints added in 445.3 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: 0.88 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: 1.97 Time building geometry restraints manager: 1.15 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=" O3' U B 71 " pdb=" P U B 72 " ideal model delta sigma weight residual 1.607 1.679 -0.072 1.20e-02 6.94e+03 3.58e+01 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=" 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: 14097 2.03 - 4.05: 1663 4.05 - 6.08: 201 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: 1227 0.070 - 0.140: 372 0.140 - 0.211: 176 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.650 ------------------------------------------------------------------------------- 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= 0.627 Angle : 1.275 10.126 15995 Z= 0.951 Chirality : 0.088 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 0.00837 / 0.63 (11555) covalent geometry : angle 1.27477 / 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 : 0.311 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: 0.6913 (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: 0.0866 time to fit residues: 28.1235 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 : 0.355 ------------------------------------------------------------------------------- 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: 9.9990 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: 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 = 0.3986 r_free = 0.3986 target = 0.153003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102071 restraints weight = 17283.297| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.57 r_work: 0.3113 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11555 Z= 0.165 Angle : 0.609 9.052 15995 Z= 0.343 Chirality : 0.043 0.243 1837 Planarity : 0.004 0.035 1740 Dihedral : 18.885 178.398 2582 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.99 % Allowed : 10.87 % 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 are not related in a simple way. whole: 0.27 (0.24), residues: 1145 helix: 1.08 (0.22), residues: 539 sheet: -0.10 (0.48), residues: 119 loop : -0.71 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 685 TYR 0.019 0.002 TYR A 256 PHE 0.014 0.002 PHE A 72 TRP 0.011 0.001 TRP A 408 HIS 0.012 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (11555) covalent geometry : angle 0.60927 / 0.34 (15995) hydrogen bonds : bond 0.06527 / 4.41 ( 492) hydrogen bonds : angle 5.26046 / 3.80 ( 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 184 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.390 Fit side-chains REVERT: A 232 MET cc_start: 0.8137 (mmt) cc_final: 0.6997 (ttp) REVERT: A 239 TYR cc_start: 0.7769 (m-80) cc_final: 0.7527 (m-80) REVERT: A 362 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6869 (tm-30) REVERT: A 366 GLU cc_start: 0.8177 (tt0) cc_final: 0.7894 (tt0) REVERT: A 386 LEU cc_start: 0.8430 (mt) cc_final: 0.7987 (mt) REVERT: A 406 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6813 (tp30) REVERT: A 478 LEU cc_start: 0.8505 (tp) cc_final: 0.8253 (tt) REVERT: A 534 CYS cc_start: 0.6933 (t) cc_final: 0.6599 (t) REVERT: A 605 LYS cc_start: 0.9326 (tmtt) cc_final: 0.9037 (tptt) REVERT: A 657 MET cc_start: 0.8297 (mmm) cc_final: 0.7962 (mmt) REVERT: A 677 ASN cc_start: 0.7512 (t0) cc_final: 0.6236 (m-40) REVERT: A 696 LYS cc_start: 0.8377 (mmtm) cc_final: 0.7774 (pttt) REVERT: A 833 ASP cc_start: 0.7654 (t70) cc_final: 0.6772 (t70) REVERT: A 987 ASP cc_start: 0.8584 (p0) cc_final: 0.8244 (p0) REVERT: A 996 MET cc_start: 0.7681 (mtm) cc_final: 0.6956 (mtm) REVERT: A 1008 MET cc_start: 0.9086 (mtm) cc_final: 0.8861 (mtm) REVERT: A 1024 THR cc_start: 0.9297 (m) cc_final: 0.8953 (p) REVERT: C 93 ASP cc_start: 0.9109 (t0) cc_final: 0.8873 (t0) REVERT: C 95 TYR cc_start: 0.8150 (m-80) cc_final: 0.7621 (m-80) REVERT: C 97 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.8121 (t80) outliers start: 20 outliers final: 13 residues processed: 175 average time/residue: 0.0892 time to fit residues: 23.3639 Evaluate side-chains 162 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 64 ILE 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: 9.9990 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 141 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN C 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.152239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099522 restraints weight = 17673.644| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.68 r_work: 0.3083 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11555 Z= 0.175 Angle : 0.557 8.676 15995 Z= 0.310 Chirality : 0.041 0.191 1837 Planarity : 0.003 0.034 1740 Dihedral : 18.601 178.390 2579 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.09 % Allowed : 12.36 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.24), residues: 1145 helix: 1.04 (0.22), residues: 552 sheet: -0.45 (0.46), residues: 119 loop : -0.80 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 685 TYR 0.034 0.002 TYR A 855 PHE 0.014 0.002 PHE A 925 TRP 0.009 0.001 TRP A 408 HIS 0.010 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (11555) covalent geometry : angle 0.55699 / 0.31 (15995) hydrogen bonds : bond 0.05525 / 3.78 ( 492) hydrogen bonds : angle 4.80934 / 3.49 ( 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 180 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7871 (t70) cc_final: 0.7489 (t70) REVERT: A 232 MET cc_start: 0.8210 (mmt) cc_final: 0.7205 (ttp) REVERT: A 362 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6755 (tm-30) REVERT: A 366 GLU cc_start: 0.8173 (tt0) cc_final: 0.7794 (mm-30) REVERT: A 386 LEU cc_start: 0.8456 (mt) cc_final: 0.8010 (mt) REVERT: A 406 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6783 (tp30) REVERT: A 478 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8288 (tt) REVERT: A 534 CYS cc_start: 0.7065 (t) cc_final: 0.6714 (t) REVERT: A 605 LYS cc_start: 0.9358 (tmtt) cc_final: 0.9060 (tptt) REVERT: A 677 ASN cc_start: 0.7494 (t0) cc_final: 0.6311 (m110) REVERT: A 696 LYS cc_start: 0.8229 (mmtm) cc_final: 0.7392 (pttp) REVERT: A 833 ASP cc_start: 0.7721 (t70) cc_final: 0.6690 (t70) REVERT: A 860 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8528 (mp0) REVERT: A 987 ASP cc_start: 0.8562 (p0) cc_final: 0.8221 (p0) REVERT: A 996 MET cc_start: 0.7569 (mtm) cc_final: 0.6906 (mtm) REVERT: A 1008 MET cc_start: 0.9134 (mtm) cc_final: 0.8901 (mtm) REVERT: A 1024 THR cc_start: 0.9313 (m) cc_final: 0.8971 (p) REVERT: C 74 ASN cc_start: 0.8868 (m-40) cc_final: 0.8531 (m110) REVERT: C 93 ASP cc_start: 0.9061 (t0) cc_final: 0.8844 (t0) REVERT: C 95 TYR cc_start: 0.8179 (m-80) cc_final: 0.7711 (m-80) REVERT: C 97 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.8220 (t80) outliers start: 21 outliers final: 15 residues processed: 169 average time/residue: 0.0769 time to fit residues: 19.3817 Evaluate side-chains 161 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 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 230 TYR Chi-restraints excluded: chain A residue 238 THR 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 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 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: 8.9990 chunk 122 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 645 ASN C 108 GLN C 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099068 restraints weight = 17377.668| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.58 r_work: 0.3082 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11555 Z= 0.184 Angle : 0.547 6.860 15995 Z= 0.299 Chirality : 0.040 0.181 1837 Planarity : 0.004 0.039 1740 Dihedral : 18.482 179.674 2579 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.59 % Allowed : 13.76 % Favored : 83.65 % 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: 0.24 (0.24), residues: 1145 helix: 1.18 (0.22), residues: 547 sheet: -0.52 (0.46), residues: 119 loop : -0.80 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 685 TYR 0.027 0.002 TYR A 855 PHE 0.022 0.002 PHE A 105 TRP 0.012 0.001 TRP A 408 HIS 0.004 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (11555) covalent geometry : angle 0.54700 / 0.30 (15995) hydrogen bonds : bond 0.05152 / 3.52 ( 492) hydrogen bonds : angle 4.64063 / 3.37 ( 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 182 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 ILE cc_start: 0.8496 (tt) cc_final: 0.8292 (pt) REVERT: A 232 MET cc_start: 0.8357 (mmt) cc_final: 0.7276 (ttt) REVERT: A 243 GLU cc_start: 0.7517 (tp30) cc_final: 0.7265 (tp30) REVERT: A 362 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6707 (tm-30) REVERT: A 366 GLU cc_start: 0.8195 (tt0) cc_final: 0.7801 (mm-30) REVERT: A 386 LEU cc_start: 0.8488 (mt) cc_final: 0.8024 (mt) REVERT: A 406 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6738 (tp30) REVERT: A 432 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8327 (pt0) REVERT: A 478 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 605 LYS cc_start: 0.9367 (tmtt) cc_final: 0.9052 (tptt) REVERT: A 657 MET cc_start: 0.8408 (mmt) cc_final: 0.7935 (mmm) REVERT: A 677 ASN cc_start: 0.7521 (t0) cc_final: 0.6340 (m-40) REVERT: A 696 LYS cc_start: 0.8263 (mmtm) cc_final: 0.7445 (pttp) REVERT: A 813 ASN cc_start: 0.8757 (t0) cc_final: 0.8044 (t0) REVERT: A 833 ASP cc_start: 0.7709 (t70) cc_final: 0.6683 (t70) REVERT: A 860 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8536 (mp0) REVERT: A 987 ASP cc_start: 0.8660 (p0) cc_final: 0.8352 (p0) REVERT: A 1024 THR cc_start: 0.9303 (m) cc_final: 0.8957 (p) REVERT: C 89 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7854 (t0) REVERT: C 93 ASP cc_start: 0.9000 (t0) cc_final: 0.8799 (t0) REVERT: C 95 TYR cc_start: 0.8227 (m-80) cc_final: 0.7715 (m-80) REVERT: C 97 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8404 (t80) outliers start: 26 outliers final: 16 residues processed: 171 average time/residue: 0.0852 time to fit residues: 21.3257 Evaluate side-chains 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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 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 154 GLU 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: 0.7980 chunk 98 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 43 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.154444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102171 restraints weight = 17243.742| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.67 r_work: 0.3123 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11555 Z= 0.107 Angle : 0.476 7.109 15995 Z= 0.265 Chirality : 0.038 0.165 1837 Planarity : 0.003 0.032 1740 Dihedral : 18.420 179.239 2579 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.79 % Allowed : 14.56 % Favored : 83.65 % 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: 0.52 (0.24), residues: 1145 helix: 1.42 (0.22), residues: 545 sheet: -0.43 (0.47), residues: 114 loop : -0.66 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 137 TYR 0.031 0.001 TYR A 939 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/Z covalent geometry : bond 0.00222 / 0.11 (11555) covalent geometry : angle 0.47607 / 0.27 (15995) hydrogen bonds : bond 0.04382 / 2.99 ( 492) hydrogen bonds : angle 4.41584 / 3.19 ( 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: 18 poor density : 162 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8432 (mttt) cc_final: 0.8149 (mtmt) REVERT: A 168 ILE cc_start: 0.8496 (tt) cc_final: 0.8282 (pt) REVERT: A 229 TRP cc_start: 0.7381 (t60) cc_final: 0.7109 (t60) REVERT: A 232 MET cc_start: 0.8333 (mmt) cc_final: 0.7220 (ttt) REVERT: A 234 MET cc_start: 0.8090 (mmm) cc_final: 0.7859 (mmt) REVERT: A 362 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6664 (tm-30) REVERT: A 366 GLU cc_start: 0.8158 (tt0) cc_final: 0.7780 (mm-30) REVERT: A 386 LEU cc_start: 0.8454 (mt) cc_final: 0.7983 (mt) REVERT: A 406 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6683 (tp30) REVERT: A 432 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8318 (pt0) REVERT: A 478 LEU cc_start: 0.8496 (tp) cc_final: 0.8269 (tt) REVERT: A 605 LYS cc_start: 0.9354 (tmtt) cc_final: 0.9043 (tptt) REVERT: A 657 MET cc_start: 0.8449 (mmt) cc_final: 0.8155 (mmm) REVERT: A 677 ASN cc_start: 0.7460 (t0) cc_final: 0.6261 (m-40) REVERT: A 687 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7717 (ttpp) REVERT: A 696 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7402 (pttp) REVERT: A 810 ASP cc_start: 0.7596 (t70) cc_final: 0.7390 (t70) REVERT: A 813 ASN cc_start: 0.8778 (t0) cc_final: 0.7983 (t0) REVERT: A 833 ASP cc_start: 0.7636 (t70) cc_final: 0.6659 (t70) REVERT: A 860 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8562 (mp0) REVERT: A 987 ASP cc_start: 0.8651 (p0) cc_final: 0.8355 (p0) REVERT: A 996 MET cc_start: 0.7447 (mtp) cc_final: 0.6766 (mtm) REVERT: A 1024 THR cc_start: 0.9287 (m) cc_final: 0.8948 (p) REVERT: C 95 TYR cc_start: 0.8163 (m-80) cc_final: 0.7800 (m-80) REVERT: C 128 ASN cc_start: 0.8251 (t0) cc_final: 0.7928 (m-40) outliers start: 18 outliers final: 14 residues processed: 170 average time/residue: 0.0922 time to fit residues: 23.1959 Evaluate side-chains 176 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 233 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 772 SER Chi-restraints excluded: chain A residue 887 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.152391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099738 restraints weight = 17480.431| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.66 r_work: 0.3094 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2857 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= 0.159 Angle : 0.508 6.577 15995 Z= 0.278 Chirality : 0.039 0.155 1837 Planarity : 0.003 0.031 1740 Dihedral : 18.305 178.304 2579 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.99 % Allowed : 15.65 % 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 are not related in a simple way. whole: 0.56 (0.25), residues: 1145 helix: 1.47 (0.22), residues: 545 sheet: -0.49 (0.47), residues: 114 loop : -0.64 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 338 TYR 0.024 0.001 TYR A 329 PHE 0.013 0.001 PHE A 925 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 0.00345 / 0.16 (11555) covalent geometry : angle 0.50847 / 0.28 (15995) hydrogen bonds : bond 0.04408 / 3.01 ( 492) hydrogen bonds : angle 4.37468 / 3.16 ( 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 174 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 168 ILE cc_start: 0.8479 (tt) cc_final: 0.8250 (pt) REVERT: A 229 TRP cc_start: 0.7468 (t60) cc_final: 0.7174 (t60) REVERT: A 232 MET cc_start: 0.8355 (mmt) cc_final: 0.7222 (ttp) REVERT: A 243 GLU cc_start: 0.7298 (tp30) cc_final: 0.7000 (tp30) REVERT: A 362 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6718 (tm-30) REVERT: A 366 GLU cc_start: 0.8131 (tt0) cc_final: 0.7738 (mm-30) REVERT: A 386 LEU cc_start: 0.8459 (mt) cc_final: 0.7924 (mt) REVERT: A 406 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6696 (tp30) REVERT: A 432 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8288 (pt0) REVERT: A 478 LEU cc_start: 0.8529 (tp) cc_final: 0.8306 (tt) REVERT: A 605 LYS cc_start: 0.9370 (tmtt) cc_final: 0.9049 (tptt) REVERT: A 657 MET cc_start: 0.8404 (mmt) cc_final: 0.8203 (mmm) REVERT: A 677 ASN cc_start: 0.7508 (t0) cc_final: 0.6306 (m-40) REVERT: A 687 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7742 (ttpp) REVERT: A 696 LYS cc_start: 0.8247 (mmtm) cc_final: 0.7476 (pttp) REVERT: A 810 ASP cc_start: 0.7692 (t70) cc_final: 0.7464 (t70) REVERT: A 813 ASN cc_start: 0.8787 (t0) cc_final: 0.8027 (t0) REVERT: A 833 ASP cc_start: 0.7695 (t70) cc_final: 0.6167 (p0) REVERT: A 860 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8540 (mp0) REVERT: A 939 TYR cc_start: 0.6256 (p90) cc_final: 0.6031 (p90) REVERT: A 987 ASP cc_start: 0.8653 (p0) cc_final: 0.8377 (p0) REVERT: A 1024 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.8949 (p) REVERT: C 95 TYR cc_start: 0.8315 (m-80) cc_final: 0.7872 (m-80) REVERT: C 97 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8387 (t80) REVERT: C 128 ASN cc_start: 0.8263 (t0) cc_final: 0.7933 (m-40) REVERT: C 135 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8747 (tm-30) outliers start: 20 outliers final: 16 residues processed: 164 average time/residue: 0.0815 time to fit residues: 19.9483 Evaluate side-chains 172 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 905 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.152455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099883 restraints weight = 17423.522| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.67 r_work: 0.3092 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3007 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= 0.150 Angle : 0.501 8.665 15995 Z= 0.275 Chirality : 0.039 0.148 1837 Planarity : 0.004 0.065 1740 Dihedral : 18.256 178.126 2579 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.09 % Allowed : 16.45 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1145 helix: 1.52 (0.22), residues: 546 sheet: -0.54 (0.47), residues: 114 loop : -0.62 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 685 TYR 0.024 0.001 TYR A 855 PHE 0.022 0.002 PHE A 635 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 0.00327 / 0.15 (11555) covalent geometry : angle 0.50139 / 0.27 (15995) hydrogen bonds : bond 0.04257 / 2.90 ( 492) hydrogen bonds : angle 4.34196 / 3.14 ( 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 181 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 229 TRP cc_start: 0.7451 (t60) cc_final: 0.7172 (t60) REVERT: A 232 MET cc_start: 0.8368 (mmt) cc_final: 0.7250 (ttp) REVERT: A 234 MET cc_start: 0.7798 (mmt) cc_final: 0.7519 (mmm) REVERT: A 243 GLU cc_start: 0.7244 (tp30) cc_final: 0.6909 (tp30) REVERT: A 244 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6923 (mt) REVERT: A 291 LYS cc_start: 0.7505 (mtmm) cc_final: 0.7208 (ttmm) REVERT: A 362 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6752 (tm-30) REVERT: A 366 GLU cc_start: 0.8112 (tt0) cc_final: 0.7741 (mm-30) REVERT: A 386 LEU cc_start: 0.8413 (mt) cc_final: 0.7878 (mt) REVERT: A 432 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8305 (pt0) REVERT: A 605 LYS cc_start: 0.9391 (tmtt) cc_final: 0.9073 (tptt) REVERT: A 677 ASN cc_start: 0.7474 (t0) cc_final: 0.6270 (m-40) REVERT: A 687 LYS cc_start: 0.8291 (mmmt) cc_final: 0.7737 (ttpp) REVERT: A 696 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7472 (pttp) REVERT: A 813 ASN cc_start: 0.8791 (t0) cc_final: 0.8453 (t0) REVERT: A 829 MET cc_start: 0.8171 (mtp) cc_final: 0.7013 (ttp) REVERT: A 833 ASP cc_start: 0.7715 (t70) cc_final: 0.6316 (p0) REVERT: A 860 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8530 (mp0) REVERT: A 987 ASP cc_start: 0.8658 (p0) cc_final: 0.8388 (p0) REVERT: A 1024 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.8937 (p) REVERT: C 95 TYR cc_start: 0.8294 (m-80) cc_final: 0.7839 (m-80) REVERT: C 119 ASP cc_start: 0.8518 (m-30) cc_final: 0.8276 (m-30) REVERT: C 125 ASP cc_start: 0.8482 (t70) cc_final: 0.7919 (t0) REVERT: C 128 ASN cc_start: 0.8262 (t0) cc_final: 0.7924 (m-40) REVERT: C 135 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8731 (tm-30) outliers start: 21 outliers final: 18 residues processed: 169 average time/residue: 0.0884 time to fit residues: 22.4523 Evaluate side-chains 175 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 244 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.153247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100808 restraints weight = 17366.676| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.67 r_work: 0.3105 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11555 Z= 0.122 Angle : 0.492 7.326 15995 Z= 0.270 Chirality : 0.038 0.148 1837 Planarity : 0.003 0.038 1740 Dihedral : 18.178 178.527 2579 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.19 % Allowed : 16.95 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1145 helix: 1.64 (0.23), residues: 539 sheet: -0.56 (0.47), residues: 114 loop : -0.54 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 685 TYR 0.018 0.001 TYR A 18 PHE 0.013 0.001 PHE A 914 TRP 0.009 0.001 TRP A 408 HIS 0.002 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11555) covalent geometry : angle 0.49227 / 0.27 (15995) hydrogen bonds : bond 0.04050 / 2.76 ( 492) hydrogen bonds : angle 4.28483 / 3.09 ( 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 185 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7929 (tpp80) cc_final: 0.7556 (tpp80) REVERT: A 148 LYS cc_start: 0.8445 (mttt) cc_final: 0.8109 (mtmt) REVERT: A 229 TRP cc_start: 0.7436 (t60) cc_final: 0.7171 (t60) REVERT: A 232 MET cc_start: 0.8356 (mmt) cc_final: 0.7258 (ttp) REVERT: A 234 MET cc_start: 0.7892 (mmt) cc_final: 0.7641 (mmm) REVERT: A 243 GLU cc_start: 0.7325 (tp30) cc_final: 0.7006 (tp30) REVERT: A 244 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6917 (mt) REVERT: A 291 LYS cc_start: 0.7479 (mtmm) cc_final: 0.7154 (ttmm) REVERT: A 329 TYR cc_start: 0.8261 (t80) cc_final: 0.8036 (t80) REVERT: A 362 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6793 (tm-30) REVERT: A 366 GLU cc_start: 0.8107 (tt0) cc_final: 0.7733 (mm-30) REVERT: A 386 LEU cc_start: 0.8431 (mt) cc_final: 0.7901 (mt) REVERT: A 432 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8249 (pt0) REVERT: A 605 LYS cc_start: 0.9382 (tmtt) cc_final: 0.9070 (tptt) REVERT: A 657 MET cc_start: 0.7941 (mmt) cc_final: 0.7679 (mmm) REVERT: A 677 ASN cc_start: 0.7440 (t0) cc_final: 0.6264 (m-40) REVERT: A 687 LYS cc_start: 0.8331 (mmmt) cc_final: 0.7769 (ttpp) REVERT: A 696 LYS cc_start: 0.8262 (mmtm) cc_final: 0.7500 (pttp) REVERT: A 813 ASN cc_start: 0.8740 (t0) cc_final: 0.8438 (t0) REVERT: A 829 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7266 (mtp) REVERT: A 833 ASP cc_start: 0.7754 (t70) cc_final: 0.6382 (p0) REVERT: A 860 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8347 (mp0) REVERT: A 987 ASP cc_start: 0.8655 (p0) cc_final: 0.8385 (p0) REVERT: C 95 TYR cc_start: 0.8281 (m-80) cc_final: 0.7814 (m-80) REVERT: C 125 ASP cc_start: 0.8461 (t70) cc_final: 0.7895 (t0) REVERT: C 128 ASN cc_start: 0.8219 (t0) cc_final: 0.7909 (m-40) REVERT: C 135 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8728 (tm-30) outliers start: 22 outliers final: 18 residues processed: 173 average time/residue: 0.0928 time to fit residues: 23.9442 Evaluate side-chains 177 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 233 LEU Chi-restraints excluded: chain A residue 244 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 829 MET Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 134 ASP 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: 0.8980 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 0.0470 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.154937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102598 restraints weight = 17255.901| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.65 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: 0.6857 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11555 Z= 0.140 Angle : 0.508 7.526 15995 Z= 0.277 Chirality : 0.039 0.147 1837 Planarity : 0.003 0.036 1740 Dihedral : 18.054 179.938 2579 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.29 % Allowed : 17.25 % Favored : 80.46 % 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: 0.71 (0.25), residues: 1145 helix: 1.63 (0.23), residues: 539 sheet: -0.51 (0.47), residues: 114 loop : -0.55 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 685 TYR 0.017 0.001 TYR A 18 PHE 0.026 0.002 PHE A 635 TRP 0.015 0.001 TRP A 408 HIS 0.002 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (11555) covalent geometry : angle 0.50759 / 0.28 (15995) hydrogen bonds : bond 0.04015 / 2.76 ( 492) hydrogen bonds : angle 4.26502 / 3.08 ( 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 179 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7777 (mm-30) REVERT: A 229 TRP cc_start: 0.7323 (t60) cc_final: 0.7082 (t60) REVERT: A 232 MET cc_start: 0.8366 (mmt) cc_final: 0.7902 (mmt) REVERT: A 234 MET cc_start: 0.7922 (mmt) cc_final: 0.7638 (mmm) REVERT: A 243 GLU cc_start: 0.7336 (tp30) cc_final: 0.7007 (tp30) REVERT: A 244 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6960 (mt) REVERT: A 362 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6826 (tm-30) REVERT: A 366 GLU cc_start: 0.8118 (tt0) cc_final: 0.7744 (mm-30) REVERT: A 386 LEU cc_start: 0.8410 (mt) cc_final: 0.7833 (mt) REVERT: A 406 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6685 (tp30) REVERT: A 432 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8210 (pt0) REVERT: A 605 LYS cc_start: 0.9387 (tmtt) cc_final: 0.9068 (tptt) REVERT: A 657 MET cc_start: 0.7929 (mmt) cc_final: 0.7724 (mmm) REVERT: A 677 ASN cc_start: 0.7446 (t0) cc_final: 0.6255 (m110) REVERT: A 687 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7737 (ttpp) REVERT: A 696 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7458 (pttp) REVERT: A 813 ASN cc_start: 0.8715 (t0) cc_final: 0.8429 (t0) REVERT: A 829 MET cc_start: 0.7966 (mtp) cc_final: 0.7037 (mtp) REVERT: A 833 ASP cc_start: 0.7613 (t70) cc_final: 0.6257 (p0) REVERT: A 860 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8354 (mp0) REVERT: A 987 ASP cc_start: 0.8630 (p0) cc_final: 0.8360 (p0) REVERT: C 95 TYR cc_start: 0.8211 (m-80) cc_final: 0.7833 (m-10) REVERT: C 125 ASP cc_start: 0.8425 (t70) cc_final: 0.7911 (t0) REVERT: C 128 ASN cc_start: 0.8143 (t0) cc_final: 0.7861 (m-40) REVERT: C 135 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8758 (tm-30) outliers start: 23 outliers final: 20 residues processed: 169 average time/residue: 0.0909 time to fit residues: 23.2224 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 : 0.365 ------------------------------------------------------------------------------- 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 233 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 259 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 704 ASP 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 64 ILE Chi-restraints excluded: chain C residue 73 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 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 = 0.4017 r_free = 0.4017 target = 0.155687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103149 restraints weight = 17601.219| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.71 r_work: 0.3149 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11555 Z= 0.126 Angle : 0.507 10.710 15995 Z= 0.277 Chirality : 0.038 0.149 1837 Planarity : 0.003 0.039 1740 Dihedral : 18.003 178.105 2579 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.89 % Allowed : 18.15 % 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 are not related in a simple way. whole: 0.73 (0.25), residues: 1145 helix: 1.64 (0.23), residues: 539 sheet: -0.50 (0.47), residues: 114 loop : -0.53 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 685 TYR 0.015 0.001 TYR A 256 PHE 0.022 0.001 PHE A 635 TRP 0.007 0.001 TRP A 408 HIS 0.002 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (11555) covalent geometry : angle 0.50659 / 0.28 (15995) hydrogen bonds : bond 0.03990 / 2.74 ( 492) hydrogen bonds : angle 4.21991 / 3.04 ( 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 175 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7582 (tpp80) REVERT: A 45 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 229 TRP cc_start: 0.7291 (t60) cc_final: 0.7056 (t60) REVERT: A 232 MET cc_start: 0.8535 (mmt) cc_final: 0.8088 (mmt) REVERT: A 234 MET cc_start: 0.7924 (mmt) cc_final: 0.7649 (mmm) REVERT: A 243 GLU cc_start: 0.7309 (tp30) cc_final: 0.6974 (tp30) REVERT: A 244 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7054 (mt) REVERT: A 291 LYS cc_start: 0.7461 (mtmm) cc_final: 0.7185 (ttmm) REVERT: A 362 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6883 (tm-30) REVERT: A 366 GLU cc_start: 0.8108 (tt0) cc_final: 0.7733 (mm-30) REVERT: A 386 LEU cc_start: 0.8379 (mt) cc_final: 0.7805 (mt) REVERT: A 406 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6614 (tp30) REVERT: A 432 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8220 (pt0) REVERT: A 605 LYS cc_start: 0.9381 (tmtt) cc_final: 0.9065 (tptt) REVERT: A 677 ASN cc_start: 0.7427 (t0) cc_final: 0.6245 (m-40) REVERT: A 696 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7446 (pttp) REVERT: A 813 ASN cc_start: 0.8627 (t0) cc_final: 0.8326 (t0) REVERT: A 829 MET cc_start: 0.7982 (mtp) cc_final: 0.7049 (mtp) REVERT: A 833 ASP cc_start: 0.7651 (t70) cc_final: 0.6281 (p0) REVERT: A 860 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8342 (mp0) REVERT: A 987 ASP cc_start: 0.8653 (p0) cc_final: 0.8389 (p0) REVERT: C 95 TYR cc_start: 0.8182 (m-80) cc_final: 0.7757 (m-10) REVERT: C 125 ASP cc_start: 0.8416 (t70) cc_final: 0.7883 (t0) REVERT: C 128 ASN cc_start: 0.8131 (t0) cc_final: 0.7819 (m-40) REVERT: C 135 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8783 (tm-30) outliers start: 19 outliers final: 17 residues processed: 166 average time/residue: 0.0922 time to fit residues: 22.8643 Evaluate side-chains 172 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 233 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 ASN 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 704 ASP 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 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=1.00 ------------------------------------------------------------------------------- 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: 1.9990 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 39 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 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 = 0.4027 r_free = 0.4027 target = 0.156725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104211 restraints weight = 17552.117| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.72 r_work: 0.3161 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3476 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= 0.113 Angle : 0.515 14.021 15995 Z= 0.276 Chirality : 0.038 0.147 1837 Planarity : 0.003 0.038 1740 Dihedral : 17.942 178.181 2579 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.99 % Allowed : 17.95 % Favored : 80.06 % 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: 0.80 (0.25), residues: 1145 helix: 1.68 (0.23), residues: 537 sheet: -0.47 (0.46), residues: 114 loop : -0.47 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 685 TYR 0.031 0.001 TYR A 18 PHE 0.023 0.001 PHE A 635 TRP 0.007 0.001 TRP A 408 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11555) covalent geometry : angle 0.51525 / 0.28 (15995) hydrogen bonds : bond 0.03862 / 2.67 ( 492) hydrogen bonds : angle 4.20018 / 3.02 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2626.38 seconds wall clock time: 45 minutes 39.88 seconds (2739.88 seconds total)