Starting phenix.real_space_refine on Wed Aug 5 15:34:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iby_35349/08_2026/8iby_35349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iby_35349/08_2026/8iby_35349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iby_35349/08_2026/8iby_35349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iby_35349/08_2026/8iby_35349.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8iby_35349/08_2026/8iby_35349.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iby_35349/08_2026/8iby_35349.cif" model { file = "/net/cci-nas-00/data/ceres_data/8iby_35349/08_2026/8iby_35349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iby_35349/08_2026/8iby_35349.cif" } resolution = 3.47 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= 0.010 sd= 0.085 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 198 5.49 5 S 32 5.16 5 C 5817 2.51 5 N 1973 2.21 5 O 2482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 10503 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 4233 Classifications: {'RNAv2': 198} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 17, 'rna3p_pur': 91, 'rna3p_pyr': 75} Link IDs: {'rna2p': 32, 'rna3p': 165} Chain breaks: 3 Chain: "C" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6269 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 39, 'TRANS': 753} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9132 SG CYS C 934 59.637 71.301 25.232 1.00104.66 S ATOM 9158 SG CYS C 938 58.180 73.110 22.172 1.00109.37 S ATOM 9263 SG CYS C 951 55.829 71.305 24.654 1.00 93.60 S Time building chain proxies: 2.17, per 1000 atoms: 0.21 Number of scatterers: 10503 At special positions: 0 Unit cell: (107.594, 130.65, 119.671, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 198 15.00 O 2482 8.00 N 1973 7.00 C 5817 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: 0.75 Conformation dependent library (CDL) restraints added in 254.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 946 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 934 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 938 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 951 " Number of angles added : 3 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 54.6% alpha, 10.5% beta 57 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'C' and resid 305 through 324 Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.553A pdb=" N ALA C 328 " --> pdb=" O CYS C 324 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 365 through 373 Processing helix chain 'C' and resid 393 through 399 removed outlier: 3.928A pdb=" N LYS C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.937A pdb=" N VAL C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 469 through 487 removed outlier: 3.577A pdb=" N ILE C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 479 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 519 Processing helix chain 'C' and resid 539 through 549 Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 592 through 607 removed outlier: 3.628A pdb=" N ASN C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 3.624A pdb=" N MET C 640 " --> pdb=" O SER C 636 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN C 641 " --> pdb=" O LYS C 637 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 642 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 643 " --> pdb=" O GLY C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.564A pdb=" N GLN C 750 " --> pdb=" O ILE C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 755 removed outlier: 3.884A pdb=" N LEU C 755 " --> pdb=" O GLY C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 779 removed outlier: 3.802A pdb=" N LEU C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 791 removed outlier: 4.177A pdb=" N HIS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 816 removed outlier: 3.740A pdb=" N ILE C 807 " --> pdb=" O VAL C 803 " (cutoff:3.500A) Proline residue: C 808 - end of helix Processing helix chain 'C' and resid 817 through 821 Processing helix chain 'C' and resid 823 through 831 removed outlier: 3.508A pdb=" N ARG C 827 " --> pdb=" O TRP C 823 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 831 " --> pdb=" O ARG C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 849 Processing helix chain 'C' and resid 861 through 871 Processing helix chain 'C' and resid 875 through 879 Processing helix chain 'C' and resid 884 through 889 removed outlier: 3.590A pdb=" N THR C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 removed outlier: 3.679A pdb=" N VAL C 904 " --> pdb=" O GLY C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 922 removed outlier: 3.821A pdb=" N ARG C 922 " --> pdb=" O ARG C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 932 Processing helix chain 'C' and resid 943 through 950 Processing helix chain 'C' and resid 951 through 953 No H-bonds generated for 'chain 'C' and resid 951 through 953' Processing helix chain 'C' and resid 954 through 976 Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.736A pdb=" N LYS C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS C1029 " --> pdb=" O GLU C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1045 Processing helix chain 'C' and resid 1066 through 1077 removed outlier: 3.710A pdb=" N ILE C1077 " --> pdb=" O LEU C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1105 removed outlier: 3.819A pdb=" N LEU C1084 " --> pdb=" O ARG C1080 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C1087 " --> pdb=" O THR C1083 " (cutoff:3.500A) Proline residue: C1088 - end of helix removed outlier: 4.317A pdb=" N MET C1105 " --> pdb=" O ARG C1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 462 through 467 Processing sheet with id=AA2, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.736A pdb=" N VAL C 631 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 528 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.736A pdb=" N VAL C 631 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 528 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 537 through 538 removed outlier: 4.429A pdb=" N VAL C 537 " --> pdb=" O GLY C 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 614 through 616 Processing sheet with id=AA6, first strand: chain 'C' and resid 686 through 687 Processing sheet with id=AA7, first strand: chain 'C' and resid 851 through 852 Processing sheet with id=AA8, first strand: chain 'C' and resid 979 through 982 removed outlier: 3.762A pdb=" N THR C 979 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C1000 " --> pdb=" O THR C 979 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY C1005 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR C1055 " --> pdb=" O GLY C1005 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE C1007 " --> pdb=" O THR C1055 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N CYS C1057 " --> pdb=" O ILE C1007 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP C1009 " --> pdb=" O CYS C1057 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE C1059 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN C1011 " --> pdb=" O ILE C1059 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C1064 " --> pdb=" O SER C1060 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 148 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2787 1.34 - 1.46: 3602 1.46 - 1.58: 4301 1.58 - 1.70: 394 1.70 - 1.83: 46 Bond restraints: 11130 Sorted by residual: bond pdb=" CB PRO C 366 " pdb=" CG PRO C 366 " ideal model delta sigma weight residual 1.492 1.616 -0.124 5.00e-02 4.00e+02 6.17e+00 bond pdb=" CB PRO C 915 " pdb=" CG PRO C 915 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.27e+00 bond pdb=" C3' C E 267 " pdb=" O3' C E 267 " ideal model delta sigma weight residual 1.415 1.444 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C3' U E 114 " pdb=" O3' U E 114 " ideal model delta sigma weight residual 1.415 1.443 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" CG1 ILE C 959 " pdb=" CD1 ILE C 959 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 ... (remaining 11125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 15343 2.39 - 4.79: 612 4.79 - 7.18: 52 7.18 - 9.57: 2 9.57 - 11.96: 5 Bond angle restraints: 16014 Sorted by residual: angle pdb=" CA PRO C 366 " pdb=" N PRO C 366 " pdb=" CD PRO C 366 " ideal model delta sigma weight residual 112.00 104.01 7.99 1.40e+00 5.10e-01 3.26e+01 angle pdb=" C3' C E 267 " pdb=" O3' C E 267 " pdb=" P C E 268 " ideal model delta sigma weight residual 119.70 125.96 -6.26 1.20e+00 6.94e-01 2.72e+01 angle pdb=" C3' U E 114 " pdb=" O3' U E 114 " pdb=" P A E 115 " ideal model delta sigma weight residual 119.70 125.16 -5.46 1.20e+00 6.94e-01 2.07e+01 angle pdb=" CB MET C 428 " pdb=" CG MET C 428 " pdb=" SD MET C 428 " ideal model delta sigma weight residual 112.70 124.66 -11.96 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C SER C 469 " pdb=" N ILE C 470 " pdb=" CA ILE C 470 " ideal model delta sigma weight residual 120.33 123.31 -2.98 8.00e-01 1.56e+00 1.39e+01 ... (remaining 16009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 5637 33.93 - 67.85: 582 67.85 - 101.78: 44 101.78 - 135.71: 1 135.71 - 169.63: 2 Dihedral angle restraints: 6266 sinusoidal: 3992 harmonic: 2274 Sorted by residual: dihedral pdb=" C4' C E 170 " pdb=" C3' C E 170 " pdb=" C2' C E 170 " pdb=" C1' C E 170 " ideal model delta sinusoidal sigma weight residual 36.34 -40.69 77.04 1 3.10e+00 1.04e-01 7.75e+02 dihedral pdb=" C4' A E 80 " pdb=" C3' A E 80 " pdb=" C2' A E 80 " pdb=" C1' A E 80 " ideal model delta sinusoidal sigma weight residual 36.34 -39.75 76.10 1 3.10e+00 1.04e-01 7.59e+02 dihedral pdb=" C4' C E 255 " pdb=" C3' C E 255 " pdb=" C2' C E 255 " pdb=" C1' C E 255 " ideal model delta sinusoidal sigma weight residual 36.34 -37.70 74.04 1 3.10e+00 1.04e-01 7.24e+02 ... (remaining 6263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1615 0.090 - 0.179: 66 0.179 - 0.269: 219 0.269 - 0.358: 41 0.358 - 0.448: 1 Chirality restraints: 1942 Sorted by residual: chirality pdb=" P C E 268 " pdb=" OP1 C E 268 " pdb=" OP2 C E 268 " pdb=" O5' C E 268 " both_signs ideal model delta sigma weight residual True 2.17 -2.62 -0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" P A E 115 " pdb=" OP1 A E 115 " pdb=" OP2 A E 115 " pdb=" O5' A E 115 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C3' A E 80 " pdb=" C4' A E 80 " pdb=" O3' A E 80 " pdb=" C2' A E 80 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 1939 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 365 " -0.056 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO C 366 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 366 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 366 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C E 78 " 0.031 2.00e-02 2.50e+03 1.97e-02 8.77e+00 pdb=" N1 C E 78 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C E 78 " 0.023 2.00e-02 2.50e+03 pdb=" O2 C E 78 " -0.018 2.00e-02 2.50e+03 pdb=" N3 C E 78 " -0.011 2.00e-02 2.50e+03 pdb=" C4 C E 78 " 0.019 2.00e-02 2.50e+03 pdb=" N4 C E 78 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C E 78 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C E 78 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 914 " -0.047 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO C 915 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 915 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 915 " -0.038 5.00e-02 4.00e+02 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 909 2.73 - 3.27: 10255 3.27 - 3.81: 18936 3.81 - 4.36: 21763 4.36 - 4.90: 33231 Nonbonded interactions: 85094 Sorted by model distance: nonbonded pdb=" O2' G E 112 " pdb=" O4' A E 113 " model vdw 2.187 3.040 nonbonded pdb=" O LEU C 878 " pdb=" OG SER C 881 " model vdw 2.206 3.040 nonbonded pdb=" O2 U E 136 " pdb=" N2 G E 152 " model vdw 2.207 2.496 nonbonded pdb=" NZ LYS C 389 " pdb=" O PRO C 390 " model vdw 2.230 3.120 nonbonded pdb=" N2 G E 33 " pdb=" OP2 A E 36 " model vdw 2.233 3.120 ... (remaining 85089 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: 0.330 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.004 0.124 11134 Z= 0.159 Angle : 0.862 11.963 16017 Z= 0.382 Chirality : 0.096 0.448 1942 Planarity : 0.005 0.081 1316 Dihedral : 21.779 169.634 4798 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 25.52 % Favored : 74.48 % 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: 0.06 (0.31), residues: 789 helix: 1.47 (0.28), residues: 371 sheet: -2.02 (0.62), residues: 63 loop : -1.11 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 316 TYR 0.015 0.001 TYR C 703 PHE 0.025 0.002 PHE C 555 TRP 0.031 0.002 TRP C 388 HIS 0.010 0.001 HIS C 955 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (11130) covalent geometry : angle 0.86246 / 0.38 (16014) hydrogen bonds : bond 0.14845 / 7.71 ( 444) hydrogen bonds : angle 5.74314 / 2.36 ( 1133) metal coordination : bond 0.00546 / 0.27 ( 4) metal coordination : angle 0.50472 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7331 (mtmm) cc_final: 0.6763 (ptpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1076 time to fit residues: 11.5153 Evaluate side-chains 77 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 30.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS C 659 ASN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.176296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.115342 restraints weight = 22449.909| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.81 r_work: 0.3441 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11134 Z= 0.212 Angle : 1.331 25.529 16017 Z= 0.522 Chirality : 0.124 1.733 1942 Planarity : 0.005 0.043 1316 Dihedral : 19.556 179.065 3259 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Rotamer: Outliers : 2.09 % Allowed : 22.84 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.31), residues: 789 helix: 1.51 (0.28), residues: 387 sheet: -1.77 (0.63), residues: 64 loop : -1.08 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 316 TYR 0.012 0.001 TYR C1070 PHE 0.008 0.001 PHE C 749 TRP 0.019 0.001 TRP C 388 HIS 0.008 0.001 HIS C 955 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (11130) covalent geometry : angle 1.33126 / 0.52 (16014) hydrogen bonds : bond 0.05378 / 2.96 ( 444) hydrogen bonds : angle 4.47908 / 1.80 ( 1133) metal coordination : bond 0.00252 / 0.13 ( 4) metal coordination : angle 1.11738 / 0.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7308 (mtmm) cc_final: 0.6936 (mtmm) REVERT: C 446 ARG cc_start: 0.7865 (ptp-110) cc_final: 0.7186 (ptp-110) REVERT: C 618 MET cc_start: 0.8078 (tmm) cc_final: 0.7858 (tmm) REVERT: C 765 MET cc_start: 0.8612 (mmt) cc_final: 0.8093 (mmt) REVERT: C 868 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.8043 (m90) REVERT: C 963 ASN cc_start: 0.8657 (t0) cc_final: 0.8281 (t0) outliers start: 14 outliers final: 5 residues processed: 96 average time/residue: 0.1060 time to fit residues: 13.6781 Evaluate side-chains 76 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 868 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 15 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.175827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.115612 restraints weight = 22358.838| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.01 r_work: 0.3399 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11134 Z= 0.173 Angle : 1.008 15.486 16017 Z= 0.405 Chirality : 0.083 1.099 1942 Planarity : 0.005 0.047 1316 Dihedral : 19.481 179.876 3259 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.82 % Rotamer: Outliers : 3.88 % Allowed : 22.24 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.31), residues: 789 helix: 1.47 (0.28), residues: 389 sheet: -1.83 (0.62), residues: 64 loop : -1.09 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 901 TYR 0.011 0.001 TYR C 563 PHE 0.007 0.001 PHE C 864 TRP 0.017 0.001 TRP C 388 HIS 0.009 0.001 HIS C 955 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (11130) covalent geometry : angle 1.00813 / 0.41 (16014) hydrogen bonds : bond 0.05589 / 3.10 ( 444) hydrogen bonds : angle 4.22081 / 1.69 ( 1133) metal coordination : bond 0.00331 / 0.17 ( 4) metal coordination : angle 1.00248 / 0.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.290 Fit side-chains REVERT: C 309 LYS cc_start: 0.7423 (mtmm) cc_final: 0.6910 (mtmm) REVERT: C 563 TYR cc_start: 0.7634 (m-80) cc_final: 0.7407 (m-80) REVERT: C 765 MET cc_start: 0.8828 (mmp) cc_final: 0.8182 (mmt) REVERT: C 868 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8235 (m90) REVERT: C 963 ASN cc_start: 0.8733 (t0) cc_final: 0.8390 (t0) REVERT: C 973 MET cc_start: 0.8579 (mtm) cc_final: 0.8277 (mtm) REVERT: C 994 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8142 (mmmt) REVERT: C 1025 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8457 (mm-30) REVERT: C 1105 MET cc_start: 0.8196 (ppp) cc_final: 0.7641 (ppp) outliers start: 26 outliers final: 13 residues processed: 106 average time/residue: 0.1008 time to fit residues: 14.6002 Evaluate side-chains 85 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 14 optimal weight: 30.0000 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS C 598 ASN C1016 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.176877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.122227 restraints weight = 22454.603| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.84 r_work: 0.3436 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11134 Z= 0.143 Angle : 0.970 14.712 16017 Z= 0.389 Chirality : 0.077 0.908 1942 Planarity : 0.005 0.052 1316 Dihedral : 19.252 179.253 3259 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 3.58 % Allowed : 21.79 % Favored : 74.63 % 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 (0.31), residues: 789 helix: 1.55 (0.28), residues: 389 sheet: -1.87 (0.61), residues: 64 loop : -1.04 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 611 TYR 0.013 0.002 TYR C 626 PHE 0.008 0.001 PHE C 749 TRP 0.024 0.001 TRP C 388 HIS 0.008 0.001 HIS C 955 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (11130) covalent geometry : angle 0.97016 / 0.39 (16014) hydrogen bonds : bond 0.05432 / 3.14 ( 444) hydrogen bonds : angle 3.97354 / 1.59 ( 1133) metal coordination : bond 0.01053 / 0.53 ( 4) metal coordination : angle 0.78998 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 455 ARG cc_start: 0.8092 (tpm170) cc_final: 0.7665 (mmm160) REVERT: C 551 MET cc_start: 0.6338 (mmp) cc_final: 0.6073 (mmp) REVERT: C 703 TYR cc_start: 0.6665 (m-80) cc_final: 0.6333 (m-80) REVERT: C 868 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.8285 (m90) REVERT: C 963 ASN cc_start: 0.8819 (t0) cc_final: 0.8421 (t0) REVERT: C 994 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8126 (mmmt) REVERT: C 1025 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8469 (mm-30) REVERT: C 1105 MET cc_start: 0.8071 (ppp) cc_final: 0.7513 (ppp) outliers start: 24 outliers final: 13 residues processed: 101 average time/residue: 0.1027 time to fit residues: 14.2416 Evaluate side-chains 87 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 30.0000 chunk 62 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS C1016 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.174048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.114606 restraints weight = 21798.995| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.89 r_work: 0.3359 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11134 Z= 0.195 Angle : 0.981 14.257 16017 Z= 0.397 Chirality : 0.076 0.889 1942 Planarity : 0.005 0.051 1316 Dihedral : 19.193 179.441 3259 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 4.18 % Allowed : 21.04 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.31), residues: 789 helix: 1.51 (0.28), residues: 384 sheet: -2.28 (0.56), residues: 69 loop : -1.06 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1001 TYR 0.011 0.002 TYR C 626 PHE 0.009 0.002 PHE C 864 TRP 0.023 0.002 TRP C 388 HIS 0.007 0.001 HIS C 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (11130) covalent geometry : angle 0.98058 / 0.40 (16014) hydrogen bonds : bond 0.05780 / 3.31 ( 444) hydrogen bonds : angle 4.09285 / 1.65 ( 1133) metal coordination : bond 0.00389 / 0.19 ( 4) metal coordination : angle 1.54120 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7370 (mtmm) cc_final: 0.6962 (mtmm) REVERT: C 388 TRP cc_start: 0.7195 (m-10) cc_final: 0.6820 (m-10) REVERT: C 395 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: C 618 MET cc_start: 0.7854 (tmm) cc_final: 0.7596 (tmm) REVERT: C 703 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: C 994 LYS cc_start: 0.8358 (mmmt) cc_final: 0.8000 (mmmt) REVERT: C 1105 MET cc_start: 0.8260 (ppp) cc_final: 0.7589 (ppp) outliers start: 28 outliers final: 20 residues processed: 99 average time/residue: 0.0811 time to fit residues: 11.3458 Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1002 ASP Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 0.0970 chunk 36 optimal weight: 0.0010 chunk 37 optimal weight: 0.0070 chunk 24 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.178925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.118666 restraints weight = 22177.937| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.81 r_work: 0.3488 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11134 Z= 0.128 Angle : 0.937 15.278 16017 Z= 0.377 Chirality : 0.073 0.861 1942 Planarity : 0.005 0.063 1316 Dihedral : 19.091 179.907 3259 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.84 % Allowed : 21.94 % Favored : 75.22 % 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: 0.35 (0.31), residues: 789 helix: 1.74 (0.28), residues: 381 sheet: -2.01 (0.56), residues: 69 loop : -1.03 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1027 TYR 0.009 0.002 TYR C 563 PHE 0.009 0.001 PHE C 749 TRP 0.022 0.001 TRP C 388 HIS 0.005 0.001 HIS C 955 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (11130) covalent geometry : angle 0.93641 / 0.38 (16014) hydrogen bonds : bond 0.05545 / 3.32 ( 444) hydrogen bonds : angle 3.81867 / 1.54 ( 1133) metal coordination : bond 0.01475 / 0.74 ( 4) metal coordination : angle 1.43578 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 388 TRP cc_start: 0.7344 (m-10) cc_final: 0.7105 (m-10) REVERT: C 395 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: C 618 MET cc_start: 0.7878 (tmm) cc_final: 0.7596 (tmm) REVERT: C 868 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7954 (m90) REVERT: C 994 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7862 (mmmt) outliers start: 19 outliers final: 13 residues processed: 105 average time/residue: 0.0951 time to fit residues: 13.7959 Evaluate side-chains 81 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 951 CYS Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 13 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS C 659 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.176574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.117075 restraints weight = 22025.851| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.91 r_work: 0.3409 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11134 Z= 0.150 Angle : 0.948 15.116 16017 Z= 0.382 Chirality : 0.072 0.791 1942 Planarity : 0.005 0.050 1316 Dihedral : 19.055 179.635 3259 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.44 % Rotamer: Outliers : 3.13 % Allowed : 22.69 % Favored : 74.18 % 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: 0.32 (0.31), residues: 789 helix: 1.75 (0.28), residues: 377 sheet: -2.07 (0.56), residues: 69 loop : -1.04 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 953 TYR 0.008 0.001 TYR C 626 PHE 0.012 0.001 PHE C1102 TRP 0.017 0.001 TRP C 388 HIS 0.005 0.001 HIS C 955 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (11130) covalent geometry : angle 0.94828 / 0.38 (16014) hydrogen bonds : bond 0.05784 / 3.38 ( 444) hydrogen bonds : angle 3.92605 / 1.59 ( 1133) metal coordination : bond 0.00989 / 0.49 ( 4) metal coordination : angle 0.85029 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7469 (mtmm) cc_final: 0.7098 (mtmm) REVERT: C 388 TRP cc_start: 0.7206 (m-10) cc_final: 0.7004 (m-10) REVERT: C 395 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: C 446 ARG cc_start: 0.7961 (ptp-110) cc_final: 0.7448 (ptp-110) REVERT: C 618 MET cc_start: 0.7831 (tmm) cc_final: 0.7505 (tmm) REVERT: C 868 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.8188 (m90) REVERT: C 1105 MET cc_start: 0.7398 (ppp) cc_final: 0.7176 (ppp) outliers start: 21 outliers final: 17 residues processed: 94 average time/residue: 0.0805 time to fit residues: 10.7679 Evaluate side-chains 87 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 951 CYS Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1050 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.177056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.115762 restraints weight = 21869.879| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.75 r_work: 0.3438 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11134 Z= 0.144 Angle : 0.935 15.416 16017 Z= 0.375 Chirality : 0.071 0.778 1942 Planarity : 0.004 0.051 1316 Dihedral : 19.072 179.487 3259 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 3.73 % Allowed : 21.49 % Favored : 74.78 % 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: 0.32 (0.31), residues: 789 helix: 1.74 (0.28), residues: 383 sheet: -2.10 (0.55), residues: 69 loop : -1.08 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1001 TYR 0.012 0.002 TYR C 563 PHE 0.010 0.001 PHE C1102 TRP 0.017 0.001 TRP C 388 HIS 0.005 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11130) covalent geometry : angle 0.93525 / 0.38 (16014) hydrogen bonds : bond 0.05794 / 3.46 ( 444) hydrogen bonds : angle 3.89919 / 1.57 ( 1133) metal coordination : bond 0.00785 / 0.39 ( 4) metal coordination : angle 0.97003 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 395 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: C 446 ARG cc_start: 0.7965 (ptp-110) cc_final: 0.7454 (ptp-110) REVERT: C 618 MET cc_start: 0.7845 (tmm) cc_final: 0.7511 (tmm) REVERT: C 868 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8200 (m90) REVERT: C 994 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7820 (mmmt) REVERT: C 1105 MET cc_start: 0.7700 (ppp) cc_final: 0.7252 (ppp) outliers start: 25 outliers final: 21 residues processed: 95 average time/residue: 0.0908 time to fit residues: 12.3207 Evaluate side-chains 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 951 CYS Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1050 GLU Chi-restraints excluded: chain C residue 1077 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 59 optimal weight: 0.3980 chunk 17 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.175980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.115921 restraints weight = 22040.083| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.92 r_work: 0.3404 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11134 Z= 0.161 Angle : 0.948 15.688 16017 Z= 0.383 Chirality : 0.071 0.730 1942 Planarity : 0.005 0.050 1316 Dihedral : 19.119 179.585 3259 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 4.03 % Allowed : 21.64 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.31), residues: 789 helix: 1.69 (0.28), residues: 383 sheet: -2.12 (0.55), residues: 69 loop : -1.08 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 400 TYR 0.010 0.001 TYR C 563 PHE 0.009 0.002 PHE C1102 TRP 0.044 0.002 TRP C 388 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (11130) covalent geometry : angle 0.94818 / 0.38 (16014) hydrogen bonds : bond 0.06020 / 3.56 ( 444) hydrogen bonds : angle 3.95113 / 1.60 ( 1133) metal coordination : bond 0.00642 / 0.32 ( 4) metal coordination : angle 0.90890 / 0.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 388 TRP cc_start: 0.7273 (m-10) cc_final: 0.6975 (m-10) REVERT: C 395 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: C 400 ARG cc_start: 0.7024 (mmm160) cc_final: 0.6781 (mmp80) REVERT: C 618 MET cc_start: 0.7904 (tmm) cc_final: 0.7603 (tmm) REVERT: C 868 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.8244 (m90) REVERT: C 994 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7820 (mmmt) REVERT: C 1101 ARG cc_start: 0.7653 (tpt170) cc_final: 0.7312 (tpt170) REVERT: C 1105 MET cc_start: 0.7768 (ppp) cc_final: 0.7174 (ppp) outliers start: 27 outliers final: 23 residues processed: 95 average time/residue: 0.0868 time to fit residues: 11.7509 Evaluate side-chains 98 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 951 CYS Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1050 GLU Chi-restraints excluded: chain C residue 1077 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1033 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.177272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.118490 restraints weight = 21716.270| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.88 r_work: 0.3418 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11134 Z= 0.136 Angle : 0.937 16.269 16017 Z= 0.377 Chirality : 0.070 0.711 1942 Planarity : 0.004 0.050 1316 Dihedral : 19.094 179.967 3259 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 4.03 % Allowed : 22.24 % Favored : 73.73 % 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: 0.32 (0.31), residues: 789 helix: 1.73 (0.28), residues: 383 sheet: -2.07 (0.54), residues: 69 loop : -1.08 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 482 TYR 0.009 0.002 TYR C 626 PHE 0.010 0.001 PHE C1102 TRP 0.040 0.001 TRP C 388 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (11130) covalent geometry : angle 0.93720 / 0.38 (16014) hydrogen bonds : bond 0.05977 / 3.57 ( 444) hydrogen bonds : angle 3.89720 / 1.58 ( 1133) metal coordination : bond 0.01007 / 0.50 ( 4) metal coordination : angle 1.02635 / 0.34 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 395 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: C 400 ARG cc_start: 0.7054 (mmm160) cc_final: 0.6813 (mmp80) REVERT: C 618 MET cc_start: 0.7843 (tmm) cc_final: 0.7536 (tmm) REVERT: C 868 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8225 (m90) REVERT: C 994 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7823 (mmmt) REVERT: C 1101 ARG cc_start: 0.7677 (tpt170) cc_final: 0.7375 (tpt170) REVERT: C 1105 MET cc_start: 0.7719 (ppp) cc_final: 0.7068 (ppp) outliers start: 27 outliers final: 23 residues processed: 96 average time/residue: 0.0814 time to fit residues: 10.9510 Evaluate side-chains 95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 951 CYS Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1050 GLU Chi-restraints excluded: chain C residue 1077 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 16 optimal weight: 30.0000 chunk 81 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.174554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114869 restraints weight = 22036.363| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.86 r_work: 0.3362 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11134 Z= 0.190 Angle : 0.973 16.709 16017 Z= 0.395 Chirality : 0.071 0.687 1942 Planarity : 0.005 0.050 1316 Dihedral : 19.139 178.486 3259 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.45 % Favored : 94.42 % Rotamer: Outliers : 3.88 % Allowed : 22.39 % Favored : 73.73 % 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: 0.14 (0.31), residues: 789 helix: 1.59 (0.28), residues: 383 sheet: -2.20 (0.54), residues: 69 loop : -1.15 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1001 TYR 0.010 0.002 TYR C 626 PHE 0.010 0.002 PHE C 864 TRP 0.031 0.002 TRP C 388 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (11130) covalent geometry : angle 0.97298 / 0.39 (16014) hydrogen bonds : bond 0.06432 / 3.76 ( 444) hydrogen bonds : angle 4.10290 / 1.67 ( 1133) metal coordination : bond 0.00609 / 0.30 ( 4) metal coordination : angle 1.26620 / 0.42 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.29 seconds wall clock time: 43 minutes 15.43 seconds (2595.43 seconds total)