Starting phenix.real_space_refine on Thu Jul 2 21:54:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iby_35349/07_2026/8iby_35349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iby_35349/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8iby_35349/07_2026/8iby_35349.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iby_35349/07_2026/8iby_35349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iby_35349/07_2026/8iby_35349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iby_35349/07_2026/8iby_35349.map" model { file = "/net/cci-nas-00/data/ceres_data/8iby_35349/07_2026/8iby_35349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iby_35349/07_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-dev-6108/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: {'RNA': 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: 2.21, 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: 0.70 Conformation dependent library (CDL) restraints added in 250.7 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: 1.26 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: 2.26 Time building geometry restraints manager: 1.04 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=" 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 bond pdb=" CB GLU C 974 " pdb=" CG GLU C 974 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" C PRO C 364 " pdb=" N THR C 365 " ideal model delta sigma weight residual 1.327 1.347 -0.020 1.71e-02 3.42e+03 1.40e+00 ... (remaining 11125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 15828 2.39 - 4.79: 155 4.79 - 7.18: 24 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=" 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=" C3' C E 267 " pdb=" O3' C E 267 " pdb=" P C E 268 " ideal model delta sigma weight residual 120.20 125.96 -5.76 1.50e+00 4.44e-01 1.47e+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 angle pdb=" CA PRO C 915 " pdb=" N PRO C 915 " pdb=" CD PRO C 915 " ideal model delta sigma weight residual 112.00 106.78 5.22 1.40e+00 5.10e-01 1.39e+01 ... (remaining 16009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 5915 35.45 - 70.90: 323 70.90 - 106.35: 19 106.35 - 141.80: 6 141.80 - 177.25: 3 Dihedral angle restraints: 6266 sinusoidal: 3992 harmonic: 2274 Sorted by residual: dihedral pdb=" O4' C E 145 " pdb=" C1' C E 145 " pdb=" N1 C E 145 " pdb=" C2 C E 145 " ideal model delta sinusoidal sigma weight residual -128.00 49.25 -177.25 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C4' U E 101 " pdb=" C3' U E 101 " pdb=" O3' U E 101 " pdb=" P G E 102 " ideal model delta sinusoidal sigma weight residual -140.00 29.63 -169.63 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" O4' G E 110 " pdb=" C1' G E 110 " pdb=" N9 G E 110 " pdb=" C4 G E 110 " ideal model delta sinusoidal sigma weight residual -106.00 -163.81 57.81 1 1.70e+01 3.46e-03 1.55e+01 ... (remaining 6263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1651 0.046 - 0.091: 225 0.091 - 0.137: 57 0.137 - 0.183: 6 0.183 - 0.229: 3 Chirality restraints: 1942 Sorted by residual: chirality pdb=" C1' A E 56 " pdb=" O4' A E 56 " pdb=" C2' A E 56 " pdb=" N9 A E 56 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.31e+00 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 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' U E 114 " pdb=" C4' U E 114 " pdb=" O3' U E 114 " pdb=" C2' U E 114 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (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: 0.250 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- 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 : 0.003 0.124 11134 Z= 0.140 Angle : 0.622 11.963 16017 Z= 0.319 Chirality : 0.035 0.229 1942 Planarity : 0.005 0.081 1316 Dihedral : 18.620 177.250 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 0.00333 / 0.14 (11130) covalent geometry : angle 0.62208 / 0.32 (16014) hydrogen bonds : bond 0.14845 / 8.69 ( 444) hydrogen bonds : angle 5.74314 / 3.35 ( 1133) metal coordination : bond 0.00546 / 0.36 ( 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 : 0.291 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: 0.1109 time to fit residues: 11.8714 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 : 0.258 ------------------------------------------------------------------------------- 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: 20.0000 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 C 769 GLN ** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.177083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.116352 restraints weight = 22165.742| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.01 r_work: 0.3415 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11134 Z= 0.135 Angle : 0.578 10.137 16017 Z= 0.291 Chirality : 0.035 0.224 1942 Planarity : 0.005 0.041 1316 Dihedral : 17.555 177.343 3259 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.82 % Rotamer: Outliers : 2.39 % Allowed : 22.24 % Favored : 75.37 % 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: 0.23 (0.31), residues: 789 helix: 1.52 (0.28), residues: 387 sheet: -1.76 (0.63), residues: 64 loop : -1.07 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 316 TYR 0.012 0.001 TYR C1070 PHE 0.008 0.001 PHE C 749 TRP 0.017 0.001 TRP C 388 HIS 0.007 0.001 HIS C 955 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (11130) covalent geometry : angle 0.57760 / 0.29 (16014) hydrogen bonds : bond 0.05050 / 3.11 ( 444) hydrogen bonds : angle 4.41372 / 2.56 ( 1133) metal coordination : bond 0.00276 / 0.16 ( 4) metal coordination : angle 1.12334 / 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: 16 poor density : 82 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7321 (mtmm) cc_final: 0.6977 (mtmm) REVERT: C 446 ARG cc_start: 0.7862 (ptp-110) cc_final: 0.7172 (ptp-110) REVERT: C 618 MET cc_start: 0.8115 (tmm) cc_final: 0.7893 (tmm) REVERT: C 868 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.8088 (m90) outliers start: 16 outliers final: 5 residues processed: 96 average time/residue: 0.1046 time to fit residues: 13.6168 Evaluate side-chains 75 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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: 30.0000 chunk 87 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 0.0040 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 0.0870 chunk 94 optimal weight: 0.6980 chunk 54 optimal weight: 0.0070 chunk 39 optimal weight: 6.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS C 598 ASN ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 HIS C1016 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.179661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.119089 restraints weight = 22307.276| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.76 r_work: 0.3490 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11134 Z= 0.099 Angle : 0.544 10.123 16017 Z= 0.271 Chirality : 0.034 0.212 1942 Planarity : 0.004 0.049 1316 Dihedral : 17.388 177.451 3259 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.53 % Favored : 97.34 % Rotamer: Outliers : 2.69 % Allowed : 21.79 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.31), residues: 789 helix: 1.67 (0.28), residues: 387 sheet: -1.68 (0.64), residues: 64 loop : -1.03 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 316 TYR 0.009 0.001 TYR C1070 PHE 0.008 0.001 PHE C 753 TRP 0.018 0.001 TRP C 388 HIS 0.010 0.001 HIS C 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (11130) covalent geometry : angle 0.54400 / 0.27 (16014) hydrogen bonds : bond 0.04732 / 2.93 ( 444) hydrogen bonds : angle 4.02805 / 2.34 ( 1133) metal coordination : bond 0.01118 / 0.74 ( 4) metal coordination : angle 0.96793 / 0.32 ( 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 106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7227 (mtmm) cc_final: 0.6763 (mtmm) REVERT: C 446 ARG cc_start: 0.8000 (ptp-110) cc_final: 0.7411 (ptp-110) REVERT: C 654 MET cc_start: 0.9375 (mmm) cc_final: 0.8800 (mmt) REVERT: C 765 MET cc_start: 0.8210 (mmt) cc_final: 0.7930 (mmt) REVERT: C 868 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.8011 (m90) REVERT: C 1025 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8466 (mm-30) REVERT: C 1105 MET cc_start: 0.8043 (ppp) cc_final: 0.7502 (ppp) outliers start: 18 outliers final: 7 residues processed: 102 average time/residue: 0.0920 time to fit residues: 12.8594 Evaluate side-chains 78 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 528 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 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: 2.9990 chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS C 659 ASN C 718 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.175134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.113161 restraints weight = 22195.644| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.83 r_work: 0.3392 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11134 Z= 0.182 Angle : 0.597 10.121 16017 Z= 0.299 Chirality : 0.036 0.213 1942 Planarity : 0.005 0.050 1316 Dihedral : 17.589 177.297 3259 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.45 % Favored : 94.42 % Rotamer: Outliers : 3.43 % Allowed : 21.49 % 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: 0.17 (0.31), residues: 789 helix: 1.51 (0.28), residues: 384 sheet: -2.04 (0.60), residues: 64 loop : -1.07 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 455 TYR 0.012 0.001 TYR C 563 PHE 0.010 0.001 PHE C 849 TRP 0.019 0.002 TRP C 388 HIS 0.008 0.001 HIS C 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (11130) covalent geometry : angle 0.59710 / 0.30 (16014) hydrogen bonds : bond 0.05143 / 3.19 ( 444) hydrogen bonds : angle 4.08699 / 2.40 ( 1133) metal coordination : bond 0.00505 / 0.33 ( 4) metal coordination : angle 1.12642 / 0.38 ( 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: 23 poor density : 80 time to evaluate : 0.216 Fit side-chains REVERT: C 309 LYS cc_start: 0.7330 (mtmm) cc_final: 0.6779 (mtmm) REVERT: C 971 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8522 (tppt) REVERT: C 973 MET cc_start: 0.8635 (mtm) cc_final: 0.8376 (mtm) REVERT: C 994 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8117 (mmmt) REVERT: C 1025 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8471 (mm-30) REVERT: C 1105 MET cc_start: 0.8184 (ppp) cc_final: 0.7589 (ppp) outliers start: 23 outliers final: 16 residues processed: 100 average time/residue: 0.0882 time to fit residues: 12.2279 Evaluate side-chains 92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 738 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1077 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS C 659 ASN C 718 HIS C 868 HIS C1016 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.174184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.111937 restraints weight = 21876.881| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.80 r_work: 0.3388 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11134 Z= 0.168 Angle : 0.588 10.230 16017 Z= 0.295 Chirality : 0.036 0.229 1942 Planarity : 0.005 0.052 1316 Dihedral : 17.723 177.376 3259 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.06 % Rotamer: Outliers : 4.78 % Allowed : 21.19 % Favored : 74.03 % 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: 0.10 (0.31), residues: 789 helix: 1.48 (0.28), residues: 384 sheet: -2.31 (0.55), residues: 69 loop : -1.05 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 455 TYR 0.015 0.002 TYR C 626 PHE 0.013 0.002 PHE C 597 TRP 0.024 0.002 TRP C 388 HIS 0.006 0.001 HIS C 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (11130) covalent geometry : angle 0.58812 / 0.29 (16014) hydrogen bonds : bond 0.05081 / 3.16 ( 444) hydrogen bonds : angle 4.04693 / 2.38 ( 1133) metal coordination : bond 0.00323 / 0.20 ( 4) metal coordination : angle 1.34208 / 0.45 ( 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 110 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: C 388 TRP cc_start: 0.7236 (m-10) cc_final: 0.6995 (m-10) REVERT: C 395 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: C 618 MET cc_start: 0.7934 (tmm) cc_final: 0.7661 (tmm) REVERT: C 703 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6022 (m-80) REVERT: C 971 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8596 (tppt) REVERT: C 994 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8120 (mmmt) REVERT: C 1073 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8863 (tt) REVERT: C 1101 ARG cc_start: 0.7610 (tpt170) cc_final: 0.7409 (tpt170) REVERT: C 1105 MET cc_start: 0.8197 (ppp) cc_final: 0.7501 (ppp) outliers start: 32 outliers final: 20 residues processed: 103 average time/residue: 0.0929 time to fit residues: 13.2486 Evaluate side-chains 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 438 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 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 746 ILE Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 947 ILE 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 Chi-restraints excluded: chain C residue 1073 LEU Chi-restraints excluded: chain C residue 1077 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 0.0470 chunk 37 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 66 optimal weight: 0.0050 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS C 659 ASN C 868 HIS ** C 955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.178071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.117917 restraints weight = 22568.667| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.84 r_work: 0.3455 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11134 Z= 0.102 Angle : 0.558 12.088 16017 Z= 0.276 Chirality : 0.034 0.212 1942 Planarity : 0.004 0.052 1316 Dihedral : 17.579 177.436 3259 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 3.58 % Allowed : 22.54 % 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: 0.28 (0.31), residues: 789 helix: 1.62 (0.28), residues: 383 sheet: -2.12 (0.56), residues: 69 loop : -0.99 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 611 TYR 0.012 0.001 TYR C 626 PHE 0.013 0.001 PHE C 429 TRP 0.018 0.001 TRP C 388 HIS 0.023 0.001 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (11130) covalent geometry : angle 0.55816 / 0.28 (16014) hydrogen bonds : bond 0.04785 / 3.00 ( 444) hydrogen bonds : angle 3.84899 / 2.25 ( 1133) metal coordination : bond 0.01210 / 0.81 ( 4) metal coordination : angle 1.00151 / 0.33 ( 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 102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7353 (mtmm) cc_final: 0.6939 (mtmm) REVERT: C 395 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7540 (pm20) REVERT: C 618 MET cc_start: 0.7974 (tmm) cc_final: 0.7669 (tmm) REVERT: C 765 MET cc_start: 0.8390 (mmt) cc_final: 0.8150 (mmt) REVERT: C 971 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8590 (tppt) REVERT: C 1105 MET cc_start: 0.8066 (ppp) cc_final: 0.7325 (ppp) outliers start: 24 outliers final: 18 residues processed: 96 average time/residue: 0.0792 time to fit residues: 10.9144 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 : 0.170 ------------------------------------------------------------------------------- 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 438 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 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 Chi-restraints excluded: chain C residue 1077 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 13 optimal weight: 40.0000 chunk 22 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 34 optimal weight: 0.0670 chunk 55 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS C 659 ASN C 718 HIS C 868 HIS ** C 955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.171911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110891 restraints weight = 22004.872| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.87 r_work: 0.3328 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11134 Z= 0.261 Angle : 0.679 10.577 16017 Z= 0.339 Chirality : 0.039 0.224 1942 Planarity : 0.005 0.051 1316 Dihedral : 17.962 177.373 3259 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.92 % Rotamer: Outliers : 4.33 % Allowed : 22.54 % Favored : 73.13 % 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: -0.20 (0.31), residues: 789 helix: 1.25 (0.27), residues: 384 sheet: -2.49 (0.55), residues: 69 loop : -1.23 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 866 TYR 0.013 0.002 TYR C 626 PHE 0.016 0.002 PHE C 849 TRP 0.037 0.002 TRP C 388 HIS 0.013 0.002 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.26 (11130) covalent geometry : angle 0.67885 / 0.34 (16014) hydrogen bonds : bond 0.05744 / 3.57 ( 444) hydrogen bonds : angle 4.21372 / 2.49 ( 1133) metal coordination : bond 0.00531 / 0.33 ( 4) metal coordination : angle 1.97767 / 0.66 ( 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 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.228 Fit side-chains REVERT: C 388 TRP cc_start: 0.7289 (m-10) cc_final: 0.6396 (m-10) REVERT: C 395 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: C 618 MET cc_start: 0.7946 (tmm) cc_final: 0.7641 (tmm) REVERT: C 703 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: C 902 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8706 (t0) REVERT: C 971 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8595 (ttmt) REVERT: C 994 LYS cc_start: 0.8338 (mmmt) cc_final: 0.8018 (mmmt) REVERT: C 1026 LYS cc_start: 0.7499 (mtpp) cc_final: 0.7257 (mtpt) REVERT: C 1105 MET cc_start: 0.8341 (ppp) cc_final: 0.7485 (ppp) outliers start: 29 outliers final: 25 residues processed: 95 average time/residue: 0.0876 time to fit residues: 11.7952 Evaluate side-chains 95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 438 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 608 LEU 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 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 899 THR Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 976 ASN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1010 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 0.0370 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 598 ASN C 659 ASN C 718 HIS C 868 HIS C 955 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.176154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.115012 restraints weight = 22106.858| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.79 r_work: 0.3423 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11134 Z= 0.106 Angle : 0.574 10.214 16017 Z= 0.283 Chirality : 0.035 0.214 1942 Planarity : 0.004 0.052 1316 Dihedral : 17.786 177.426 3259 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.82 % Rotamer: Outliers : 3.58 % Allowed : 23.28 % Favored : 73.13 % 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 (0.31), residues: 789 helix: 1.61 (0.28), residues: 376 sheet: -2.13 (0.57), residues: 69 loop : -1.11 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 866 TYR 0.010 0.001 TYR C 626 PHE 0.013 0.001 PHE C 429 TRP 0.029 0.002 TRP C 388 HIS 0.012 0.001 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (11130) covalent geometry : angle 0.57365 / 0.28 (16014) hydrogen bonds : bond 0.05045 / 3.17 ( 444) hydrogen bonds : angle 3.88289 / 2.27 ( 1133) metal coordination : bond 0.01451 / 0.97 ( 4) metal coordination : angle 1.30707 / 0.44 ( 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 98 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.235 Fit side-chains REVERT: C 309 LYS cc_start: 0.7288 (mtmm) cc_final: 0.7079 (mtmm) REVERT: C 388 TRP cc_start: 0.7009 (m-10) cc_final: 0.6588 (m-10) REVERT: C 395 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: C 618 MET cc_start: 0.7905 (tmm) cc_final: 0.7564 (tmm) REVERT: C 994 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7948 (mmmt) REVERT: C 1105 MET cc_start: 0.8196 (ppp) cc_final: 0.7278 (ppp) outliers start: 24 outliers final: 19 residues processed: 91 average time/residue: 0.0766 time to fit residues: 10.0802 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 438 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 7 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 40.0000 chunk 58 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS C 598 ASN C 868 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.177129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.120741 restraints weight = 22330.127| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.91 r_work: 0.3418 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11134 Z= 0.105 Angle : 0.561 10.107 16017 Z= 0.278 Chirality : 0.035 0.211 1942 Planarity : 0.004 0.052 1316 Dihedral : 17.737 177.410 3259 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.94 % Rotamer: Outliers : 3.13 % Allowed : 22.99 % 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: 0.24 (0.31), residues: 789 helix: 1.68 (0.28), residues: 377 sheet: -2.11 (0.56), residues: 69 loop : -1.08 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 400 TYR 0.010 0.001 TYR C 626 PHE 0.014 0.001 PHE C 429 TRP 0.028 0.001 TRP C 388 HIS 0.011 0.001 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (11130) covalent geometry : angle 0.56047 / 0.28 (16014) hydrogen bonds : bond 0.05108 / 3.22 ( 444) hydrogen bonds : angle 3.83110 / 2.25 ( 1133) metal coordination : bond 0.01158 / 0.77 ( 4) metal coordination : angle 1.16859 / 0.39 ( 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 95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 309 LYS cc_start: 0.7283 (mtmm) cc_final: 0.6701 (mtmm) REVERT: C 388 TRP cc_start: 0.6952 (m-10) cc_final: 0.6535 (m-10) REVERT: C 395 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: C 428 MET cc_start: 0.6337 (mtp) cc_final: 0.5769 (tpt) REVERT: C 618 MET cc_start: 0.7907 (tmm) cc_final: 0.7583 (tmm) REVERT: C 953 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7730 (mtp180) REVERT: C 994 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7848 (mmmt) outliers start: 21 outliers final: 19 residues processed: 90 average time/residue: 0.0880 time to fit residues: 11.1333 Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 438 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 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 802 SER Chi-restraints excluded: chain C residue 868 HIS 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: 1.9990 chunk 24 optimal weight: 0.4980 chunk 77 optimal weight: 0.1980 chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 30.0000 chunk 97 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 963 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.177352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.116616 restraints weight = 21761.687| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.68 r_work: 0.3460 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11134 Z= 0.105 Angle : 0.561 10.113 16017 Z= 0.277 Chirality : 0.035 0.211 1942 Planarity : 0.004 0.052 1316 Dihedral : 17.721 177.402 3259 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.55 % Favored : 96.32 % Rotamer: Outliers : 3.28 % Allowed : 22.69 % Favored : 74.03 % 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: 0.33 (0.31), residues: 789 helix: 1.77 (0.28), residues: 377 sheet: -2.11 (0.55), residues: 69 loop : -1.06 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 400 TYR 0.010 0.001 TYR C 626 PHE 0.013 0.001 PHE C 864 TRP 0.029 0.001 TRP C 388 HIS 0.013 0.001 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (11130) covalent geometry : angle 0.56034 / 0.28 (16014) hydrogen bonds : bond 0.05168 / 3.26 ( 444) hydrogen bonds : angle 3.80705 / 2.23 ( 1133) metal coordination : bond 0.01145 / 0.76 ( 4) metal coordination : angle 1.20199 / 0.40 ( 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 96 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 388 TRP cc_start: 0.6986 (m-10) cc_final: 0.6583 (m-10) REVERT: C 395 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: C 400 ARG cc_start: 0.7079 (mmm160) cc_final: 0.6878 (mmp80) REVERT: C 428 MET cc_start: 0.6197 (mtp) cc_final: 0.5616 (tpt) REVERT: C 618 MET cc_start: 0.7861 (tmm) cc_final: 0.7543 (tmm) REVERT: C 765 MET cc_start: 0.8139 (mmt) cc_final: 0.7617 (mmt) REVERT: C 953 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7659 (mtp180) REVERT: C 994 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7798 (mmmt) outliers start: 22 outliers final: 19 residues processed: 91 average time/residue: 0.0817 time to fit residues: 10.5717 Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 438 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 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 802 SER 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: 20.0000 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 718 HIS C 868 HIS C 963 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.173212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.111607 restraints weight = 21948.184| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.74 r_work: 0.3377 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11134 Z= 0.191 Angle : 0.616 10.090 16017 Z= 0.308 Chirality : 0.037 0.208 1942 Planarity : 0.005 0.051 1316 Dihedral : 17.933 177.484 3259 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.58 % Favored : 94.30 % Rotamer: Outliers : 2.99 % Allowed : 23.13 % 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: 0.13 (0.31), residues: 789 helix: 1.59 (0.28), residues: 383 sheet: -2.37 (0.56), residues: 69 loop : -1.14 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1001 TYR 0.017 0.002 TYR C 788 PHE 0.013 0.002 PHE C 864 TRP 0.031 0.002 TRP C 388 HIS 0.008 0.002 HIS C 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (11130) covalent geometry : angle 0.61569 / 0.31 (16014) hydrogen bonds : bond 0.05756 / 3.62 ( 444) hydrogen bonds : angle 4.02651 / 2.37 ( 1133) metal coordination : bond 0.00437 / 0.28 ( 4) metal coordination : angle 1.50354 / 0.50 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.29 seconds wall clock time: 44 minutes 3.39 seconds (2643.39 seconds total)