Starting phenix.real_space_refine on Wed Aug 5 15:18:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ibz_35350/08_2026/8ibz_35350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibz_35350/08_2026/8ibz_35350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ibz_35350/08_2026/8ibz_35350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibz_35350/08_2026/8ibz_35350.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ibz_35350/08_2026/8ibz_35350.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ibz_35350/08_2026/8ibz_35350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ibz_35350/08_2026/8ibz_35350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibz_35350/08_2026/8ibz_35350.map" } resolution = 3.04 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= 0.002 sd= 0.069 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 180 5.49 5 S 33 5.16 5 C 5747 2.51 5 N 1936 2.21 5 O 2376 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: 10273 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 6419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6419 Classifications: {'peptide': 817} Link IDs: {'PTRANS': 40, 'TRANS': 776} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 3853 Classifications: {'RNAv2': 180} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 13, 'rna3p_pur': 84, 'rna3p_pyr': 68} Link IDs: {'rna2p': 27, 'rna3p': 152} Chain breaks: 3 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 5049 SG CYS C 934 23.361 91.141 71.596 1.00 19.77 S ATOM 5075 SG CYS C 938 21.307 94.372 71.712 1.00 27.76 S ATOM 5180 SG CYS C 951 24.106 93.871 74.236 1.00 14.04 S Time building chain proxies: 2.37, per 1000 atoms: 0.23 Number of scatterers: 10273 At special positions: 0 Unit cell: (114.745, 142.89, 123.405, 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 33 16.00 P 180 15.00 O 2376 8.00 N 1936 7.00 C 5747 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 248.1 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 938 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 951 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 934 " Number of angles added : 3 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 55.8% alpha, 9.7% beta 46 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'C' and resid 260 through 283 Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 347 through 356 Proline residue: C 353 - end of helix Processing helix chain 'C' and resid 365 through 374 Processing helix chain 'C' and resid 393 through 399 removed outlier: 3.675A pdb=" N LYS C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.649A pdb=" N GLN C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) 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: 3.662A pdb=" N ILE C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 479 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 519 removed outlier: 4.322A pdb=" N ALA C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 549 Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 592 through 607 removed outlier: 3.850A pdb=" N ASN C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 654 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 Processing helix chain 'C' and resid 751 through 755 Processing helix chain 'C' and resid 759 through 779 removed outlier: 3.806A pdb=" N LEU C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 791 removed outlier: 4.047A pdb=" N TYR C 789 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 817 Proline residue: C 808 - end of helix removed outlier: 4.394A pdb=" N GLY C 817 " --> pdb=" O ARG C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 821 Processing helix chain 'C' and resid 823 through 831 removed outlier: 3.839A pdb=" N ARG C 827 " --> pdb=" O TRP C 823 " (cutoff:3.500A) removed outlier: 3.658A 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 878 through 883 removed outlier: 4.096A pdb=" N THR C 882 " --> pdb=" O ARG C 879 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 883 " --> pdb=" O GLU C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 889 removed outlier: 3.615A pdb=" N THR C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 Processing helix chain 'C' and resid 918 through 922 removed outlier: 3.513A pdb=" N SER C 921 " --> pdb=" O ILE C 918 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG C 922 " --> pdb=" O ARG C 919 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 918 through 922' 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: 3.507A pdb=" N LEU C1022 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS C1029 " --> pdb=" O GLU C1025 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR C1030 " --> pdb=" O LYS C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1045 Processing helix chain 'C' and resid 1066 through 1076 Processing helix chain 'C' and resid 1080 through 1085 Processing helix chain 'C' and resid 1086 through 1105 removed outlier: 3.711A 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 625 Processing sheet with id=AA3, first strand: chain 'C' and resid 623 through 625 Processing sheet with id=AA4, first strand: chain 'C' and resid 614 through 615 Processing sheet with id=AA5, first strand: chain 'C' and resid 686 through 687 removed outlier: 3.644A pdb=" N LYS C 690 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 851 through 852 Processing sheet with id=AA7, first strand: chain 'C' and resid 981 through 982 removed outlier: 6.894A pdb=" N GLY C1005 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR C1055 " --> pdb=" O GLY C1005 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE C1007 " --> pdb=" O THR C1055 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS C1057 " --> pdb=" O ILE C1007 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP C1009 " --> pdb=" O CYS C1057 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE C1059 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN C1011 " --> pdb=" O ILE C1059 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 116 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2312 1.33 - 1.45: 3196 1.45 - 1.57: 4946 1.57 - 1.69: 356 1.69 - 1.81: 47 Bond restraints: 10857 Sorted by residual: bond pdb=" CG PRO C 822 " pdb=" CD PRO C 822 " ideal model delta sigma weight residual 1.503 1.571 -0.068 3.40e-02 8.65e+02 4.02e+00 bond pdb=" C3' A E 179 " pdb=" O3' A E 179 " ideal model delta sigma weight residual 1.415 1.446 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C3' A E 181 " pdb=" O3' A E 181 " ideal model delta sigma weight residual 1.415 1.444 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C SER C 821 " pdb=" N PRO C 822 " ideal model delta sigma weight residual 1.331 1.343 -0.011 7.90e-03 1.60e+04 2.03e+00 bond pdb=" C3' U E 114 " pdb=" O3' U E 114 " ideal model delta sigma weight residual 1.415 1.442 -0.027 2.00e-02 2.50e+03 1.80e+00 ... (remaining 10852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 14926 2.26 - 4.52: 557 4.52 - 6.78: 68 6.78 - 9.04: 3 9.04 - 11.30: 1 Bond angle restraints: 15555 Sorted by residual: angle pdb=" C3' U E 114 " pdb=" O3' U E 114 " pdb=" P A E 115 " ideal model delta sigma weight residual 119.70 125.61 -5.91 1.20e+00 6.94e-01 2.43e+01 angle pdb=" C3' A E 179 " pdb=" O3' A E 179 " pdb=" P A E 180 " ideal model delta sigma weight residual 119.70 125.38 -5.68 1.20e+00 6.94e-01 2.24e+01 angle pdb=" C3' U E 131 " pdb=" O3' U E 131 " pdb=" P G E 132 " ideal model delta sigma weight residual 119.70 124.44 -4.74 1.20e+00 6.94e-01 1.56e+01 angle pdb=" C3' A E 181 " pdb=" O3' A E 181 " pdb=" P A E 182 " ideal model delta sigma weight residual 119.70 124.37 -4.67 1.20e+00 6.94e-01 1.52e+01 angle pdb=" C3' U E 133 " pdb=" O3' U E 133 " pdb=" P G E 134 " ideal model delta sigma weight residual 119.70 124.03 -4.33 1.20e+00 6.94e-01 1.30e+01 ... (remaining 15550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 5582 35.58 - 71.17: 526 71.17 - 106.75: 32 106.75 - 142.33: 1 142.33 - 177.91: 5 Dihedral angle restraints: 6146 sinusoidal: 3805 harmonic: 2341 Sorted by residual: 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 -38.59 74.93 1 3.10e+00 1.04e-01 7.39e+02 dihedral pdb=" C4' C E 156 " pdb=" C3' C E 156 " pdb=" C2' C E 156 " pdb=" C1' C E 156 " ideal model delta sinusoidal sigma weight residual 36.34 -38.19 74.54 1 3.10e+00 1.04e-01 7.33e+02 dihedral pdb=" C4' C E 130 " pdb=" C3' C E 130 " pdb=" C2' C E 130 " pdb=" C1' C E 130 " ideal model delta sinusoidal sigma weight residual 36.34 -38.13 74.47 1 3.10e+00 1.04e-01 7.32e+02 ... (remaining 6143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1548 0.081 - 0.161: 98 0.161 - 0.242: 161 0.242 - 0.322: 65 0.322 - 0.403: 6 Chirality restraints: 1878 Sorted by residual: 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 -2.58 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" P G E 134 " pdb=" OP1 G E 134 " pdb=" OP2 G E 134 " pdb=" O5' G E 134 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.89e+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 -2.83 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 1875 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 701 " 0.021 2.00e-02 2.50e+03 1.84e-02 8.46e+00 pdb=" CG TRP C 701 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 701 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 701 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 701 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 701 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 701 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 701 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 701 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 701 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 78 " -0.032 2.00e-02 2.50e+03 1.67e-02 6.30e+00 pdb=" N1 C E 78 " 0.035 2.00e-02 2.50e+03 pdb=" C2 C E 78 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C E 78 " 0.006 2.00e-02 2.50e+03 pdb=" N3 C E 78 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C E 78 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C E 78 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C E 78 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C E 78 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 117 " -0.006 2.00e-02 2.50e+03 1.58e-02 5.62e+00 pdb=" N1 C E 117 " 0.003 2.00e-02 2.50e+03 pdb=" C2 C E 117 " 0.039 2.00e-02 2.50e+03 pdb=" O2 C E 117 " -0.021 2.00e-02 2.50e+03 pdb=" N3 C E 117 " -0.006 2.00e-02 2.50e+03 pdb=" C4 C E 117 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C E 117 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C E 117 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C E 117 " -0.006 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 932 2.73 - 3.27: 9727 3.27 - 3.82: 18691 3.82 - 4.36: 21932 4.36 - 4.90: 33764 Nonbonded interactions: 85046 Sorted by model distance: nonbonded pdb=" O ALA C1091 " pdb=" OG SER C1095 " model vdw 2.190 3.040 nonbonded pdb=" O2 U E 109 " pdb=" O2' G E 110 " model vdw 2.193 3.040 nonbonded pdb=" O2' U E 131 " pdb=" OP1 G E 132 " model vdw 2.214 3.040 nonbonded pdb=" O2' A E 79 " pdb=" O4' A E 80 " model vdw 2.248 3.040 nonbonded pdb=" O LEU C 878 " pdb=" OG SER C 881 " model vdw 2.254 3.040 ... (remaining 85041 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.560 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 0.068 10861 Z= 0.167 Angle : 0.824 11.303 15558 Z= 0.360 Chirality : 0.093 0.403 1878 Planarity : 0.005 0.055 1322 Dihedral : 21.924 177.913 4634 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 0.29 % Allowed : 23.75 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.31), residues: 811 helix: 1.83 (0.27), residues: 390 sheet: -0.13 (0.66), residues: 62 loop : -1.02 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 748 TYR 0.012 0.002 TYR C 703 PHE 0.015 0.002 PHE C 753 TRP 0.050 0.002 TRP C 701 HIS 0.005 0.001 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (10857) covalent geometry : angle 0.82371 / 0.36 (15555) hydrogen bonds : bond 0.14567 / 9.69 ( 431) hydrogen bonds : angle 5.30120 / 3.82 ( 1144) metal coordination : bond 0.00247 / 0.12 ( 4) metal coordination : angle 1.24801 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.281 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.1317 time to fit residues: 10.5640 Evaluate side-chains 54 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1021 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 0.0040 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 653 GLN C 769 GLN ** C 946 HIS ** 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 = 0.4488 r_free = 0.4488 target = 0.186063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.140968 restraints weight = 15743.037| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.48 r_work: 0.3497 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10861 Z= 0.193 Angle : 1.254 18.227 15558 Z= 0.493 Chirality : 0.115 1.463 1878 Planarity : 0.005 0.063 1322 Dihedral : 19.690 176.192 3069 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 2.51 % Allowed : 23.60 % Favored : 73.89 % 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: 0.86 (0.31), residues: 811 helix: 2.06 (0.27), residues: 396 sheet: 0.51 (0.71), residues: 56 loop : -1.19 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 901 TYR 0.010 0.001 TYR C 703 PHE 0.012 0.001 PHE C 749 TRP 0.018 0.001 TRP C 701 HIS 0.004 0.001 HIS C1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (10857) covalent geometry : angle 1.25363 / 0.49 (15555) hydrogen bonds : bond 0.06105 / 3.64 ( 431) hydrogen bonds : angle 3.69551 / 2.68 ( 1144) metal coordination : bond 0.01135 / 0.57 ( 4) metal coordination : angle 1.50922 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.315 Fit side-chains REVERT: C 401 PHE cc_start: 0.7342 (t80) cc_final: 0.7097 (t80) REVERT: C 704 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6549 (pp) REVERT: C 814 ARG cc_start: 0.7353 (ttt180) cc_final: 0.6752 (ttt180) REVERT: C 1072 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: C 1105 MET cc_start: 0.7434 (ppp) cc_final: 0.6803 (ppp) outliers start: 17 outliers final: 9 residues processed: 76 average time/residue: 0.1189 time to fit residues: 12.4592 Evaluate side-chains 66 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 493 GLN C 870 HIS ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.179723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.135138 restraints weight = 15805.327| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.93 r_work: 0.3347 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 10861 Z= 0.288 Angle : 1.116 15.621 15558 Z= 0.461 Chirality : 0.087 1.244 1878 Planarity : 0.006 0.069 1322 Dihedral : 19.488 172.716 3066 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.41 % Favored : 93.46 % Rotamer: Outliers : 5.60 % Allowed : 21.68 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.07 (0.30), residues: 811 helix: 1.29 (0.26), residues: 405 sheet: -0.03 (0.67), residues: 57 loop : -1.46 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 584 TYR 0.021 0.003 TYR C 703 PHE 0.024 0.003 PHE C 749 TRP 0.038 0.002 TRP C 701 HIS 0.006 0.002 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.29 (10857) covalent geometry : angle 1.11500 / 0.46 (15555) hydrogen bonds : bond 0.06114 / 4.20 ( 431) hydrogen bonds : angle 4.03812 / 2.90 ( 1144) metal coordination : bond 0.00923 / 0.46 ( 4) metal coordination : angle 3.48843 / 1.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 57 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: C 337 CYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6274 (m) REVERT: C 548 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7662 (tp) REVERT: C 776 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: C 814 ARG cc_start: 0.7625 (ttt180) cc_final: 0.7117 (ttt180) REVERT: C 883 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7503 (ptm160) REVERT: C 987 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.3808 (mmp-170) REVERT: C 1072 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: C 1105 MET cc_start: 0.7608 (ppp) cc_final: 0.6943 (ppp) outliers start: 38 outliers final: 20 residues processed: 87 average time/residue: 0.1093 time to fit residues: 13.3960 Evaluate side-chains 80 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 987 ARG Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.183691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.139901 restraints weight = 15827.189| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.68 r_work: 0.3442 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10861 Z= 0.148 Angle : 0.920 12.665 15558 Z= 0.374 Chirality : 0.072 0.665 1878 Planarity : 0.005 0.064 1322 Dihedral : 19.312 175.663 3066 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.21 % Favored : 96.67 % Rotamer: Outliers : 3.69 % Allowed : 24.04 % Favored : 72.27 % 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: 0.55 (0.31), residues: 811 helix: 1.75 (0.27), residues: 407 sheet: -0.01 (0.68), residues: 56 loop : -1.30 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 307 TYR 0.017 0.002 TYR C 703 PHE 0.015 0.002 PHE C 749 TRP 0.024 0.001 TRP C 701 HIS 0.004 0.001 HIS C1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (10857) covalent geometry : angle 0.91971 / 0.37 (15555) hydrogen bonds : bond 0.04856 / 3.26 ( 431) hydrogen bonds : angle 3.56606 / 2.59 ( 1144) metal coordination : bond 0.00667 / 0.33 ( 4) metal coordination : angle 1.52899 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 410 ASP cc_start: 0.6540 (OUTLIER) cc_final: 0.5804 (p0) REVERT: C 883 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7322 (ptm160) REVERT: C 950 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7244 (pp30) REVERT: C 1026 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7865 (mmmt) REVERT: C 1072 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: C 1105 MET cc_start: 0.7592 (ppp) cc_final: 0.6987 (ppp) outliers start: 25 outliers final: 12 residues processed: 78 average time/residue: 0.1129 time to fit residues: 12.4806 Evaluate side-chains 68 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 950 GLN Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.180951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.135140 restraints weight = 15832.768| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.00 r_work: 0.3367 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10861 Z= 0.218 Angle : 0.952 11.710 15558 Z= 0.392 Chirality : 0.073 0.681 1878 Planarity : 0.005 0.067 1322 Dihedral : 19.150 178.419 3066 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.41 % Favored : 93.46 % Rotamer: Outliers : 5.46 % Allowed : 22.86 % Favored : 71.68 % 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: 811 helix: 1.53 (0.27), residues: 409 sheet: -0.20 (0.66), residues: 56 loop : -1.38 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 549 TYR 0.028 0.003 TYR C 703 PHE 0.021 0.002 PHE C 749 TRP 0.031 0.002 TRP C 701 HIS 0.004 0.001 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 (10857) covalent geometry : angle 0.95188 / 0.39 (15555) hydrogen bonds : bond 0.05332 / 3.58 ( 431) hydrogen bonds : angle 3.71151 / 2.68 ( 1144) metal coordination : bond 0.00762 / 0.38 ( 4) metal coordination : angle 2.55024 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 55 time to evaluate : 0.289 Fit side-chains REVERT: C 337 CYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6362 (m) REVERT: C 410 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6101 (p0) REVERT: C 435 ARG cc_start: 0.7051 (ttp-170) cc_final: 0.6728 (ttp-170) REVERT: C 758 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6634 (tp) REVERT: C 776 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: C 883 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7370 (ptm160) REVERT: C 950 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7353 (pp30) REVERT: C 1026 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7886 (mmmt) REVERT: C 1072 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: C 1105 MET cc_start: 0.7673 (ppp) cc_final: 0.7192 (ppp) outliers start: 37 outliers final: 23 residues processed: 85 average time/residue: 0.1098 time to fit residues: 13.1224 Evaluate side-chains 85 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 950 GLN Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1083 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.0060 chunk 57 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.183806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.139612 restraints weight = 15910.468| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.70 r_work: 0.3443 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10861 Z= 0.136 Angle : 0.868 11.566 15558 Z= 0.354 Chirality : 0.068 0.635 1878 Planarity : 0.005 0.060 1322 Dihedral : 19.119 178.560 3066 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.58 % Favored : 96.30 % Rotamer: Outliers : 4.72 % Allowed : 23.45 % Favored : 71.83 % 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: 0.61 (0.31), residues: 811 helix: 1.82 (0.27), residues: 408 sheet: -0.11 (0.66), residues: 56 loop : -1.29 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 748 TYR 0.026 0.002 TYR C 703 PHE 0.015 0.002 PHE C 749 TRP 0.024 0.001 TRP C 701 HIS 0.003 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (10857) covalent geometry : angle 0.86740 / 0.35 (15555) hydrogen bonds : bond 0.04769 / 3.20 ( 431) hydrogen bonds : angle 3.46874 / 2.52 ( 1144) metal coordination : bond 0.00684 / 0.34 ( 4) metal coordination : angle 1.39418 / 0.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.313 Fit side-chains REVERT: C 435 ARG cc_start: 0.6970 (ttp-170) cc_final: 0.6635 (ttp-170) REVERT: C 551 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6975 (mtt) REVERT: C 758 ILE cc_start: 0.6341 (OUTLIER) cc_final: 0.6101 (tt) REVERT: C 776 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: C 814 ARG cc_start: 0.7476 (ttt180) cc_final: 0.7144 (ttt180) REVERT: C 883 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7300 (ptm160) REVERT: C 950 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7290 (pp30) REVERT: C 1026 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7895 (mmmt) REVERT: C 1072 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: C 1105 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7103 (ppp) outliers start: 32 outliers final: 17 residues processed: 84 average time/residue: 0.1033 time to fit residues: 12.5798 Evaluate side-chains 80 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 950 GLN Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1105 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.181024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136187 restraints weight = 15642.258| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.70 r_work: 0.3381 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10861 Z= 0.220 Angle : 0.927 11.138 15558 Z= 0.384 Chirality : 0.070 0.628 1878 Planarity : 0.005 0.060 1322 Dihedral : 19.105 175.426 3066 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.92 % Favored : 93.96 % Rotamer: Outliers : 5.16 % Allowed : 22.57 % Favored : 72.27 % 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 (0.30), residues: 811 helix: 1.58 (0.27), residues: 408 sheet: -0.28 (0.67), residues: 56 loop : -1.40 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1062 TYR 0.025 0.002 TYR C 703 PHE 0.020 0.002 PHE C 749 TRP 0.029 0.002 TRP C 701 HIS 0.004 0.001 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (10857) covalent geometry : angle 0.92616 / 0.38 (15555) hydrogen bonds : bond 0.05326 / 3.58 ( 431) hydrogen bonds : angle 3.68769 / 2.67 ( 1144) metal coordination : bond 0.00555 / 0.27 ( 4) metal coordination : angle 2.52109 / 1.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: C 337 CYS cc_start: 0.6746 (OUTLIER) cc_final: 0.6374 (m) REVERT: C 410 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6062 (p0) REVERT: C 435 ARG cc_start: 0.7126 (ttp-170) cc_final: 0.6747 (ttp-170) REVERT: C 551 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7002 (mtt) REVERT: C 704 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6990 (pp) REVERT: C 758 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6663 (tp) REVERT: C 776 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: C 883 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7411 (ptm160) REVERT: C 950 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7348 (pp30) REVERT: C 1026 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7887 (mmmt) REVERT: C 1072 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: C 1105 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7102 (ppp) outliers start: 35 outliers final: 19 residues processed: 85 average time/residue: 0.1011 time to fit residues: 12.2670 Evaluate side-chains 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 950 GLN Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1083 THR Chi-restraints excluded: chain C residue 1105 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 41 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.181966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.137138 restraints weight = 15628.535| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.70 r_work: 0.3402 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10861 Z= 0.178 Angle : 0.881 11.994 15558 Z= 0.364 Chirality : 0.067 0.604 1878 Planarity : 0.005 0.058 1322 Dihedral : 19.006 177.300 3066 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.44 % Favored : 95.44 % Rotamer: Outliers : 4.87 % Allowed : 23.60 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.30), residues: 811 helix: 1.72 (0.27), residues: 407 sheet: -0.20 (0.67), residues: 56 loop : -1.41 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 748 TYR 0.023 0.002 TYR C 703 PHE 0.019 0.002 PHE C 749 TRP 0.027 0.002 TRP C 701 HIS 0.004 0.001 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (10857) covalent geometry : angle 0.88103 / 0.36 (15555) hydrogen bonds : bond 0.05032 / 3.38 ( 431) hydrogen bonds : angle 3.57347 / 2.60 ( 1144) metal coordination : bond 0.00614 / 0.31 ( 4) metal coordination : angle 2.05441 / 1.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.298 Fit side-chains REVERT: C 337 CYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6639 (m) REVERT: C 435 ARG cc_start: 0.7097 (ttp-170) cc_final: 0.6746 (ttp-170) REVERT: C 551 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.7003 (mtt) REVERT: C 704 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6652 (pp) REVERT: C 758 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6458 (tp) REVERT: C 776 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: C 883 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7367 (ptm160) REVERT: C 950 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7337 (pp30) REVERT: C 1026 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7943 (mmmm) REVERT: C 1072 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: C 1105 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7034 (ppp) outliers start: 33 outliers final: 21 residues processed: 82 average time/residue: 0.1136 time to fit residues: 13.0741 Evaluate side-chains 83 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 950 GLN Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1083 THR Chi-restraints excluded: chain C residue 1105 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.185156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.141814 restraints weight = 15595.403| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.62 r_work: 0.3490 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10861 Z= 0.131 Angle : 0.824 10.491 15558 Z= 0.339 Chirality : 0.064 0.558 1878 Planarity : 0.004 0.056 1322 Dihedral : 18.826 178.933 3066 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 4.87 % Allowed : 23.45 % Favored : 71.68 % 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: 0.74 (0.31), residues: 811 helix: 1.98 (0.27), residues: 406 sheet: 0.01 (0.67), residues: 56 loop : -1.29 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 748 TYR 0.019 0.001 TYR C 703 PHE 0.015 0.002 PHE C 749 TRP 0.023 0.001 TRP C 701 HIS 0.004 0.001 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10857) covalent geometry : angle 0.82419 / 0.34 (15555) hydrogen bonds : bond 0.04780 / 3.22 ( 431) hydrogen bonds : angle 3.38587 / 2.47 ( 1144) metal coordination : bond 0.00861 / 0.43 ( 4) metal coordination : angle 1.43751 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: C 704 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6104 (pp) REVERT: C 758 ILE cc_start: 0.6177 (OUTLIER) cc_final: 0.5928 (tt) REVERT: C 767 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: C 776 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: C 868 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.8289 (m-70) REVERT: C 883 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7253 (ptm160) REVERT: C 950 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7282 (pp30) REVERT: C 1080 ARG cc_start: 0.7444 (mpp-170) cc_final: 0.7113 (mtt180) REVERT: C 1105 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7017 (ppp) outliers start: 33 outliers final: 20 residues processed: 82 average time/residue: 0.1008 time to fit residues: 12.0023 Evaluate side-chains 83 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 767 ASP Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 950 GLN Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1083 THR Chi-restraints excluded: chain C residue 1105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.185871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.141792 restraints weight = 15629.051| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.61 r_work: 0.3487 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10861 Z= 0.128 Angle : 0.823 12.384 15558 Z= 0.338 Chirality : 0.063 0.522 1878 Planarity : 0.004 0.056 1322 Dihedral : 18.750 179.629 3066 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.45 % Favored : 96.42 % Rotamer: Outliers : 3.98 % Allowed : 24.19 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.31), residues: 811 helix: 2.05 (0.27), residues: 408 sheet: 0.01 (0.67), residues: 56 loop : -1.31 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 748 TYR 0.021 0.001 TYR C 703 PHE 0.014 0.001 PHE C 749 TRP 0.024 0.001 TRP C 701 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10857) covalent geometry : angle 0.82283 / 0.34 (15555) hydrogen bonds : bond 0.04737 / 3.20 ( 431) hydrogen bonds : angle 3.32972 / 2.42 ( 1144) metal coordination : bond 0.00948 / 0.47 ( 4) metal coordination : angle 1.62578 / 0.88 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: C 704 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6201 (pp) REVERT: C 711 SER cc_start: 0.6452 (p) cc_final: 0.6139 (t) REVERT: C 758 ILE cc_start: 0.6410 (OUTLIER) cc_final: 0.6132 (tt) REVERT: C 767 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: C 776 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: C 950 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7286 (pp30) REVERT: C 1080 ARG cc_start: 0.7426 (mpp-170) cc_final: 0.7103 (mtt180) REVERT: C 1105 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6986 (ppp) outliers start: 27 outliers final: 20 residues processed: 78 average time/residue: 0.0970 time to fit residues: 11.1178 Evaluate side-chains 81 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 767 ASP Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 950 GLN Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1083 THR Chi-restraints excluded: chain C residue 1105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.0050 chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.184172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.137301 restraints weight = 15707.372| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.54 r_work: 0.3457 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10861 Z= 0.162 Angle : 0.839 10.540 15558 Z= 0.347 Chirality : 0.064 0.494 1878 Planarity : 0.005 0.056 1322 Dihedral : 18.766 179.896 3066 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.81 % Favored : 95.07 % Rotamer: Outliers : 3.98 % Allowed : 23.89 % Favored : 72.12 % 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: 0.68 (0.31), residues: 811 helix: 1.97 (0.27), residues: 407 sheet: -0.12 (0.66), residues: 56 loop : -1.37 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 748 TYR 0.024 0.002 TYR C 703 PHE 0.017 0.002 PHE C 749 TRP 0.027 0.001 TRP C 701 HIS 0.004 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (10857) covalent geometry : angle 0.83897 / 0.35 (15555) hydrogen bonds : bond 0.04914 / 3.32 ( 431) hydrogen bonds : angle 3.44377 / 2.50 ( 1144) metal coordination : bond 0.00604 / 0.30 ( 4) metal coordination : angle 1.99572 / 1.08 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3011.45 seconds wall clock time: 52 minutes 13.25 seconds (3133.25 seconds total)