Starting phenix.real_space_refine on Mon Jul 28 14:47:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibz_35350/07_2025/8ibz_35350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibz_35350/07_2025/8ibz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ibz_35350/07_2025/8ibz_35350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibz_35350/07_2025/8ibz_35350.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibz_35350/07_2025/8ibz_35350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibz_35350/07_2025/8ibz_35350.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 3853 Classifications: {'RNA': 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: 6.74, per 1000 atoms: 0.66 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: 2.66 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 4.10 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: 5.29 Time building geometry restraints manager: 3.18 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=" 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' A E 179 " pdb=" O3' A E 179 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.50e-02 4.44e+03 1.58e+00 bond pdb=" CB GLU C 975 " pdb=" CG GLU C 975 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" C3' A E 181 " pdb=" O3' A E 181 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.23e+00 ... (remaining 10852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 15354 2.26 - 4.52: 171 4.52 - 6.78: 26 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 120.20 125.61 -5.41 1.50e+00 4.44e-01 1.30e+01 angle pdb=" C3' A E 179 " pdb=" O3' A E 179 " pdb=" P A E 180 " ideal model delta sigma weight residual 120.20 125.38 -5.18 1.50e+00 4.44e-01 1.19e+01 angle pdb=" CA PRO C 822 " pdb=" N PRO C 822 " pdb=" CD PRO C 822 " ideal model delta sigma weight residual 112.00 107.33 4.67 1.40e+00 5.10e-01 1.11e+01 angle pdb=" CA LEU C 755 " pdb=" CB LEU C 755 " pdb=" CG LEU C 755 " ideal model delta sigma weight residual 116.30 127.60 -11.30 3.50e+00 8.16e-02 1.04e+01 angle pdb=" O3' C E 186 " pdb=" C3' C E 186 " pdb=" C2' C E 186 " ideal model delta sigma weight residual 109.50 114.08 -4.58 1.50e+00 4.44e-01 9.33e+00 ... (remaining 15550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 6113 35.58 - 71.17: 606 71.17 - 106.75: 72 106.75 - 142.33: 4 142.33 - 177.91: 5 Dihedral angle restraints: 6800 sinusoidal: 4459 harmonic: 2341 Sorted by residual: dihedral pdb=" C4' C E 186 " pdb=" C3' C E 186 " pdb=" C2' C E 186 " pdb=" C1' C E 186 " ideal model delta sinusoidal sigma weight residual -35.00 35.06 -70.06 1 8.00e+00 1.56e-02 9.88e+01 dihedral pdb=" C5' C E 186 " pdb=" C4' C E 186 " pdb=" C3' C E 186 " pdb=" O3' C E 186 " ideal model delta sinusoidal sigma weight residual 147.00 80.84 66.16 1 8.00e+00 1.56e-02 8.94e+01 dihedral pdb=" O4' C E 186 " pdb=" C4' C E 186 " pdb=" C3' C E 186 " pdb=" C2' C E 186 " ideal model delta sinusoidal sigma weight residual 24.00 -34.97 58.97 1 8.00e+00 1.56e-02 7.27e+01 ... (remaining 6797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1676 0.060 - 0.121: 183 0.121 - 0.181: 15 0.181 - 0.241: 3 0.241 - 0.302: 1 Chirality restraints: 1878 Sorted by residual: chirality pdb=" C3' C E 186 " pdb=" C4' C E 186 " pdb=" O3' C E 186 " pdb=" C2' C E 186 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C2' C E 186 " pdb=" C3' C E 186 " pdb=" O2' C E 186 " pdb=" C1' C E 186 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C1' C E 78 " pdb=" O4' C E 78 " pdb=" C2' C E 78 " pdb=" N1 C E 78 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.04e+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: 0.820 Set stop_for_unknowns flag: 0.010 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 33.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 0.068 10861 Z= 0.152 Angle : 0.603 11.303 15558 Z= 0.308 Chirality : 0.038 0.302 1878 Planarity : 0.005 0.055 1322 Dihedral : 23.457 177.913 5288 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.050 0.002 TRP C 701 HIS 0.005 0.001 HIS C 868 PHE 0.015 0.002 PHE C 753 TYR 0.012 0.002 TYR C 703 ARG 0.006 0.000 ARG C 748 Details of bonding type rmsd hydrogen bonds : bond 0.14567 ( 431) hydrogen bonds : angle 5.30120 ( 1144) metal coordination : bond 0.00247 ( 4) metal coordination : angle 1.24801 ( 3) covalent geometry : bond 0.00335 (10857) covalent geometry : angle 0.60257 (15555) *********************** 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 : 0.911 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.3053 time to fit residues: 24.7556 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 : 0.831 ------------------------------------------------------------------------------- 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 83 optimal weight: 20.0000 chunk 75 optimal weight: 0.0050 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4464 r_free = 0.4464 target = 0.183741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.140409 restraints weight = 15750.762| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.85 r_work: 0.3426 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10861 Z= 0.152 Angle : 0.622 8.954 15558 Z= 0.309 Chirality : 0.038 0.217 1878 Planarity : 0.005 0.066 1322 Dihedral : 24.122 171.218 3723 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 3.24 % Allowed : 23.30 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.31), residues: 811 helix: 1.82 (0.27), residues: 402 sheet: 0.42 (0.69), residues: 57 loop : -1.25 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 701 HIS 0.004 0.001 HIS C 677 PHE 0.017 0.002 PHE C 749 TYR 0.011 0.002 TYR C 703 ARG 0.005 0.000 ARG C 814 Details of bonding type rmsd hydrogen bonds : bond 0.06366 ( 431) hydrogen bonds : angle 3.75232 ( 1144) metal coordination : bond 0.01255 ( 4) metal coordination : angle 2.14492 ( 3) covalent geometry : bond 0.00327 (10857) covalent geometry : angle 0.62111 (15555) *********************** 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 81 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: C 410 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.5586 (p0) REVERT: C 1072 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: C 1105 MET cc_start: 0.7510 (ppp) cc_final: 0.6843 (ppp) outliers start: 22 outliers final: 11 residues processed: 77 average time/residue: 0.2306 time to fit residues: 25.1279 Evaluate side-chains 70 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 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 45 optimal weight: 0.3980 chunk 59 optimal weight: 0.0020 chunk 95 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4468 r_free = 0.4468 target = 0.184203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.138255 restraints weight = 15984.444| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.00 r_work: 0.3429 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1133 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= 0.130 Angle : 0.575 8.778 15558 Z= 0.287 Chirality : 0.037 0.210 1878 Planarity : 0.004 0.066 1322 Dihedral : 23.909 170.725 3720 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.95 % Favored : 95.93 % Rotamer: Outliers : 3.69 % Allowed : 23.16 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.31), residues: 811 helix: 1.97 (0.27), residues: 399 sheet: 0.12 (0.69), residues: 56 loop : -1.30 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 701 HIS 0.004 0.001 HIS C 423 PHE 0.015 0.002 PHE C 749 TYR 0.026 0.002 TYR C 703 ARG 0.004 0.000 ARG C 748 Details of bonding type rmsd hydrogen bonds : bond 0.05193 ( 431) hydrogen bonds : angle 3.51614 ( 1144) metal coordination : bond 0.00647 ( 4) metal coordination : angle 1.51070 ( 3) covalent geometry : bond 0.00283 (10857) covalent geometry : angle 0.57429 (15555) *********************** 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 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.781 Fit side-chains REVERT: C 551 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6965 (mtt) REVERT: C 883 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7308 (ptm160) REVERT: C 1072 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: C 1105 MET cc_start: 0.7560 (ppp) cc_final: 0.6781 (ppp) outliers start: 25 outliers final: 14 residues processed: 82 average time/residue: 0.2659 time to fit residues: 30.3040 Evaluate side-chains 73 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 551 MET 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 711 SER Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1046 LEU 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 72 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4471 r_free = 0.4471 target = 0.184634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.140883 restraints weight = 15746.614| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.84 r_work: 0.3444 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1387 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= 0.120 Angle : 0.553 8.692 15558 Z= 0.277 Chirality : 0.036 0.206 1878 Planarity : 0.005 0.065 1322 Dihedral : 23.779 170.410 3720 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.70 % Favored : 96.18 % Rotamer: Outliers : 4.42 % Allowed : 22.71 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.31), residues: 811 helix: 1.92 (0.27), residues: 407 sheet: 0.11 (0.69), residues: 56 loop : -1.26 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 701 HIS 0.003 0.001 HIS C 868 PHE 0.016 0.002 PHE C 749 TYR 0.015 0.002 TYR C 703 ARG 0.005 0.000 ARG C1053 Details of bonding type rmsd hydrogen bonds : bond 0.04893 ( 431) hydrogen bonds : angle 3.40924 ( 1144) metal coordination : bond 0.00720 ( 4) metal coordination : angle 1.47109 ( 3) covalent geometry : bond 0.00256 (10857) covalent geometry : angle 0.55267 (15555) *********************** 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 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.811 Fit side-chains REVERT: C 576 MET cc_start: 0.6634 (mmm) cc_final: 0.5922 (pmm) REVERT: C 776 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: C 883 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7296 (ptm160) REVERT: C 950 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7232 (pp30) REVERT: C 987 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.4122 (mmp-170) REVERT: C 1026 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7861 (mmmt) REVERT: C 1072 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: C 1105 MET cc_start: 0.7599 (ppp) cc_final: 0.7056 (ppp) outliers start: 30 outliers final: 16 residues processed: 80 average time/residue: 0.2536 time to fit residues: 28.1023 Evaluate side-chains 74 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 765 MET Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 784 VAL 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 960 LEU 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 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 9 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4480 r_free = 0.4480 target = 0.185574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.142321 restraints weight = 15770.424| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.92 r_work: 0.3459 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10861 Z= 0.110 Angle : 0.542 8.639 15558 Z= 0.270 Chirality : 0.035 0.194 1878 Planarity : 0.004 0.063 1322 Dihedral : 23.602 170.267 3720 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.95 % Favored : 95.93 % Rotamer: Outliers : 5.31 % Allowed : 22.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.31), residues: 811 helix: 2.01 (0.27), residues: 408 sheet: 0.18 (0.69), residues: 56 loop : -1.29 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 701 HIS 0.003 0.001 HIS C 423 PHE 0.027 0.002 PHE C 401 TYR 0.038 0.002 TYR C 703 ARG 0.004 0.000 ARG C 404 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 431) hydrogen bonds : angle 3.30662 ( 1144) metal coordination : bond 0.00650 ( 4) metal coordination : angle 1.13880 ( 3) covalent geometry : bond 0.00230 (10857) covalent geometry : angle 0.54159 (15555) *********************** 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 97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.895 Fit side-chains REVERT: C 401 PHE cc_start: 0.7318 (t80) cc_final: 0.6862 (t80) REVERT: C 551 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6974 (mtt) REVERT: C 576 MET cc_start: 0.6308 (mmm) cc_final: 0.5496 (pmm) REVERT: C 661 ARG cc_start: 0.8267 (mtt90) cc_final: 0.7343 (mtp85) REVERT: C 776 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: C 883 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7293 (ptm160) REVERT: C 950 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7228 (pp30) REVERT: C 1026 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7877 (mmmt) REVERT: C 1072 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: C 1080 ARG cc_start: 0.7661 (mpp-170) cc_final: 0.7446 (mtt180) REVERT: C 1105 MET cc_start: 0.7601 (ppp) cc_final: 0.7074 (ppp) outliers start: 36 outliers final: 22 residues processed: 91 average time/residue: 0.2867 time to fit residues: 35.7886 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 : 0.875 ------------------------------------------------------------------------------- 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 548 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 706 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 765 MET Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 784 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 30.0000 chunk 9 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 82 optimal weight: 40.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 870 HIS ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.178947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.134938 restraints weight = 15737.125| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 3.01 r_work: 0.3331 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 10861 Z= 0.308 Angle : 0.713 9.003 15558 Z= 0.359 Chirality : 0.044 0.204 1878 Planarity : 0.006 0.064 1322 Dihedral : 23.779 169.211 3720 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 5.75 % Allowed : 21.98 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.30), residues: 811 helix: 1.34 (0.26), residues: 406 sheet: -0.37 (0.66), residues: 56 loop : -1.50 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 701 HIS 0.007 0.002 HIS C 910 PHE 0.025 0.004 PHE C 749 TYR 0.028 0.004 TYR C 703 ARG 0.008 0.001 ARG C 814 Details of bonding type rmsd hydrogen bonds : bond 0.05852 ( 431) hydrogen bonds : angle 3.93942 ( 1144) metal coordination : bond 0.00706 ( 4) metal coordination : angle 3.61441 ( 3) covalent geometry : bond 0.00710 (10857) covalent geometry : angle 0.71095 (15555) *********************** 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 98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 59 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: C 337 CYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6349 (m) REVERT: C 410 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6594 (p0) REVERT: C 576 MET cc_start: 0.7148 (mmm) cc_final: 0.6583 (pmm) REVERT: C 758 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6869 (tp) REVERT: C 776 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: C 883 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7510 (ptm160) REVERT: C 950 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7322 (pp30) REVERT: C 1026 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7869 (mmmt) REVERT: C 1072 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: C 1105 MET cc_start: 0.7616 (ppp) cc_final: 0.7144 (ppp) outliers start: 39 outliers final: 26 residues processed: 87 average time/residue: 0.2741 time to fit residues: 32.8352 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 : 0.907 ------------------------------------------------------------------------------- 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 548 LEU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 654 MET 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 784 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 988 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 30.0000 chunk 77 optimal weight: 0.5980 chunk 8 optimal weight: 0.0030 chunk 96 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4460 r_free = 0.4460 target = 0.183537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.139752 restraints weight = 15883.823| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.79 r_work: 0.3425 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10861 Z= 0.113 Angle : 0.560 8.601 15558 Z= 0.281 Chirality : 0.036 0.195 1878 Planarity : 0.005 0.057 1322 Dihedral : 23.642 169.955 3720 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.33 % Favored : 96.55 % Rotamer: Outliers : 4.42 % Allowed : 23.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.31), residues: 811 helix: 1.86 (0.27), residues: 408 sheet: -0.17 (0.66), residues: 56 loop : -1.33 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 701 HIS 0.004 0.001 HIS C1096 PHE 0.018 0.002 PHE C 401 TYR 0.022 0.002 TYR C 703 ARG 0.008 0.000 ARG C 748 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 431) hydrogen bonds : angle 3.47537 ( 1144) metal coordination : bond 0.00666 ( 4) metal coordination : angle 1.27218 ( 3) covalent geometry : bond 0.00235 (10857) covalent geometry : angle 0.56008 (15555) *********************** 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 90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: C 551 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7019 (mtt) REVERT: C 576 MET cc_start: 0.6870 (mmm) cc_final: 0.6136 (pmm) REVERT: C 776 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: C 883 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7301 (ptm160) REVERT: C 950 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7267 (pp30) REVERT: C 1026 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7884 (mmmt) REVERT: C 1072 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: C 1105 MET cc_start: 0.7632 (ppp) cc_final: 0.7151 (ppp) outliers start: 30 outliers final: 18 residues processed: 83 average time/residue: 0.2545 time to fit residues: 29.7519 Evaluate side-chains 76 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 528 LEU Chi-restraints excluded: chain C residue 548 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 776 GLN Chi-restraints excluded: chain C residue 784 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 1046 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1083 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4442 r_free = 0.4442 target = 0.181849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.137804 restraints weight = 15711.292| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.79 r_work: 0.3388 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10861 Z= 0.164 Angle : 0.588 8.670 15558 Z= 0.295 Chirality : 0.037 0.192 1878 Planarity : 0.005 0.057 1322 Dihedral : 23.564 169.370 3720 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.33 % Rotamer: Outliers : 4.42 % Allowed : 23.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 811 helix: 1.79 (0.27), residues: 409 sheet: -0.16 (0.68), residues: 56 loop : -1.36 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 701 HIS 0.005 0.001 HIS C 423 PHE 0.018 0.002 PHE C 749 TYR 0.023 0.002 TYR C 703 ARG 0.009 0.000 ARG C 748 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 431) hydrogen bonds : angle 3.52784 ( 1144) metal coordination : bond 0.00640 ( 4) metal coordination : angle 2.06768 ( 3) covalent geometry : bond 0.00370 (10857) covalent geometry : angle 0.58735 (15555) *********************** 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 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: C 337 CYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6471 (m) REVERT: C 551 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6986 (mtt) REVERT: C 576 MET cc_start: 0.6937 (mmm) cc_final: 0.6253 (pmm) REVERT: C 704 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6736 (pp) REVERT: C 711 SER cc_start: 0.6382 (p) cc_final: 0.6062 (t) REVERT: C 776 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: C 883 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7402 (ptm160) REVERT: C 950 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7275 (pp30) REVERT: C 1026 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7873 (mmmt) REVERT: C 1053 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7901 (ttp-110) REVERT: C 1072 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: C 1105 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7102 (ppp) outliers start: 30 outliers final: 21 residues processed: 82 average time/residue: 0.2520 time to fit residues: 29.0122 Evaluate side-chains 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 548 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 776 GLN Chi-restraints excluded: chain C residue 784 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4485 r_free = 0.4485 target = 0.185872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.141434 restraints weight = 15843.205| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.65 r_work: 0.3479 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10861 Z= 0.098 Angle : 0.536 8.478 15558 Z= 0.268 Chirality : 0.035 0.197 1878 Planarity : 0.004 0.054 1322 Dihedral : 23.448 169.747 3720 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.84 % Favored : 97.04 % Rotamer: Outliers : 3.54 % Allowed : 24.48 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.31), residues: 811 helix: 2.11 (0.27), residues: 408 sheet: 0.02 (0.68), residues: 56 loop : -1.24 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 701 HIS 0.004 0.001 HIS C1096 PHE 0.017 0.001 PHE C 401 TYR 0.017 0.001 TYR C 703 ARG 0.006 0.000 ARG C 748 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 431) hydrogen bonds : angle 3.29085 ( 1144) metal coordination : bond 0.01084 ( 4) metal coordination : angle 1.06987 ( 3) covalent geometry : bond 0.00198 (10857) covalent geometry : angle 0.53588 (15555) *********************** 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 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: C 551 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6968 (mtt) REVERT: C 576 MET cc_start: 0.6716 (mmm) cc_final: 0.6002 (pmm) REVERT: C 661 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7406 (mtp180) REVERT: C 776 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: C 883 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7276 (ptm160) REVERT: C 950 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7279 (pp30) REVERT: C 1072 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: C 1080 ARG cc_start: 0.7466 (mpp-170) cc_final: 0.7157 (mtt180) REVERT: C 1105 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7173 (ppp) outliers start: 24 outliers final: 15 residues processed: 79 average time/residue: 0.4274 time to fit residues: 46.0140 Evaluate side-chains 76 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 548 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 776 GLN Chi-restraints excluded: chain C residue 784 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 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 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4473 r_free = 0.4473 target = 0.184690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138853 restraints weight = 15704.286| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.94 r_work: 0.3439 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10861 Z= 0.116 Angle : 0.542 8.552 15558 Z= 0.271 Chirality : 0.035 0.195 1878 Planarity : 0.004 0.055 1322 Dihedral : 23.384 169.344 3720 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 3.54 % Allowed : 24.48 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.31), residues: 811 helix: 2.11 (0.27), residues: 408 sheet: 0.05 (0.67), residues: 56 loop : -1.26 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 701 HIS 0.005 0.001 HIS C 423 PHE 0.017 0.002 PHE C 401 TYR 0.020 0.001 TYR C 703 ARG 0.009 0.000 ARG C1053 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 431) hydrogen bonds : angle 3.32389 ( 1144) metal coordination : bond 0.00849 ( 4) metal coordination : angle 1.57275 ( 3) covalent geometry : bond 0.00254 (10857) covalent geometry : angle 0.54136 (15555) ********************** 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: 24 poor density : 58 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 551 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6978 (mtt) REVERT: C 576 MET cc_start: 0.6787 (mmm) cc_final: 0.6030 (pmm) REVERT: C 704 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6709 (pp) REVERT: C 711 SER cc_start: 0.6628 (p) cc_final: 0.6332 (t) REVERT: C 776 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: C 883 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7283 (ptm160) REVERT: C 950 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7289 (pp30) REVERT: C 1080 ARG cc_start: 0.7514 (mpp-170) cc_final: 0.7180 (mtt180) REVERT: C 1105 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7119 (ppp) outliers start: 24 outliers final: 17 residues processed: 75 average time/residue: 0.2754 time to fit residues: 29.5123 Evaluate side-chains 80 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 548 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 776 GLN Chi-restraints excluded: chain C residue 784 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 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 38 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 56 optimal weight: 0.0570 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 82 optimal weight: 40.0000 chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.183526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.139932 restraints weight = 15475.436| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.70 r_work: 0.3429 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10861 Z= 0.134 Angle : 0.557 8.523 15558 Z= 0.279 Chirality : 0.036 0.194 1878 Planarity : 0.004 0.056 1322 Dihedral : 23.383 169.226 3720 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.70 % Favored : 96.18 % Rotamer: Outliers : 3.83 % Allowed : 24.19 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.31), residues: 811 helix: 2.05 (0.27), residues: 409 sheet: -0.11 (0.66), residues: 56 loop : -1.30 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 701 HIS 0.004 0.001 HIS C 910 PHE 0.017 0.002 PHE C 401 TYR 0.020 0.002 TYR C 703 ARG 0.009 0.000 ARG C1053 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 431) hydrogen bonds : angle 3.37943 ( 1144) metal coordination : bond 0.00658 ( 4) metal coordination : angle 1.78712 ( 3) covalent geometry : bond 0.00301 (10857) covalent geometry : angle 0.55683 (15555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6404.35 seconds wall clock time: 112 minutes 8.36 seconds (6728.36 seconds total)