Starting phenix.real_space_refine on Sat Dec 9 06:00:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/12_2023/8ibz_35350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/12_2023/8ibz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/12_2023/8ibz_35350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/12_2023/8ibz_35350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/12_2023/8ibz_35350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/12_2023/8ibz_35350.pdb" } 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 Residue "C GLU 345": "OE1" <-> "OE2" Residue "C ASP 402": "OD1" <-> "OD2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 564": "OD1" <-> "OD2" Residue "C ASP 602": "OD1" <-> "OD2" Residue "C GLU 709": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 809": "OD1" <-> "OD2" Residue "C ASP 853": "OD1" <-> "OD2" Residue "C GLU 983": "OE1" <-> "OE2" Residue "C GLU 1050": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.94, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 4.98 Conformation dependent library (CDL) restraints added in 1.3 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: 4.01 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: 4.68 Time building geometry restraints manager: 5.29 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: 99.41 - 106.32: 1210 106.32 - 113.24: 6155 113.24 - 120.16: 3877 120.16 - 127.08: 3813 127.08 - 134.00: 500 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: 6036 35.58 - 71.17: 555 71.17 - 106.75: 72 106.75 - 142.33: 4 142.33 - 177.91: 5 Dihedral angle restraints: 6672 sinusoidal: 4331 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 6669 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 2.440 nonbonded pdb=" O2 U E 109 " pdb=" O2' G E 110 " model vdw 2.193 2.440 nonbonded pdb=" O2' U E 131 " pdb=" OP1 G E 132 " model vdw 2.214 2.440 nonbonded pdb=" O2' A E 79 " pdb=" O4' A E 80 " model vdw 2.248 2.440 nonbonded pdb=" O LEU C 878 " pdb=" OG SER C 881 " model vdw 2.254 2.440 ... (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 ========== 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: 0.590 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: 3.470 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 36.330 Find NCS groups from input model: 0.230 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- 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 10857 Z= 0.221 Angle : 0.603 11.303 15555 Z= 0.308 Chirality : 0.038 0.302 1878 Planarity : 0.005 0.055 1322 Dihedral : 23.019 177.913 5160 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.912 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.3087 time to fit residues: 24.6560 Evaluate side-chains 54 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1366 time to fit residues: 1.4105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0170 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 GLN ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10857 Z= 0.149 Angle : 0.576 8.834 15555 Z= 0.290 Chirality : 0.036 0.204 1878 Planarity : 0.004 0.063 1322 Dihedral : 23.721 177.293 3592 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.44 % Favored : 95.44 % Rotamer: Outliers : 2.65 % Allowed : 22.86 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.31), residues: 811 helix: 1.99 (0.27), residues: 399 sheet: 0.40 (0.70), residues: 56 loop : -1.18 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 701 HIS 0.003 0.001 HIS C 910 PHE 0.014 0.001 PHE C 749 TYR 0.010 0.001 TYR C 703 ARG 0.003 0.000 ARG C1027 *********************** 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 79 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.830 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 75 average time/residue: 0.2554 time to fit residues: 26.7119 Evaluate side-chains 66 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0980 time to fit residues: 2.6269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 0.0970 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 444 GLN C 493 GLN ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10857 Z= 0.245 Angle : 0.589 8.862 15555 Z= 0.295 Chirality : 0.038 0.193 1878 Planarity : 0.005 0.066 1322 Dihedral : 23.526 176.687 3592 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.33 % Rotamer: Outliers : 2.95 % Allowed : 23.30 % Favored : 73.75 % 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: 0.59 (0.31), residues: 811 helix: 1.70 (0.27), residues: 411 sheet: -0.07 (0.70), residues: 58 loop : -1.18 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 701 HIS 0.004 0.001 HIS C 868 PHE 0.018 0.002 PHE C 749 TYR 0.009 0.002 TYR C 563 ARG 0.009 0.000 ARG C 404 *********************** 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 78 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.880 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 74 average time/residue: 0.2765 time to fit residues: 28.3599 Evaluate side-chains 64 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1007 time to fit residues: 2.9234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 493 GLN ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10857 Z= 0.242 Angle : 0.587 8.749 15555 Z= 0.294 Chirality : 0.038 0.190 1878 Planarity : 0.005 0.065 1322 Dihedral : 23.468 176.378 3592 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.06 % Favored : 94.82 % Rotamer: Outliers : 2.65 % Allowed : 24.19 % 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: 0.51 (0.31), residues: 811 helix: 1.65 (0.27), residues: 413 sheet: -0.22 (0.70), residues: 58 loop : -1.23 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 701 HIS 0.004 0.001 HIS C 868 PHE 0.026 0.002 PHE C 401 TYR 0.026 0.002 TYR C 703 ARG 0.008 0.000 ARG C 987 *********************** 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 78 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.900 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 75 average time/residue: 0.2895 time to fit residues: 29.3368 Evaluate side-chains 69 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0986 time to fit residues: 3.1114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10857 Z= 0.182 Angle : 0.556 9.216 15555 Z= 0.278 Chirality : 0.036 0.190 1878 Planarity : 0.004 0.060 1322 Dihedral : 23.345 176.541 3592 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 2.36 % Allowed : 25.37 % 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: 0.70 (0.31), residues: 811 helix: 1.85 (0.27), residues: 412 sheet: -0.14 (0.70), residues: 58 loop : -1.20 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP C 701 HIS 0.003 0.001 HIS C 946 PHE 0.015 0.002 PHE C 401 TYR 0.036 0.002 TYR C 703 ARG 0.005 0.000 ARG C 748 *********************** 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 79 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.891 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 75 average time/residue: 0.2694 time to fit residues: 27.8838 Evaluate side-chains 61 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0950 time to fit residues: 2.0094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 444 GLN C 769 GLN ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10857 Z= 0.301 Angle : 0.614 8.983 15555 Z= 0.308 Chirality : 0.039 0.188 1878 Planarity : 0.005 0.059 1322 Dihedral : 23.332 176.048 3592 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.92 % Favored : 93.96 % Rotamer: Outliers : 1.92 % Allowed : 25.22 % 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: 0.38 (0.31), residues: 811 helix: 1.58 (0.27), residues: 413 sheet: -0.43 (0.69), residues: 58 loop : -1.33 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 701 HIS 0.004 0.001 HIS C 910 PHE 0.021 0.003 PHE C 749 TYR 0.026 0.002 TYR C 703 ARG 0.006 0.000 ARG C1053 *********************** 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 68 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 65 average time/residue: 0.2835 time to fit residues: 25.6935 Evaluate side-chains 63 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0974 time to fit residues: 2.6368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 59 optimal weight: 0.0060 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 776 GLN ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10857 Z= 0.178 Angle : 0.555 8.628 15555 Z= 0.276 Chirality : 0.036 0.191 1878 Planarity : 0.004 0.055 1322 Dihedral : 23.248 176.444 3592 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 0.59 % Allowed : 25.81 % Favored : 73.60 % 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: 0.60 (0.31), residues: 811 helix: 1.74 (0.27), residues: 418 sheet: -0.12 (0.68), residues: 56 loop : -1.27 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 701 HIS 0.004 0.001 HIS C 423 PHE 0.016 0.001 PHE C 749 TYR 0.025 0.002 TYR C 703 ARG 0.008 0.000 ARG C1053 *********************** 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 62 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.823 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 0.2827 time to fit residues: 23.9450 Evaluate side-chains 56 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1125 time to fit residues: 1.8940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 0.0670 chunk 18 optimal weight: 0.0470 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10857 Z= 0.132 Angle : 0.532 10.081 15555 Z= 0.262 Chirality : 0.034 0.192 1878 Planarity : 0.004 0.054 1322 Dihedral : 23.047 176.530 3592 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 0.59 % Allowed : 25.66 % Favored : 73.75 % 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: 0.86 (0.31), residues: 811 helix: 2.00 (0.27), residues: 411 sheet: 0.10 (0.70), residues: 56 loop : -1.17 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 701 HIS 0.004 0.001 HIS C 910 PHE 0.013 0.001 PHE C 401 TYR 0.018 0.001 TYR C 703 ARG 0.005 0.000 ARG C1053 *********************** 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 61 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.917 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 60 average time/residue: 0.2907 time to fit residues: 23.9980 Evaluate side-chains 53 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 57 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10857 Z= 0.188 Angle : 0.546 8.550 15555 Z= 0.271 Chirality : 0.036 0.202 1878 Planarity : 0.004 0.054 1322 Dihedral : 22.978 176.242 3592 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 0.29 % Allowed : 25.52 % Favored : 74.19 % 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: 1.87 (0.27), residues: 417 sheet: 0.05 (0.68), residues: 56 loop : -1.16 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 701 HIS 0.007 0.001 HIS C 868 PHE 0.015 0.002 PHE C 749 TYR 0.020 0.002 TYR C 703 ARG 0.008 0.000 ARG C1053 *********************** 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 58 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.874 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.2616 time to fit residues: 21.6129 Evaluate side-chains 55 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0370 chunk 65 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 62 optimal weight: 0.3980 chunk 83 optimal weight: 20.0000 chunk 24 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- 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** C 955 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10857 Z= 0.129 Angle : 0.531 12.254 15555 Z= 0.261 Chirality : 0.034 0.192 1878 Planarity : 0.004 0.052 1322 Dihedral : 22.905 176.490 3592 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.96 % Favored : 96.92 % Rotamer: Outliers : 0.15 % Allowed : 25.96 % 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 (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: 0.96 (0.31), residues: 811 helix: 2.18 (0.27), residues: 404 sheet: -0.11 (0.70), residues: 58 loop : -1.15 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 701 HIS 0.009 0.001 HIS C 955 PHE 0.013 0.001 PHE C 749 TYR 0.016 0.001 TYR C 703 ARG 0.008 0.000 ARG C1053 ********************** 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 61 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.897 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.2839 time to fit residues: 24.0904 Evaluate side-chains 57 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0920 time to fit residues: 1.2595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.4465 r_free = 0.4465 target = 0.183807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.140161 restraints weight = 15558.575| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.04 r_work: 0.3412 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10857 Z= 0.216 Angle : 0.555 8.574 15555 Z= 0.277 Chirality : 0.036 0.241 1878 Planarity : 0.004 0.054 1322 Dihedral : 22.892 176.070 3592 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 26.11 % 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 (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: 0.83 (0.31), residues: 811 helix: 2.03 (0.27), residues: 409 sheet: -0.26 (0.69), residues: 58 loop : -1.18 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 701 HIS 0.007 0.001 HIS C 868 PHE 0.016 0.002 PHE C 749 TYR 0.022 0.002 TYR C 703 ARG 0.008 0.000 ARG C1053 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2040.44 seconds wall clock time: 38 minutes 2.50 seconds (2282.50 seconds total)