Starting phenix.real_space_refine on Wed May 8 12:53:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/05_2024/8ibz_35350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/05_2024/8ibz_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_35350/05_2024/8ibz_35350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/05_2024/8ibz_35350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/05_2024/8ibz_35350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibz_35350/05_2024/8ibz_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-dev-5322/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: 5.65, per 1000 atoms: 0.55 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: 4.51 Conformation dependent library (CDL) restraints added in 1.1 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: 3.98 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: 5.05 Time building geometry restraints manager: 4.93 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: 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 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: 0.820 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: 0.020 Extract box with map and model: 3.520 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 36.050 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.880 ------------------------------------------------------------------------------- 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 : 23.457 177.913 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 *********************** 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 : 0.892 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.2919 time to fit residues: 23.4727 Evaluate side-chains 54 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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: 0.0170 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: 0.7105 moved from start: 0.0654 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= 0.149 Angle : 0.575 8.878 15555 Z= 0.290 Chirality : 0.036 0.204 1878 Planarity : 0.004 0.064 1322 Dihedral : 24.244 176.786 3723 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 2.51 % Allowed : 23.30 % 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: 0.80 (0.31), residues: 811 helix: 1.97 (0.27), residues: 399 sheet: 0.37 (0.70), residues: 56 loop : -1.18 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 701 HIS 0.003 0.001 HIS C1096 PHE 0.012 0.001 PHE C 749 TYR 0.010 0.001 TYR C 703 ARG 0.002 0.000 ARG C 700 *********************** 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 78 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.857 Fit side-chains REVERT: C 704 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6240 (pp) REVERT: C 1105 MET cc_start: 0.6154 (ppp) cc_final: 0.5858 (ppp) outliers start: 17 outliers final: 9 residues processed: 75 average time/residue: 0.2597 time to fit residues: 27.0246 Evaluate side-chains 67 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 714 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 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: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.7210 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10857 Z= 0.300 Angle : 0.615 8.981 15555 Z= 0.309 Chirality : 0.039 0.193 1878 Planarity : 0.005 0.067 1322 Dihedral : 24.063 176.546 3720 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 4.57 % Allowed : 22.71 % Favored : 72.71 % 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: 0.43 (0.31), residues: 811 helix: 1.58 (0.27), residues: 411 sheet: -0.22 (0.69), residues: 58 loop : -1.27 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 701 HIS 0.005 0.001 HIS C 910 PHE 0.021 0.002 PHE C 749 TYR 0.011 0.002 TYR C 563 ARG 0.007 0.001 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 90 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 59 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: C 883 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6806 (ptm160) REVERT: C 987 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.2812 (mmp-170) REVERT: C 1105 MET cc_start: 0.6345 (ppp) cc_final: 0.5962 (ppp) outliers start: 31 outliers final: 18 residues processed: 82 average time/residue: 0.2686 time to fit residues: 30.4251 Evaluate side-chains 75 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 987 ARG Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1046 LEU 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: 0.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 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: 0.7980 chunk 85 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.7161 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10857 Z= 0.186 Angle : 0.558 8.637 15555 Z= 0.279 Chirality : 0.036 0.190 1878 Planarity : 0.005 0.064 1322 Dihedral : 23.931 176.594 3720 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.95 % Favored : 95.93 % Rotamer: Outliers : 3.83 % Allowed : 22.71 % 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: 0.61 (0.31), residues: 811 helix: 1.77 (0.27), residues: 412 sheet: -0.21 (0.70), residues: 58 loop : -1.22 (0.35), residues: 341 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 0.015 0.002 PHE C 749 TYR 0.009 0.001 TYR C 703 ARG 0.005 0.000 ARG C1053 *********************** 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 84 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 58 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: C 776 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: C 883 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6793 (ptm160) REVERT: C 950 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7039 (pp30) REVERT: C 1105 MET cc_start: 0.6316 (ppp) cc_final: 0.6097 (ppp) outliers start: 26 outliers final: 18 residues processed: 80 average time/residue: 0.2580 time to fit residues: 28.7392 Evaluate side-chains 75 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 54 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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 709 GLU Chi-restraints excluded: chain C residue 714 VAL 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 803 VAL Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 887 SER 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 1046 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 769 GLN C 870 HIS ** 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: 0.7233 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10857 Z= 0.307 Angle : 0.614 8.819 15555 Z= 0.309 Chirality : 0.039 0.188 1878 Planarity : 0.005 0.066 1322 Dihedral : 23.888 176.104 3720 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 5.75 % Allowed : 22.12 % 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: 0.33 (0.31), residues: 811 helix: 1.53 (0.27), residues: 413 sheet: -0.46 (0.67), residues: 58 loop : -1.35 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 701 HIS 0.004 0.001 HIS C 868 PHE 0.022 0.003 PHE C 401 TYR 0.030 0.003 TYR C 703 ARG 0.004 0.001 ARG C1053 *********************** 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 fitting. rotamer outliers: 39 poor density : 58 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 551 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6822 (mtt) REVERT: C 776 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: C 883 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6824 (ptm160) REVERT: C 950 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7041 (pp30) REVERT: C 1105 MET cc_start: 0.6484 (ppp) cc_final: 0.6189 (ppp) outliers start: 39 outliers final: 27 residues processed: 90 average time/residue: 0.2534 time to fit residues: 31.8636 Evaluate side-chains 86 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 55 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 666 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 709 GLU Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 950 GLN Chi-restraints excluded: chain C residue 954 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 1083 THR 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 86 optimal weight: 10.0000 chunk 18 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 30.0000 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 444 GLN C 870 HIS ** 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: 0.7149 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10857 Z= 0.154 Angle : 0.545 9.732 15555 Z= 0.272 Chirality : 0.035 0.191 1878 Planarity : 0.004 0.059 1322 Dihedral : 23.755 176.569 3720 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 3.98 % Allowed : 23.75 % 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: 0.68 (0.31), residues: 811 helix: 1.87 (0.27), residues: 412 sheet: -0.28 (0.69), residues: 58 loop : -1.23 (0.34), residues: 341 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 0.014 0.001 PHE C 749 TYR 0.040 0.002 TYR C 703 ARG 0.007 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 87 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 60 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 551 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6804 (mtt) REVERT: C 767 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: C 776 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: C 950 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7101 (pp30) REVERT: C 1105 MET cc_start: 0.6437 (ppp) cc_final: 0.6173 (ppp) outliers start: 27 outliers final: 18 residues processed: 81 average time/residue: 0.2475 time to fit residues: 28.3493 Evaluate side-chains 77 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 55 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 767 ASP Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 861 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.8413 > 50: distance: 49 - 65: 22.728 distance: 61 - 65: 22.929 distance: 65 - 66: 14.896 distance: 66 - 67: 50.224 distance: 66 - 69: 9.774 distance: 67 - 68: 16.846 distance: 67 - 70: 42.701 distance: 70 - 71: 37.658 distance: 70 - 76: 42.619 distance: 71 - 72: 30.362 distance: 71 - 74: 20.906 distance: 72 - 73: 23.413 distance: 72 - 77: 23.238 distance: 74 - 75: 24.208 distance: 75 - 76: 44.250 distance: 77 - 78: 16.284 distance: 78 - 79: 6.187 distance: 78 - 81: 47.876 distance: 79 - 85: 49.951 distance: 81 - 82: 31.910 distance: 82 - 84: 45.990 distance: 85 - 86: 29.934 distance: 86 - 87: 11.076 distance: 86 - 89: 20.050 distance: 87 - 88: 39.018 distance: 87 - 94: 46.942 distance: 88 - 119: 31.574 distance: 89 - 90: 20.236 distance: 90 - 91: 40.377 distance: 91 - 92: 40.589 distance: 92 - 93: 52.921 distance: 94 - 95: 30.108 distance: 94 - 100: 40.155 distance: 95 - 96: 41.465 distance: 95 - 98: 18.877 distance: 96 - 97: 36.447 distance: 96 - 101: 9.754 distance: 97 - 130: 43.515 distance: 98 - 99: 32.078 distance: 99 - 100: 42.579 distance: 101 - 102: 18.155 distance: 102 - 103: 31.879 distance: 103 - 104: 29.027 distance: 103 - 110: 11.590 distance: 104 - 138: 42.978 distance: 105 - 106: 37.435 distance: 106 - 107: 7.502 distance: 107 - 108: 7.213 distance: 107 - 109: 31.773 distance: 110 - 111: 25.079 distance: 111 - 112: 29.454 distance: 111 - 114: 40.842 distance: 112 - 113: 22.482 distance: 112 - 119: 33.272 distance: 113 - 147: 35.476 distance: 114 - 115: 49.376 distance: 115 - 116: 12.408 distance: 116 - 117: 35.749 distance: 116 - 118: 23.697 distance: 119 - 120: 38.894 distance: 120 - 121: 33.528 distance: 121 - 122: 53.204 distance: 121 - 130: 55.410 distance: 122 - 155: 25.623 distance: 123 - 124: 36.291 distance: 124 - 125: 21.010 distance: 125 - 126: 26.617 distance: 126 - 127: 19.354 distance: 127 - 128: 29.547 distance: 127 - 129: 27.065 distance: 130 - 131: 39.656 distance: 131 - 132: 28.428 distance: 131 - 134: 45.234 distance: 132 - 133: 27.221 distance: 132 - 138: 33.255 distance: 133 - 162: 36.539 distance: 134 - 135: 52.581 distance: 135 - 136: 22.832 distance: 135 - 137: 8.869 distance: 138 - 139: 19.827 distance: 139 - 140: 15.719 distance: 139 - 142: 29.945 distance: 140 - 141: 39.317 distance: 140 - 147: 26.931 distance: 141 - 173: 23.155 distance: 142 - 143: 24.350 distance: 143 - 144: 12.154 distance: 144 - 145: 25.824 distance: 144 - 146: 3.439