Starting phenix.real_space_refine on Thu Jun 27 01:58:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/06_2024/8r2h_18842_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/06_2024/8r2h_18842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/06_2024/8r2h_18842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/06_2024/8r2h_18842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/06_2024/8r2h_18842_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/06_2024/8r2h_18842_updated.pdb" } resolution = 2.42 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= 0.001 sd= 0.021 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 P 4 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 7424 2.51 5 N 1897 2.21 5 O 2117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 11484 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5680 Classifications: {'peptide': 693} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 677} Chain breaks: 5 Chain: "B" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5750 Classifications: {'peptide': 701} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 685} Chain breaks: 5 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.25, per 1000 atoms: 0.63 Number of scatterers: 11484 At special positions: 0 Unit cell: (120.62, 93.98, 102.86, 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) S 40 16.00 P 4 15.00 Mg 2 11.99 O 2117 8.00 N 1897 7.00 C 7424 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: 4.59 Conformation dependent library (CDL) restraints added in 2.0 seconds 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 6 sheets defined 48.5% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 327 through 333 removed outlier: 4.155A pdb=" N THR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 376 through 389 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 399 through 402 Processing helix chain 'A' and resid 404 through 416 removed outlier: 4.282A pdb=" N TYR A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 434 through 455 Proline residue: A 438 - end of helix removed outlier: 4.016A pdb=" N LEU A 444 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 448 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL A 452 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN A 453 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 502 through 505 removed outlier: 4.484A pdb=" N LEU A 505 " --> pdb=" O LEU A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 535 through 552 removed outlier: 3.554A pdb=" N LYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 removed outlier: 3.582A pdb=" N THR A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 628 through 632' Processing helix chain 'A' and resid 634 through 646 Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 707 through 710 No H-bonds generated for 'chain 'A' and resid 707 through 710' Processing helix chain 'A' and resid 724 through 736 Processing helix chain 'A' and resid 822 through 824 No H-bonds generated for 'chain 'A' and resid 822 through 824' Processing helix chain 'A' and resid 830 through 844 removed outlier: 3.979A pdb=" N LYS A 844 " --> pdb=" O LYS A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 859 No H-bonds generated for 'chain 'A' and resid 856 through 859' Processing helix chain 'A' and resid 862 through 867 removed outlier: 3.713A pdb=" N ARG A 867 " --> pdb=" O LYS A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 905 through 907 No H-bonds generated for 'chain 'A' and resid 905 through 907' Processing helix chain 'A' and resid 911 through 915 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 946 through 950 Processing helix chain 'A' and resid 964 through 976 Processing helix chain 'A' and resid 994 through 997 No H-bonds generated for 'chain 'A' and resid 994 through 997' Processing helix chain 'A' and resid 1032 through 1039 Processing helix chain 'A' and resid 1081 through 1093 removed outlier: 3.628A pdb=" N GLU A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1100 Processing helix chain 'A' and resid 1116 through 1124 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1178 through 1184 Processing helix chain 'A' and resid 1189 through 1202 Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 327 through 333 removed outlier: 4.114A pdb=" N THR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 376 through 389 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 399 through 402 Processing helix chain 'B' and resid 404 through 416 removed outlier: 4.498A pdb=" N TYR B 416 " --> pdb=" O LYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 434 through 455 Proline residue: B 438 - end of helix removed outlier: 3.992A pdb=" N LEU B 444 " --> pdb=" O ALA B 441 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 448 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL B 452 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN B 453 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 492 through 498 Processing helix chain 'B' and resid 502 through 506 removed outlier: 4.461A pdb=" N LEU B 505 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.842A pdb=" N LYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 removed outlier: 3.604A pdb=" N THR B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 628 through 632' Processing helix chain 'B' and resid 634 through 646 Processing helix chain 'B' and resid 677 through 685 Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 724 through 736 Processing helix chain 'B' and resid 822 through 824 No H-bonds generated for 'chain 'B' and resid 822 through 824' Processing helix chain 'B' and resid 830 through 844 removed outlier: 3.909A pdb=" N LYS B 844 " --> pdb=" O LYS B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 859 No H-bonds generated for 'chain 'B' and resid 856 through 859' Processing helix chain 'B' and resid 862 through 867 removed outlier: 3.863A pdb=" N ARG B 867 " --> pdb=" O LYS B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 871 No H-bonds generated for 'chain 'B' and resid 869 through 871' Processing helix chain 'B' and resid 879 through 890 Processing helix chain 'B' and resid 905 through 915 removed outlier: 4.000A pdb=" N TYR B 910 " --> pdb=" O GLN B 907 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP B 911 " --> pdb=" O ARG B 908 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS B 915 " --> pdb=" O GLN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 946 through 950 Processing helix chain 'B' and resid 964 through 976 Processing helix chain 'B' and resid 994 through 999 Processing helix chain 'B' and resid 1032 through 1039 Processing helix chain 'B' and resid 1081 through 1093 removed outlier: 3.529A pdb=" N GLU B1092 " --> pdb=" O ILE B1088 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B1093 " --> pdb=" O LYS B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1095 through 1100 Processing helix chain 'B' and resid 1116 through 1124 Processing helix chain 'B' and resid 1142 through 1153 Processing helix chain 'B' and resid 1155 through 1159 Processing helix chain 'B' and resid 1178 through 1184 Processing helix chain 'B' and resid 1189 through 1202 Processing sheet with id= A, first strand: chain 'A' and resid 482 through 485 removed outlier: 6.649A pdb=" N THR A 743 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR A 654 " --> pdb=" O THR A 743 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 745 " --> pdb=" O TYR A 654 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP A 656 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 747 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP A 714 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N HIS A 746 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 716 " --> pdb=" O HIS A 746 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ARG A 748 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 872 through 874 removed outlier: 8.538A pdb=" N TYR A 873 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE A 850 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS A 896 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU A 851 " --> pdb=" O LYS A 896 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN A 898 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS A 925 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE A 901 " --> pdb=" O LYS A 925 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE A 927 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1162 through 1167 removed outlier: 6.004A pdb=" N ASP A1107 " --> pdb=" O ILE A1045 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE A1045 " --> pdb=" O ASP A1107 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 483 through 485 removed outlier: 6.610A pdb=" N ILE B 623 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR B 743 " --> pdb=" O ILE B 652 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR B 654 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 745 " --> pdb=" O TYR B 654 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP B 656 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL B 747 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP B 714 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS B 746 " --> pdb=" O ASP B 714 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 716 " --> pdb=" O HIS B 746 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ARG B 748 " --> pdb=" O ILE B 716 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 872 through 874 removed outlier: 8.593A pdb=" N TYR B 873 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N PHE B 850 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS B 896 " --> pdb=" O ILE B 849 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LEU B 851 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN B 898 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS B 925 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE B 901 " --> pdb=" O LYS B 925 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE B 927 " --> pdb=" O ILE B 901 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 982 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE B 928 " --> pdb=" O VAL B 982 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 984 " --> pdb=" O ILE B 928 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1162 through 1167 removed outlier: 6.049A pdb=" N ASP B1107 " --> pdb=" O ILE B1045 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE B1045 " --> pdb=" O ASP B1107 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3614 1.34 - 1.46: 1853 1.46 - 1.57: 6168 1.57 - 1.69: 6 1.69 - 1.80: 74 Bond restraints: 11715 Sorted by residual: bond pdb=" N PHE B 527 " pdb=" CA PHE B 527 " ideal model delta sigma weight residual 1.457 1.501 -0.045 1.26e-02 6.30e+03 1.25e+01 bond pdb=" C2 TPP B1302 " pdb=" S1 TPP B1302 " ideal model delta sigma weight residual 1.675 1.701 -0.026 1.00e-02 1.00e+04 6.72e+00 bond pdb=" N ASN A 870 " pdb=" CA ASN A 870 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.31e-02 5.83e+03 6.51e+00 bond pdb=" N ASN B 399 " pdb=" CA ASN B 399 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.39e+00 bond pdb=" N LYS B 526 " pdb=" CA LYS B 526 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.11e+00 ... (remaining 11710 not shown) Histogram of bond angle deviations from ideal: 89.20 - 98.16: 2 98.16 - 107.11: 214 107.11 - 116.06: 7331 116.06 - 125.01: 8156 125.01 - 133.96: 87 Bond angle restraints: 15790 Sorted by residual: angle pdb=" PA TPP A1302 " pdb=" O3A TPP A1302 " pdb=" PB TPP A1302 " ideal model delta sigma weight residual 139.87 129.63 10.24 1.00e+00 1.00e+00 1.05e+02 angle pdb=" PA TPP B1302 " pdb=" O3A TPP B1302 " pdb=" PB TPP B1302 " ideal model delta sigma weight residual 139.87 130.61 9.26 1.00e+00 1.00e+00 8.57e+01 angle pdb=" CA PHE B 527 " pdb=" CB PHE B 527 " pdb=" CG PHE B 527 " ideal model delta sigma weight residual 113.80 122.14 -8.34 1.00e+00 1.00e+00 6.95e+01 angle pdb=" CA LYS B 526 " pdb=" C LYS B 526 " pdb=" N PHE B 527 " ideal model delta sigma weight residual 117.07 123.27 -6.20 1.14e+00 7.69e-01 2.95e+01 angle pdb=" C7 TPP A1302 " pdb=" O7 TPP A1302 " pdb=" PA TPP A1302 " ideal model delta sigma weight residual 124.29 119.84 4.45 1.00e+00 1.00e+00 1.98e+01 ... (remaining 15785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6680 17.99 - 35.98: 299 35.98 - 53.97: 36 53.97 - 71.95: 9 71.95 - 89.94: 3 Dihedral angle restraints: 7027 sinusoidal: 2905 harmonic: 4122 Sorted by residual: dihedral pdb=" CA LEU A 953 " pdb=" C LEU A 953 " pdb=" N ASN A 954 " pdb=" CA ASN A 954 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA TYR A 374 " pdb=" C TYR A 374 " pdb=" N ASN A 375 " pdb=" CA ASN A 375 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA TYR B 374 " pdb=" C TYR B 374 " pdb=" N ASN B 375 " pdb=" CA ASN B 375 " ideal model delta harmonic sigma weight residual 180.00 164.60 15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 7024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1196 0.040 - 0.079: 412 0.079 - 0.118: 112 0.118 - 0.158: 13 0.158 - 0.197: 1 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CA PHE B 527 " pdb=" N PHE B 527 " pdb=" C PHE B 527 " pdb=" CB PHE B 527 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA ILE A 350 " pdb=" N ILE A 350 " pdb=" C ILE A 350 " pdb=" CB ILE A 350 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL B1072 " pdb=" N VAL B1072 " pdb=" C VAL B1072 " pdb=" CB VAL B1072 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 1731 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 TPP B1302 " -0.127 2.00e-02 2.50e+03 1.46e-01 4.27e+02 pdb=" C4 TPP B1302 " 0.051 2.00e-02 2.50e+03 pdb=" C5 TPP B1302 " 0.013 2.00e-02 2.50e+03 pdb=" C6 TPP B1302 " -0.223 2.00e-02 2.50e+03 pdb=" C7' TPP B1302 " -0.078 2.00e-02 2.50e+03 pdb=" CM4 TPP B1302 " 0.160 2.00e-02 2.50e+03 pdb=" N3 TPP B1302 " -0.055 2.00e-02 2.50e+03 pdb=" S1 TPP B1302 " 0.260 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 TPP A1302 " 0.095 2.00e-02 2.50e+03 1.13e-01 2.53e+02 pdb=" C4 TPP A1302 " -0.038 2.00e-02 2.50e+03 pdb=" C5 TPP A1302 " -0.005 2.00e-02 2.50e+03 pdb=" C6 TPP A1302 " 0.171 2.00e-02 2.50e+03 pdb=" C7' TPP A1302 " 0.064 2.00e-02 2.50e+03 pdb=" CM4 TPP A1302 " -0.127 2.00e-02 2.50e+03 pdb=" N3 TPP A1302 " 0.039 2.00e-02 2.50e+03 pdb=" S1 TPP A1302 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 527 " -0.026 2.00e-02 2.50e+03 2.08e-02 7.58e+00 pdb=" CG PHE B 527 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 527 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 527 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 527 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 527 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 527 " -0.005 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 88 2.51 - 3.11: 8542 3.11 - 3.71: 17661 3.71 - 4.30: 27065 4.30 - 4.90: 44270 Nonbonded interactions: 97626 Sorted by model distance: nonbonded pdb=" O GLN B 659 " pdb="MG MG B1301 " model vdw 1.914 2.170 nonbonded pdb=" O GLN A 659 " pdb="MG MG A1301 " model vdw 1.924 2.170 nonbonded pdb=" OD1 ASN B 657 " pdb="MG MG B1301 " model vdw 1.952 2.170 nonbonded pdb="MG MG A1301 " pdb=" O2A TPP A1302 " model vdw 2.045 2.170 nonbonded pdb=" OD1 ASN A 657 " pdb="MG MG A1301 " model vdw 2.108 2.170 ... (remaining 97621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 312 through 683 or resid 705 through 998 or resid 1030 thr \ ough 1204 or resid 1301 through 1302)) } 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: 3.750 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: 12.680 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 34.220 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 0.045 11715 Z= 0.210 Angle : 0.516 10.241 15790 Z= 0.322 Chirality : 0.042 0.197 1734 Planarity : 0.005 0.146 1986 Dihedral : 10.241 89.943 4385 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.55 % Allowed : 5.97 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.09 (0.22), residues: 1370 helix: 0.42 (0.20), residues: 640 sheet: 0.97 (0.43), residues: 156 loop : -0.83 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 547 HIS 0.003 0.001 HIS B 915 PHE 0.047 0.002 PHE B 527 TYR 0.014 0.001 TYR B 983 ARG 0.003 0.000 ARG B 741 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 GLU cc_start: 0.6135 (mm-30) cc_final: 0.5799 (mm-30) REVERT: A 504 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7138 (m-80) REVERT: A 980 HIS cc_start: 0.7865 (m90) cc_final: 0.7658 (m90) outliers start: 7 outliers final: 0 residues processed: 222 average time/residue: 1.0426 time to fit residues: 253.5341 Evaluate side-chains 202 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS A 732 ASN A 990 ASN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN B 710 ASN B 732 ASN ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11715 Z= 0.270 Angle : 0.525 8.797 15790 Z= 0.281 Chirality : 0.044 0.157 1734 Planarity : 0.003 0.038 1986 Dihedral : 6.431 74.478 1536 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.89 % Allowed : 11.08 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.25 (0.22), residues: 1370 helix: 0.31 (0.20), residues: 634 sheet: 1.04 (0.47), residues: 139 loop : -0.92 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 547 HIS 0.004 0.001 HIS A1145 PHE 0.019 0.002 PHE B1146 TYR 0.018 0.002 TYR B1130 ARG 0.004 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 205 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7211 (m-80) REVERT: A 840 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7318 (ttmm) REVERT: A 885 PHE cc_start: 0.7748 (t80) cc_final: 0.7436 (t80) outliers start: 24 outliers final: 11 residues processed: 214 average time/residue: 1.0937 time to fit residues: 255.9516 Evaluate side-chains 213 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 200 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1031 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 0.0170 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 ASN ** A 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11715 Z= 0.250 Angle : 0.514 7.936 15790 Z= 0.274 Chirality : 0.043 0.148 1734 Planarity : 0.003 0.038 1986 Dihedral : 6.342 73.170 1536 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.59 % Allowed : 12.88 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.28 (0.22), residues: 1370 helix: 0.27 (0.20), residues: 627 sheet: 0.87 (0.45), residues: 149 loop : -0.88 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 547 HIS 0.003 0.001 HIS A 915 PHE 0.017 0.002 PHE B 885 TYR 0.017 0.002 TYR B1130 ARG 0.003 0.000 ARG B 741 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7208 (m-80) REVERT: A 840 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7329 (ttmm) REVERT: A 885 PHE cc_start: 0.7752 (t80) cc_final: 0.7419 (t80) REVERT: A 1123 ILE cc_start: 0.5761 (OUTLIER) cc_final: 0.5487 (mt) REVERT: B 480 TYR cc_start: 0.8419 (t80) cc_final: 0.8119 (t80) outliers start: 33 outliers final: 11 residues processed: 212 average time/residue: 1.0620 time to fit residues: 247.7852 Evaluate side-chains 205 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1031 ASP Chi-restraints excluded: chain B residue 1077 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11715 Z= 0.291 Angle : 0.540 8.049 15790 Z= 0.287 Chirality : 0.044 0.154 1734 Planarity : 0.004 0.043 1986 Dihedral : 6.358 74.275 1536 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.44 % Allowed : 14.61 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.56 (0.22), residues: 1370 helix: 0.02 (0.20), residues: 636 sheet: 0.59 (0.45), residues: 138 loop : -0.94 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 547 HIS 0.004 0.001 HIS A 915 PHE 0.019 0.002 PHE B1146 TYR 0.018 0.002 TYR B1130 ARG 0.004 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: A 840 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7366 (ttmm) REVERT: A 1123 ILE cc_start: 0.5672 (OUTLIER) cc_final: 0.5375 (mt) REVERT: B 480 TYR cc_start: 0.8423 (t80) cc_final: 0.8133 (t80) outliers start: 31 outliers final: 20 residues processed: 211 average time/residue: 1.0062 time to fit residues: 233.5040 Evaluate side-chains 218 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1031 ASP Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11715 Z= 0.274 Angle : 0.535 7.903 15790 Z= 0.284 Chirality : 0.044 0.191 1734 Planarity : 0.003 0.041 1986 Dihedral : 6.080 73.046 1534 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.91 % Allowed : 14.22 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1370 helix: 0.03 (0.20), residues: 632 sheet: 0.76 (0.44), residues: 147 loop : -0.99 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 547 HIS 0.004 0.001 HIS A 915 PHE 0.018 0.002 PHE B1146 TYR 0.017 0.002 TYR B1130 ARG 0.004 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.297 Fit side-chains REVERT: A 1123 ILE cc_start: 0.5687 (OUTLIER) cc_final: 0.5405 (mt) REVERT: B 480 TYR cc_start: 0.8423 (t80) cc_final: 0.8143 (t80) outliers start: 37 outliers final: 21 residues processed: 218 average time/residue: 0.9431 time to fit residues: 227.0750 Evaluate side-chains 218 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1031 ASP Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 134 optimal weight: 0.2980 chunk 111 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11715 Z= 0.204 Angle : 0.501 8.432 15790 Z= 0.265 Chirality : 0.043 0.186 1734 Planarity : 0.003 0.040 1986 Dihedral : 5.814 68.084 1534 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.96 % Allowed : 15.79 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.34 (0.22), residues: 1370 helix: 0.26 (0.20), residues: 623 sheet: 0.82 (0.44), residues: 147 loop : -0.94 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 547 HIS 0.002 0.001 HIS A 915 PHE 0.016 0.001 PHE B 885 TYR 0.014 0.001 TYR A1130 ARG 0.003 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.261 Fit side-chains REVERT: A 504 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: A 1123 ILE cc_start: 0.5764 (OUTLIER) cc_final: 0.5528 (mt) REVERT: B 480 TYR cc_start: 0.8406 (t80) cc_final: 0.8123 (t80) outliers start: 25 outliers final: 15 residues processed: 206 average time/residue: 1.0255 time to fit residues: 232.6350 Evaluate side-chains 212 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1031 ASP Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 133 optimal weight: 0.5980 chunk 83 optimal weight: 0.2980 chunk 81 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 11715 Z= 0.224 Angle : 0.521 9.750 15790 Z= 0.273 Chirality : 0.044 0.332 1734 Planarity : 0.003 0.039 1986 Dihedral : 5.733 67.608 1534 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.20 % Allowed : 16.50 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.27 (0.22), residues: 1370 helix: 0.30 (0.20), residues: 618 sheet: 0.94 (0.44), residues: 147 loop : -0.90 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 547 HIS 0.003 0.001 HIS A 915 PHE 0.015 0.001 PHE B 885 TYR 0.018 0.001 TYR B 474 ARG 0.003 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: A 1123 ILE cc_start: 0.5778 (OUTLIER) cc_final: 0.5527 (mt) REVERT: B 1080 MET cc_start: 0.5997 (mmm) cc_final: 0.5703 (mmm) outliers start: 28 outliers final: 19 residues processed: 216 average time/residue: 1.0013 time to fit residues: 237.9785 Evaluate side-chains 219 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1031 ASP Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.0070 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1137 ASN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11715 Z= 0.246 Angle : 0.538 9.692 15790 Z= 0.281 Chirality : 0.045 0.347 1734 Planarity : 0.003 0.039 1986 Dihedral : 5.761 67.474 1534 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.20 % Allowed : 17.12 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 (0.22), residues: 1370 helix: 0.20 (0.20), residues: 619 sheet: 0.76 (0.46), residues: 136 loop : -0.88 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 547 HIS 0.003 0.001 HIS A 915 PHE 0.016 0.002 PHE B1146 TYR 0.017 0.002 TYR B 474 ARG 0.003 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 1.229 Fit side-chains REVERT: A 504 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7218 (m-80) REVERT: A 1123 ILE cc_start: 0.5790 (OUTLIER) cc_final: 0.5546 (mt) REVERT: B 480 TYR cc_start: 0.8343 (t80) cc_final: 0.8119 (t80) outliers start: 28 outliers final: 18 residues processed: 209 average time/residue: 0.9691 time to fit residues: 223.2794 Evaluate side-chains 212 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1031 ASP Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1083 ASN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 11715 Z= 0.331 Angle : 0.594 9.750 15790 Z= 0.310 Chirality : 0.047 0.414 1734 Planarity : 0.004 0.039 1986 Dihedral : 5.961 66.042 1534 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.59 % Allowed : 16.73 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 (0.22), residues: 1370 helix: 0.00 (0.20), residues: 622 sheet: 0.68 (0.45), residues: 136 loop : -0.98 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 547 HIS 0.004 0.001 HIS A 915 PHE 0.021 0.002 PHE B1146 TYR 0.022 0.002 TYR B 949 ARG 0.003 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 628 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7311 (p0) REVERT: A 1118 MET cc_start: 0.6313 (tpp) cc_final: 0.6085 (tpp) REVERT: A 1123 ILE cc_start: 0.5712 (OUTLIER) cc_final: 0.5406 (mt) REVERT: B 480 TYR cc_start: 0.8362 (t80) cc_final: 0.8064 (t80) outliers start: 33 outliers final: 22 residues processed: 210 average time/residue: 0.9158 time to fit residues: 212.8148 Evaluate side-chains 215 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 954 ASN Chi-restraints excluded: chain B residue 1031 ASP Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.2587 > 50: distance: 154 - 155: 5.631 distance: 154 - 160: 9.547 distance: 155 - 156: 8.431 distance: 155 - 158: 8.578 distance: 156 - 157: 3.533 distance: 156 - 161: 8.994 distance: 158 - 159: 15.272 distance: 159 - 160: 9.304 distance: 162 - 163: 7.681 distance: 162 - 165: 10.902 distance: 163 - 164: 17.910 distance: 163 - 169: 11.031 distance: 165 - 166: 9.816 distance: 166 - 167: 13.444 distance: 166 - 168: 4.063 distance: 169 - 170: 5.783 distance: 170 - 171: 8.252 distance: 170 - 173: 9.342 distance: 171 - 172: 11.957 distance: 171 - 177: 17.029 distance: 173 - 174: 6.097 distance: 174 - 175: 6.465 distance: 174 - 176: 5.945 distance: 177 - 178: 9.595 distance: 178 - 179: 8.704 distance: 178 - 181: 18.335 distance: 179 - 180: 19.055 distance: 179 - 184: 14.469 distance: 181 - 182: 4.107 distance: 181 - 183: 15.085 distance: 184 - 185: 5.720 distance: 185 - 186: 16.129 distance: 185 - 188: 4.719 distance: 186 - 187: 12.492 distance: 186 - 196: 26.406 distance: 188 - 189: 6.094 distance: 189 - 191: 5.922 distance: 190 - 192: 4.782 distance: 191 - 193: 10.201 distance: 192 - 194: 4.748 distance: 193 - 194: 4.909 distance: 194 - 195: 7.286 distance: 196 - 197: 16.053 distance: 197 - 198: 6.904 distance: 197 - 200: 12.913 distance: 198 - 199: 12.302 distance: 198 - 204: 17.281 distance: 200 - 201: 5.910 distance: 201 - 202: 5.139 distance: 201 - 203: 10.945 distance: 204 - 205: 8.820 distance: 205 - 208: 14.426 distance: 206 - 207: 27.172 distance: 206 - 211: 12.073 distance: 208 - 209: 21.582 distance: 208 - 210: 9.944 distance: 211 - 212: 13.100 distance: 212 - 213: 34.013 distance: 213 - 214: 16.702 distance: 213 - 215: 11.403 distance: 215 - 216: 26.412 distance: 216 - 217: 19.991 distance: 216 - 219: 15.242 distance: 217 - 218: 18.742 distance: 217 - 223: 28.386 distance: 219 - 220: 25.466 distance: 220 - 222: 16.682 distance: 223 - 224: 20.204 distance: 224 - 225: 3.573 distance: 224 - 227: 16.438 distance: 225 - 226: 11.919 distance: 225 - 228: 27.080