Starting phenix.real_space_refine on Sat Aug 3 22:17:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5r_44222/08_2024/9b5r_44222.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5r_44222/08_2024/9b5r_44222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5r_44222/08_2024/9b5r_44222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5r_44222/08_2024/9b5r_44222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5r_44222/08_2024/9b5r_44222.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5r_44222/08_2024/9b5r_44222.cif" } resolution = 2.95 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= 0.000 sd= 0.062 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 3 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 5703 2.51 5 N 1470 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8935 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.77, per 1000 atoms: 0.76 Number of scatterers: 8935 At special positions: 0 Unit cell: (85.12, 100.016, 119.168, 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 41 16.00 P 3 15.00 Mg 2 11.99 O 1716 8.00 N 1470 7.00 C 5703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.90 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.6 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 9 sheets defined 47.5% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.714A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.694A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.973A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.641A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.810A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.420A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.657A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.317A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.541A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.724A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.773A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.602A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.577A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.647A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.963A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.661A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 835 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.531A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.642A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.897A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR A 385 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.137A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.137A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.491A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA7, first strand: chain 'A' and resid 919 through 922 removed outlier: 6.452A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 919 through 922 removed outlier: 6.452A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A1003 " --> pdb=" O CYS A 995 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 26 removed outlier: 3.657A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1209 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: 3.55 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1512 1.27 - 1.40: 2173 1.40 - 1.54: 5284 1.54 - 1.67: 109 1.67 - 1.81: 62 Bond restraints: 9140 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.20e+00 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.404 0.012 1.30e-02 5.92e+03 9.14e-01 bond pdb=" C05 A1AIV D 201 " pdb=" N06 A1AIV D 201 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.02e-01 bond pdb=" C PHE A 360 " pdb=" O PHE A 360 " ideal model delta sigma weight residual 1.236 1.242 -0.006 1.15e-02 7.56e+03 2.70e-01 ... (remaining 9135 not shown) Histogram of bond angle deviations from ideal: 100.03 - 115.88: 5960 115.88 - 131.73: 6418 131.73 - 147.58: 11 147.58 - 163.44: 0 163.44 - 179.29: 1 Bond angle restraints: 12390 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.82 -7.12 1.80e+00 3.09e-01 1.56e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.12 3.41 1.18e+00 7.24e-01 8.44e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.61 4.58 1.76e+00 3.23e-01 6.78e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.39 6.44 2.67e+00 1.40e-01 5.83e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 104.22 6.36 2.79e+00 1.28e-01 5.18e+00 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5334 17.55 - 35.09: 170 35.09 - 52.64: 37 52.64 - 70.19: 8 70.19 - 87.73: 3 Dihedral angle restraints: 5552 sinusoidal: 2262 harmonic: 3290 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -142.26 56.26 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" N CYS C 85 " pdb=" CA CYS C 85 " pdb=" CB CYS C 85 " pdb=" SG CYS C 85 " ideal model delta sinusoidal sigma weight residual -180.00 -122.79 -57.21 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1213 0.057 - 0.114: 134 0.114 - 0.171: 24 0.171 - 0.229: 1 0.229 - 0.286: 2 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.90 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" C5' ATP A1103 " pdb=" O4' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.49 -2.72 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1371 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO C 95 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 17 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO C 18 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.017 5.00e-02 4.00e+02 2.53e-02 1.03e+00 pdb=" N PRO C 121 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.014 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 57 2.58 - 3.16: 7398 3.16 - 3.74: 12983 3.74 - 4.32: 19327 4.32 - 4.90: 32792 Nonbonded interactions: 72557 Sorted by model distance: nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.006 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.040 2.170 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.186 3.040 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.189 2.170 nonbonded pdb=" N GLU A 489 " pdb=" OE1 GLU A 489 " model vdw 2.236 3.120 ... (remaining 72552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.060 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 29.700 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 0.072 9140 Z= 0.192 Angle : 0.453 7.119 12390 Z= 0.227 Chirality : 0.042 0.286 1374 Planarity : 0.003 0.030 1604 Dihedral : 9.740 87.732 3425 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.31 % Allowed : 2.52 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % 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: 1.02 (0.26), residues: 1126 helix: 1.50 (0.25), residues: 476 sheet: 0.44 (0.39), residues: 174 loop : 0.04 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 608 HIS 0.002 0.000 HIS A 818 PHE 0.010 0.001 PHE A 842 TYR 0.008 0.001 TYR A 732 ARG 0.002 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ILE cc_start: 0.8643 (mt) cc_final: 0.8431 (mm) REVERT: A 218 MET cc_start: 0.7338 (mtt) cc_final: 0.7065 (mtt) REVERT: A 262 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8376 (mtpm) REVERT: A 270 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7954 (mt-10) REVERT: A 273 LYS cc_start: 0.7776 (mttt) cc_final: 0.7536 (mtmt) REVERT: A 353 ASP cc_start: 0.8389 (t0) cc_final: 0.8108 (t0) REVERT: A 368 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 526 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8878 (m-80) REVERT: A 562 LEU cc_start: 0.8323 (tp) cc_final: 0.8062 (tt) REVERT: A 596 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8206 (tttt) REVERT: A 755 ASN cc_start: 0.8783 (m-40) cc_final: 0.8144 (p0) REVERT: A 832 MET cc_start: 0.8213 (mtp) cc_final: 0.7949 (mtp) REVERT: A 879 LYS cc_start: 0.8449 (mmmm) cc_final: 0.7704 (mtmm) REVERT: A 909 ASN cc_start: 0.7453 (t0) cc_final: 0.7123 (t0) REVERT: A 937 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: A 979 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7733 (mmmt) REVERT: A 980 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7490 (ttpp) REVERT: A 1011 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7629 (tppt) outliers start: 13 outliers final: 3 residues processed: 159 average time/residue: 1.5658 time to fit residues: 262.0328 Evaluate side-chains 103 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9140 Z= 0.337 Angle : 0.537 6.183 12390 Z= 0.282 Chirality : 0.044 0.151 1374 Planarity : 0.005 0.046 1604 Dihedral : 6.992 75.531 1256 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 9.38 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % 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: 0.90 (0.26), residues: 1126 helix: 1.39 (0.25), residues: 486 sheet: 0.46 (0.39), residues: 173 loop : -0.10 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 147 PHE 0.012 0.001 PHE A 237 TYR 0.011 0.001 TYR A 81 ARG 0.007 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.992 Fit side-chains REVERT: A 32 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8263 (mmm) REVERT: A 85 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: A 182 THR cc_start: 0.8625 (t) cc_final: 0.8332 (m) REVERT: A 185 ILE cc_start: 0.8630 (mt) cc_final: 0.8375 (mm) REVERT: A 228 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8172 (tppt) REVERT: A 262 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8362 (mtpm) REVERT: A 270 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 273 LYS cc_start: 0.7790 (mttt) cc_final: 0.7534 (mtmt) REVERT: A 353 ASP cc_start: 0.8400 (t0) cc_final: 0.8061 (t0) REVERT: A 368 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8329 (mm-30) REVERT: A 562 LEU cc_start: 0.8326 (tp) cc_final: 0.8117 (tt) REVERT: A 596 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7906 (tttt) REVERT: A 668 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7688 (mmt) REVERT: A 699 GLN cc_start: 0.8496 (mp10) cc_final: 0.8192 (mp10) REVERT: A 755 ASN cc_start: 0.8785 (m-40) cc_final: 0.8141 (p0) REVERT: A 879 LYS cc_start: 0.8460 (mmmm) cc_final: 0.8013 (mtmm) REVERT: A 909 ASN cc_start: 0.7425 (t0) cc_final: 0.7073 (t0) REVERT: A 979 LYS cc_start: 0.7933 (mmtp) cc_final: 0.7716 (mmmt) REVERT: A 980 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7518 (ttpp) REVERT: A 1011 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7717 (tppt) REVERT: C 32 HIS cc_start: 0.8230 (t-170) cc_final: 0.7895 (t70) REVERT: C 38 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7741 (mtm) REVERT: C 143 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7713 (tmm-80) outliers start: 19 outliers final: 6 residues processed: 111 average time/residue: 1.6679 time to fit residues: 194.9833 Evaluate side-chains 110 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.0470 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 0.0000 chunk 100 optimal weight: 1.9990 overall best weight: 0.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9140 Z= 0.179 Angle : 0.503 11.657 12390 Z= 0.261 Chirality : 0.042 0.176 1374 Planarity : 0.004 0.046 1604 Dihedral : 6.228 80.124 1250 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.12 % Allowed : 10.48 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % 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: 0.97 (0.25), residues: 1126 helix: 1.52 (0.25), residues: 486 sheet: 0.41 (0.37), residues: 181 loop : -0.11 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 702 HIS 0.001 0.000 HIS A 818 PHE 0.009 0.001 PHE A 237 TYR 0.013 0.001 TYR C 145 ARG 0.007 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 1.009 Fit side-chains REVERT: A 32 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8219 (mmm) REVERT: A 85 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: A 182 THR cc_start: 0.8647 (t) cc_final: 0.8365 (m) REVERT: A 184 MET cc_start: 0.7606 (mtp) cc_final: 0.7345 (ptp) REVERT: A 185 ILE cc_start: 0.8628 (mt) cc_final: 0.8398 (mm) REVERT: A 228 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8251 (mmmt) REVERT: A 262 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8344 (mtpm) REVERT: A 270 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 273 LYS cc_start: 0.7772 (mttt) cc_final: 0.7511 (mtmt) REVERT: A 353 ASP cc_start: 0.8438 (t0) cc_final: 0.8055 (t0) REVERT: A 368 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8307 (mm-30) REVERT: A 526 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: A 562 LEU cc_start: 0.8336 (tp) cc_final: 0.8127 (tt) REVERT: A 596 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7780 (tttt) REVERT: A 668 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7711 (mmm) REVERT: A 699 GLN cc_start: 0.8486 (mp10) cc_final: 0.8165 (mp10) REVERT: A 755 ASN cc_start: 0.8786 (m-40) cc_final: 0.8159 (p0) REVERT: A 879 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8015 (mtmm) REVERT: A 909 ASN cc_start: 0.7409 (t0) cc_final: 0.7075 (t0) REVERT: A 979 LYS cc_start: 0.7919 (mmtp) cc_final: 0.7700 (mmmt) REVERT: A 980 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7494 (ttpp) REVERT: A 1011 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7716 (tppt) REVERT: C 32 HIS cc_start: 0.8220 (t-170) cc_final: 0.7895 (t70) REVERT: C 38 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7732 (mtm) outliers start: 21 outliers final: 6 residues processed: 109 average time/residue: 1.4867 time to fit residues: 171.4317 Evaluate side-chains 109 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9140 Z= 0.302 Angle : 0.518 11.053 12390 Z= 0.269 Chirality : 0.043 0.168 1374 Planarity : 0.004 0.048 1604 Dihedral : 6.458 87.726 1250 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.42 % Allowed : 10.69 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % 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: 0.84 (0.25), residues: 1126 helix: 1.42 (0.25), residues: 486 sheet: 0.28 (0.37), residues: 181 loop : -0.17 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.011 0.001 PHE A 677 TYR 0.012 0.001 TYR C 145 ARG 0.007 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 0.999 Fit side-chains REVERT: A 32 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8220 (mmm) REVERT: A 85 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: A 112 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8484 (m) REVERT: A 184 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7585 (ptp) REVERT: A 218 MET cc_start: 0.6854 (mtt) cc_final: 0.6148 (mmt) REVERT: A 228 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8276 (mmmt) REVERT: A 262 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8352 (mtpm) REVERT: A 270 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8058 (mt-10) REVERT: A 273 LYS cc_start: 0.7745 (mttt) cc_final: 0.7438 (mtmt) REVERT: A 353 ASP cc_start: 0.8422 (t0) cc_final: 0.8026 (t0) REVERT: A 368 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8325 (mm-30) REVERT: A 526 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8886 (m-80) REVERT: A 562 LEU cc_start: 0.8353 (tp) cc_final: 0.8136 (tt) REVERT: A 596 LYS cc_start: 0.7988 (tmtt) cc_final: 0.7711 (tttt) REVERT: A 668 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7707 (mmm) REVERT: A 699 GLN cc_start: 0.8537 (mp10) cc_final: 0.8213 (mp10) REVERT: A 755 ASN cc_start: 0.8788 (m-40) cc_final: 0.8129 (p0) REVERT: A 879 LYS cc_start: 0.8501 (mmmm) cc_final: 0.8024 (mtmm) REVERT: A 909 ASN cc_start: 0.7431 (t0) cc_final: 0.7103 (t0) REVERT: A 979 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7710 (mmmt) REVERT: A 980 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7517 (ttpp) REVERT: A 1011 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7736 (tppt) REVERT: C 32 HIS cc_start: 0.8222 (t-170) cc_final: 0.7849 (t70) REVERT: C 38 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7707 (mtm) REVERT: C 72 ARG cc_start: 0.8360 (tpp80) cc_final: 0.8159 (ttm-80) REVERT: C 143 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7826 (tmm-80) outliers start: 24 outliers final: 9 residues processed: 113 average time/residue: 1.4755 time to fit residues: 176.5742 Evaluate side-chains 114 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9140 Z= 0.261 Angle : 0.507 9.988 12390 Z= 0.264 Chirality : 0.043 0.161 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.378 84.694 1250 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.22 % Allowed : 10.99 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1126 helix: 1.42 (0.24), residues: 486 sheet: 0.28 (0.37), residues: 181 loop : -0.19 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 PHE 0.010 0.001 PHE A 123 TYR 0.010 0.001 TYR A 81 ARG 0.009 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.060 Fit side-chains REVERT: A 32 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8195 (mmm) REVERT: A 85 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: A 184 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7524 (ptp) REVERT: A 218 MET cc_start: 0.6913 (mtt) cc_final: 0.6264 (mmt) REVERT: A 228 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8295 (mmmt) REVERT: A 262 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8361 (mtpm) REVERT: A 270 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8060 (mt-10) REVERT: A 273 LYS cc_start: 0.7736 (mttt) cc_final: 0.7438 (mtmt) REVERT: A 353 ASP cc_start: 0.8483 (t0) cc_final: 0.8066 (t0) REVERT: A 368 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8322 (mm-30) REVERT: A 526 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.8879 (m-80) REVERT: A 562 LEU cc_start: 0.8350 (tp) cc_final: 0.8127 (tt) REVERT: A 596 LYS cc_start: 0.8054 (tmtt) cc_final: 0.7810 (tttt) REVERT: A 699 GLN cc_start: 0.8553 (mp10) cc_final: 0.8250 (mp10) REVERT: A 755 ASN cc_start: 0.8794 (m-40) cc_final: 0.8148 (p0) REVERT: A 804 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7836 (mmm-85) REVERT: A 879 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8014 (mtmm) REVERT: A 909 ASN cc_start: 0.7435 (t0) cc_final: 0.7130 (t0) REVERT: A 979 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7707 (mmmt) REVERT: A 980 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7520 (ttpp) REVERT: A 1011 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7737 (tppt) REVERT: C 32 HIS cc_start: 0.8159 (t-170) cc_final: 0.7849 (t70) REVERT: C 117 ASP cc_start: 0.8507 (t0) cc_final: 0.8177 (t0) REVERT: C 144 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8430 (ttpp) outliers start: 22 outliers final: 10 residues processed: 113 average time/residue: 1.5500 time to fit residues: 185.2891 Evaluate side-chains 110 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 54.2779 > 50: distance: 32 - 142: 6.104 distance: 35 - 139: 4.373 distance: 46 - 126: 16.450 distance: 49 - 123: 12.144 distance: 72 - 82: 11.471 distance: 82 - 83: 7.985 distance: 82 - 88: 21.769 distance: 83 - 84: 12.900 distance: 83 - 86: 10.970 distance: 84 - 85: 18.592 distance: 84 - 89: 9.051 distance: 86 - 87: 18.063 distance: 87 - 88: 14.559 distance: 89 - 90: 20.132 distance: 90 - 91: 10.964 distance: 90 - 93: 23.887 distance: 91 - 92: 17.019 distance: 91 - 100: 9.806 distance: 93 - 94: 9.551 distance: 94 - 95: 6.378 distance: 94 - 96: 4.701 distance: 96 - 98: 7.262 distance: 97 - 99: 3.063 distance: 98 - 99: 4.305 distance: 100 - 101: 3.806 distance: 101 - 102: 5.036 distance: 101 - 104: 7.742 distance: 102 - 103: 5.500 distance: 102 - 109: 3.889 distance: 104 - 105: 9.168 distance: 105 - 106: 11.432 distance: 106 - 107: 10.060 distance: 107 - 108: 13.057 distance: 109 - 110: 4.720 distance: 109 - 115: 9.900 distance: 110 - 111: 13.826 distance: 110 - 113: 11.380 distance: 111 - 112: 12.111 distance: 111 - 116: 6.399 distance: 113 - 114: 9.952 distance: 114 - 115: 16.691 distance: 116 - 117: 11.233 distance: 116 - 122: 7.582 distance: 117 - 118: 4.126 distance: 117 - 120: 10.640 distance: 118 - 119: 6.490 distance: 118 - 123: 20.297 distance: 120 - 121: 12.826 distance: 121 - 122: 16.958 distance: 123 - 124: 5.760 distance: 124 - 125: 4.507 distance: 124 - 127: 6.773 distance: 125 - 126: 20.519 distance: 125 - 132: 3.422 distance: 127 - 128: 4.261 distance: 128 - 129: 5.587 distance: 129 - 130: 18.511 distance: 130 - 131: 10.648 distance: 133 - 134: 3.176 distance: 133 - 136: 12.973 distance: 136 - 137: 28.895 distance: 136 - 138: 32.311 distance: 139 - 140: 15.643 distance: 140 - 141: 8.957 distance: 140 - 143: 15.655 distance: 141 - 142: 3.153 distance: 141 - 147: 5.088 distance: 143 - 144: 9.594 distance: 144 - 145: 13.407 distance: 144 - 146: 6.915 distance: 147 - 148: 8.083 distance: 148 - 149: 8.593 distance: 148 - 151: 8.057 distance: 149 - 150: 12.531 distance: 149 - 158: 6.355 distance: 151 - 152: 6.761 distance: 152 - 153: 5.705 distance: 152 - 154: 13.909 distance: 153 - 155: 9.506 distance: 154 - 156: 7.432 distance: 155 - 157: 12.302 distance: 156 - 157: 4.045 distance: 159 - 160: 5.279 distance: 159 - 162: 9.662 distance: 160 - 161: 17.800 distance: 160 - 165: 3.043 distance: 162 - 163: 4.297 distance: 162 - 164: 11.111