Starting phenix.real_space_refine on Mon May 12 13:21:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5q_44221/05_2025/9b5q_44221.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5q_44221/05_2025/9b5q_44221.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/cci-nas-00/data/ceres_data/9b5q_44221/05_2025/9b5q_44221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5q_44221/05_2025/9b5q_44221.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5q_44221/05_2025/9b5q_44221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5q_44221/05_2025/9b5q_44221.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= 0.066 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. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.21, per 1000 atoms: 0.70 Number of scatterers: 8935 At special positions: 0 Unit cell: (85.12, 100.016, 120.232, 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.1 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: 49 helices and 10 sheets defined 48.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.879A 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: 3.817A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.028A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.455A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.576A 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 144 removed outlier: 3.763A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.368A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.616A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.635A 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: 4.282A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.554A 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: 3.807A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.619A 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: 3.749A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.963A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.577A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.569A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 removed outlier: 3.519A pdb=" N THR A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.561A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.658A 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: 3.597A 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: 3.964A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 Processing helix chain 'A' and resid 796 through 800 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: 3.506A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.661A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.660A 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: 6.771A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.312A 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: 4.053A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.446A 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: 4.053A 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: 6.435A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.081A 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 920 through 922 removed outlier: 6.331A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP A 996 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 942 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.331A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 22 removed outlier: 6.165A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 22 441 hydrogen bonds defined for protein. 1212 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: 3.48 Time building geometry restraints manager: 2.92 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: 5256 1.54 - 1.67: 137 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 1.30e+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 1.21e+00 bond pdb=" C05 A1AIV D 201 " pdb=" N06 A1AIV D 201 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 9.60e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.405 0.011 1.30e-02 5.92e+03 7.69e-01 bond pdb=" CA SER A 789 " pdb=" C SER A 789 " ideal model delta sigma weight residual 1.524 1.517 0.007 1.27e-02 6.20e+03 2.85e-01 ... (remaining 9135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 12219 1.34 - 2.67: 95 2.67 - 4.01: 67 4.01 - 5.35: 5 5.35 - 6.68: 4 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 121.70 128.38 -6.68 1.80e+00 3.09e-01 1.38e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.01 3.52 1.18e+00 7.24e-01 8.95e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.48 4.71 1.76e+00 3.23e-01 7.16e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.15 6.68 2.67e+00 1.40e-01 6.27e+00 angle pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 111.83 105.71 6.12 2.67e+00 1.40e-01 5.25e+00 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5342 17.90 - 35.81: 166 35.81 - 53.71: 37 53.71 - 71.61: 5 71.61 - 89.52: 2 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 -138.05 52.05 1 1.00e+01 1.00e-02 3.70e+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 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+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 -60.00 -119.10 59.10 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1218 0.058 - 0.115: 130 0.115 - 0.173: 23 0.173 - 0.231: 1 0.231 - 0.288: 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 2.08e+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 -2.91 0.28 2.00e-01 2.50e+01 1.93e+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 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1371 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 143 " 0.131 9.50e-02 1.11e+02 5.86e-02 2.11e+00 pdb=" NE ARG C 143 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG C 143 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 143 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 143 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO C 95 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 17 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO C 18 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.016 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 50 2.59 - 3.16: 7400 3.16 - 3.74: 13021 3.74 - 4.32: 19330 4.32 - 4.90: 32850 Nonbonded interactions: 72651 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.007 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.022 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.040 2.170 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.085 2.170 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.175 3.040 ... (remaining 72646 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: 5.150 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.930 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.010 0.868 9143 Z= 0.485 Angle : 0.628 44.277 12392 Z= 0.310 Chirality : 0.042 0.288 1374 Planarity : 0.004 0.059 1604 Dihedral : 9.514 89.519 3425 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.31 % Allowed : 2.22 % Favored : 96.47 % 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 (0.25), residues: 1126 helix: 1.45 (0.24), residues: 477 sheet: 0.13 (0.40), residues: 183 loop : 0.24 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 608 HIS 0.003 0.001 HIS C 75 PHE 0.010 0.001 PHE A 842 TYR 0.008 0.001 TYR A 732 ARG 0.003 0.000 ARG A 919 Details of bonding type rmsd hydrogen bonds : bond 0.14919 ( 426) hydrogen bonds : angle 5.84327 ( 1212) SS BOND : bond 0.86752 ( 1) SS BOND : angle 33.27292 ( 2) covalent geometry : bond 0.00302 ( 9140) covalent geometry : angle 0.46467 (12390) Misc. bond : bond 0.07812 ( 2) *********************** 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 149 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8156 (t70) cc_final: 0.7398 (p0) REVERT: A 442 MET cc_start: 0.8825 (tpp) cc_final: 0.8500 (mmm) REVERT: A 582 SER cc_start: 0.8262 (m) cc_final: 0.7927 (p) REVERT: A 832 MET cc_start: 0.8437 (mtp) cc_final: 0.8216 (mtp) REVERT: A 911 LYS cc_start: 0.7289 (mtmt) cc_final: 0.7038 (mtpp) REVERT: A 937 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 983 GLU cc_start: 0.8423 (mp0) cc_final: 0.8045 (mp0) REVERT: C 42 ASP cc_start: 0.8288 (p0) cc_final: 0.7866 (p0) REVERT: C 59 ASP cc_start: 0.8211 (m-30) cc_final: 0.7561 (t70) REVERT: C 72 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8058 (mmm-85) outliers start: 13 outliers final: 4 residues processed: 145 average time/residue: 1.3826 time to fit residues: 212.8049 Evaluate side-chains 87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 165 ASP 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: 0.6980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093448 restraints weight = 11374.036| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.19 r_work: 0.2939 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9143 Z= 0.159 Angle : 0.508 8.276 12392 Z= 0.264 Chirality : 0.043 0.139 1374 Planarity : 0.004 0.040 1604 Dihedral : 6.163 66.336 1256 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.92 % Allowed : 6.25 % Favored : 91.83 % 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: 1.06 (0.25), residues: 1126 helix: 1.49 (0.24), residues: 486 sheet: 0.30 (0.41), residues: 174 loop : 0.15 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 608 HIS 0.003 0.001 HIS A 818 PHE 0.011 0.001 PHE A 842 TYR 0.010 0.001 TYR A 732 ARG 0.005 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 426) hydrogen bonds : angle 4.70856 ( 1212) SS BOND : bond 0.01142 ( 1) SS BOND : angle 3.04339 ( 2) covalent geometry : bond 0.00391 ( 9140) covalent geometry : angle 0.50641 (12390) Misc. bond : bond 0.00150 ( 2) *********************** 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 106 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8090 (t70) cc_final: 0.7095 (p0) REVERT: A 320 GLU cc_start: 0.6990 (tt0) cc_final: 0.6679 (tt0) REVERT: A 387 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8550 (p0) REVERT: A 442 MET cc_start: 0.8547 (tpp) cc_final: 0.8225 (mmm) REVERT: A 582 SER cc_start: 0.7706 (m) cc_final: 0.7469 (p) REVERT: A 596 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7183 (tttt) REVERT: A 646 GLU cc_start: 0.7748 (mp0) cc_final: 0.7469 (mp0) REVERT: A 668 MET cc_start: 0.7919 (tpp) cc_final: 0.7682 (mmm) REVERT: A 937 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: A 983 GLU cc_start: 0.8309 (mp0) cc_final: 0.7823 (mp0) REVERT: C 59 ASP cc_start: 0.8482 (m-30) cc_final: 0.7434 (t70) REVERT: C 72 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.7938 (mmm-85) outliers start: 19 outliers final: 9 residues processed: 101 average time/residue: 1.3263 time to fit residues: 143.0232 Evaluate side-chains 94 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 105 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 91 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100345 restraints weight = 11716.216| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.78 r_work: 0.2990 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9143 Z= 0.163 Angle : 0.503 10.205 12392 Z= 0.261 Chirality : 0.043 0.158 1374 Planarity : 0.004 0.040 1604 Dihedral : 6.147 66.751 1255 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.62 % Allowed : 6.85 % Favored : 90.52 % 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: 1.05 (0.25), residues: 1126 helix: 1.52 (0.24), residues: 485 sheet: 0.23 (0.41), residues: 174 loop : 0.14 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 608 HIS 0.006 0.001 HIS C 32 PHE 0.010 0.001 PHE A 360 TYR 0.010 0.001 TYR C 145 ARG 0.006 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 426) hydrogen bonds : angle 4.51430 ( 1212) SS BOND : bond 0.01048 ( 1) SS BOND : angle 1.33873 ( 2) covalent geometry : bond 0.00404 ( 9140) covalent geometry : angle 0.50254 (12390) Misc. bond : bond 0.00082 ( 2) *********************** 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 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8103 (t70) cc_final: 0.7516 (p0) REVERT: A 596 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7680 (ttpt) REVERT: A 668 MET cc_start: 0.8445 (tpp) cc_final: 0.8165 (mmm) REVERT: A 983 GLU cc_start: 0.8616 (mp0) cc_final: 0.8260 (mp0) REVERT: C 59 ASP cc_start: 0.8223 (m-30) cc_final: 0.7654 (t70) outliers start: 26 outliers final: 16 residues processed: 99 average time/residue: 1.2858 time to fit residues: 136.1843 Evaluate side-chains 93 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 143 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097282 restraints weight = 11676.987| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.95 r_work: 0.2946 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9143 Z= 0.200 Angle : 0.518 11.044 12392 Z= 0.269 Chirality : 0.043 0.149 1374 Planarity : 0.004 0.043 1604 Dihedral : 6.073 65.839 1252 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.32 % Allowed : 8.77 % Favored : 88.91 % 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: 0.92 (0.26), residues: 1126 helix: 1.47 (0.24), residues: 485 sheet: 0.04 (0.40), residues: 187 loop : 0.06 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 608 HIS 0.004 0.001 HIS A 818 PHE 0.012 0.001 PHE A 265 TYR 0.010 0.001 TYR C 145 ARG 0.007 0.001 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 426) hydrogen bonds : angle 4.50702 ( 1212) SS BOND : bond 0.01708 ( 1) SS BOND : angle 1.85963 ( 2) covalent geometry : bond 0.00504 ( 9140) covalent geometry : angle 0.51706 (12390) Misc. bond : bond 0.00053 ( 2) *********************** 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 96 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8197 (t70) cc_final: 0.7392 (p0) REVERT: A 596 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7562 (tttt) REVERT: A 699 GLN cc_start: 0.8436 (mt0) cc_final: 0.7522 (mp10) REVERT: A 935 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7849 (tm-30) REVERT: A 983 GLU cc_start: 0.8564 (mp0) cc_final: 0.8095 (mp0) REVERT: C 59 ASP cc_start: 0.8399 (m-30) cc_final: 0.7665 (t70) outliers start: 23 outliers final: 16 residues processed: 89 average time/residue: 1.2791 time to fit residues: 121.8720 Evaluate side-chains 87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 143 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097499 restraints weight = 11513.499| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.91 r_work: 0.2958 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9143 Z= 0.144 Angle : 0.487 10.573 12392 Z= 0.253 Chirality : 0.042 0.146 1374 Planarity : 0.004 0.044 1604 Dihedral : 5.966 63.192 1252 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.22 % Allowed : 9.17 % Favored : 88.61 % 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: 0.99 (0.26), residues: 1126 helix: 1.58 (0.24), residues: 483 sheet: 0.02 (0.39), residues: 187 loop : 0.06 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 702 HIS 0.004 0.001 HIS C 32 PHE 0.009 0.001 PHE A 360 TYR 0.018 0.001 TYR C 145 ARG 0.011 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 426) hydrogen bonds : angle 4.41524 ( 1212) SS BOND : bond 0.01630 ( 1) SS BOND : angle 1.17039 ( 2) covalent geometry : bond 0.00354 ( 9140) covalent geometry : angle 0.48702 (12390) Misc. bond : bond 0.00014 ( 2) *********************** 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 94 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8461 (tp30) cc_final: 0.8002 (tp30) REVERT: A 274 ASP cc_start: 0.8199 (t70) cc_final: 0.7393 (p0) REVERT: A 465 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8475 (t70) REVERT: A 596 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7524 (tttt) REVERT: A 668 MET cc_start: 0.8360 (tpp) cc_final: 0.8089 (mmm) REVERT: A 699 GLN cc_start: 0.8434 (mt0) cc_final: 0.8181 (mp10) REVERT: A 935 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 983 GLU cc_start: 0.8562 (mp0) cc_final: 0.8089 (mp0) REVERT: C 59 ASP cc_start: 0.8357 (m-30) cc_final: 0.7631 (t70) REVERT: C 72 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: C 145 TYR cc_start: 0.8425 (m-80) cc_final: 0.7981 (m-10) outliers start: 22 outliers final: 13 residues processed: 87 average time/residue: 1.3474 time to fit residues: 125.4593 Evaluate side-chains 86 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 143 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 106 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098785 restraints weight = 11607.441| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.94 r_work: 0.2965 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9143 Z= 0.129 Angle : 0.472 10.083 12392 Z= 0.245 Chirality : 0.041 0.151 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.860 60.842 1252 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.92 % Allowed : 9.58 % Favored : 88.51 % 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: 1.06 (0.26), residues: 1126 helix: 1.65 (0.24), residues: 483 sheet: -0.02 (0.39), residues: 187 loop : 0.11 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 702 HIS 0.003 0.001 HIS C 32 PHE 0.009 0.001 PHE A 321 TYR 0.008 0.001 TYR C 145 ARG 0.007 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 426) hydrogen bonds : angle 4.33635 ( 1212) SS BOND : bond 0.00968 ( 1) SS BOND : angle 1.24203 ( 2) covalent geometry : bond 0.00316 ( 9140) covalent geometry : angle 0.47165 (12390) Misc. bond : bond 0.00262 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 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 91 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8484 (tp30) cc_final: 0.8046 (tp30) REVERT: A 274 ASP cc_start: 0.8200 (t70) cc_final: 0.7439 (p0) REVERT: A 465 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8507 (t70) REVERT: A 596 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7567 (tttt) REVERT: A 699 GLN cc_start: 0.8482 (mt0) cc_final: 0.8211 (mp10) REVERT: A 935 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 983 GLU cc_start: 0.8588 (mp0) cc_final: 0.8131 (mp0) REVERT: C 59 ASP cc_start: 0.8274 (m-30) cc_final: 0.7626 (t70) REVERT: C 139 ARG cc_start: 0.6869 (ttm-80) cc_final: 0.6144 (mtm-85) outliers start: 19 outliers final: 11 residues processed: 87 average time/residue: 1.3200 time to fit residues: 122.9690 Evaluate side-chains 84 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 143 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 102 optimal weight: 0.0060 chunk 45 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100558 restraints weight = 11640.458| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.87 r_work: 0.2996 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9143 Z= 0.111 Angle : 0.458 9.471 12392 Z= 0.237 Chirality : 0.041 0.144 1374 Planarity : 0.004 0.049 1604 Dihedral : 5.706 57.626 1250 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.02 % Allowed : 9.78 % Favored : 88.21 % 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: 1.18 (0.26), residues: 1126 helix: 1.71 (0.24), residues: 484 sheet: 0.20 (0.41), residues: 164 loop : 0.14 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.009 0.001 PHE A 613 TYR 0.010 0.001 TYR C 145 ARG 0.008 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 426) hydrogen bonds : angle 4.21868 ( 1212) SS BOND : bond 0.00846 ( 1) SS BOND : angle 1.16264 ( 2) covalent geometry : bond 0.00265 ( 9140) covalent geometry : angle 0.45743 (12390) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 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 94 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8420 (tp30) cc_final: 0.7994 (tp30) REVERT: A 274 ASP cc_start: 0.8184 (t70) cc_final: 0.7407 (p0) REVERT: A 465 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8430 (t70) REVERT: A 596 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7538 (tttt) REVERT: A 668 MET cc_start: 0.8374 (tpp) cc_final: 0.8110 (mmm) REVERT: A 699 GLN cc_start: 0.8456 (mt0) cc_final: 0.8199 (mp10) REVERT: A 935 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7820 (tm-30) REVERT: A 983 GLU cc_start: 0.8578 (mp0) cc_final: 0.8113 (mp0) REVERT: A 1005 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8071 (m) REVERT: C 59 ASP cc_start: 0.8245 (m-30) cc_final: 0.7649 (t70) outliers start: 20 outliers final: 8 residues processed: 87 average time/residue: 1.3757 time to fit residues: 127.6019 Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain C residue 91 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099112 restraints weight = 11790.743| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.81 r_work: 0.3005 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9143 Z= 0.150 Angle : 0.479 9.849 12392 Z= 0.247 Chirality : 0.042 0.161 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.750 58.789 1250 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.41 % Allowed : 10.18 % Favored : 88.41 % 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: 1.08 (0.26), residues: 1126 helix: 1.66 (0.24), residues: 484 sheet: 0.01 (0.40), residues: 174 loop : 0.11 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.003 0.001 HIS C 32 PHE 0.009 0.001 PHE A 166 TYR 0.012 0.001 TYR A 150 ARG 0.009 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 426) hydrogen bonds : angle 4.26635 ( 1212) SS BOND : bond 0.01450 ( 1) SS BOND : angle 0.65655 ( 2) covalent geometry : bond 0.00375 ( 9140) covalent geometry : angle 0.47853 (12390) Misc. bond : bond 0.00073 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 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 84 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8438 (tp30) cc_final: 0.8024 (tp30) REVERT: A 274 ASP cc_start: 0.8127 (t70) cc_final: 0.7456 (p0) REVERT: A 465 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8448 (t70) REVERT: A 596 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7678 (tttt) REVERT: A 668 MET cc_start: 0.8419 (tpp) cc_final: 0.8164 (mmm) REVERT: A 699 GLN cc_start: 0.8431 (mt0) cc_final: 0.7596 (mp10) REVERT: A 935 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 983 GLU cc_start: 0.8591 (mp0) cc_final: 0.8169 (mp0) REVERT: A 1005 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8150 (m) REVERT: C 59 ASP cc_start: 0.8176 (m-30) cc_final: 0.7715 (t70) REVERT: C 139 ARG cc_start: 0.6917 (ttm-80) cc_final: 0.6132 (mtm-85) REVERT: C 145 TYR cc_start: 0.8401 (m-10) cc_final: 0.8130 (m-10) outliers start: 14 outliers final: 8 residues processed: 81 average time/residue: 1.3910 time to fit residues: 120.1296 Evaluate side-chains 81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain C residue 91 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098727 restraints weight = 11631.198| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.93 r_work: 0.2978 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9143 Z= 0.122 Angle : 0.464 9.266 12392 Z= 0.240 Chirality : 0.041 0.144 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.673 56.669 1250 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.31 % Allowed : 10.58 % Favored : 88.10 % 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: 1.14 (0.26), residues: 1126 helix: 1.71 (0.24), residues: 484 sheet: 0.14 (0.41), residues: 164 loop : 0.10 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 669 HIS 0.003 0.001 HIS C 32 PHE 0.009 0.001 PHE A 613 TYR 0.007 0.001 TYR C 145 ARG 0.008 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 426) hydrogen bonds : angle 4.21392 ( 1212) SS BOND : bond 0.01553 ( 1) SS BOND : angle 0.53389 ( 2) covalent geometry : bond 0.00299 ( 9140) covalent geometry : angle 0.46396 (12390) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 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 88 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8451 (tp30) cc_final: 0.7978 (tp30) REVERT: A 32 MET cc_start: 0.8768 (mtp) cc_final: 0.8488 (mmm) REVERT: A 274 ASP cc_start: 0.8183 (t70) cc_final: 0.7354 (p0) REVERT: A 465 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8436 (t70) REVERT: A 596 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7540 (tttt) REVERT: A 668 MET cc_start: 0.8347 (tpp) cc_final: 0.8088 (mmm) REVERT: A 699 GLN cc_start: 0.8408 (mt0) cc_final: 0.7508 (mp10) REVERT: A 935 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 983 GLU cc_start: 0.8581 (mp0) cc_final: 0.8097 (mp0) REVERT: A 1005 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8026 (m) REVERT: C 59 ASP cc_start: 0.8296 (m-30) cc_final: 0.7681 (t70) REVERT: C 139 ARG cc_start: 0.6913 (ttm-80) cc_final: 0.6133 (mtm-85) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 1.3593 time to fit residues: 121.7056 Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain C residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 108 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098966 restraints weight = 11624.984| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.91 r_work: 0.2961 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9143 Z= 0.134 Angle : 0.481 9.447 12392 Z= 0.250 Chirality : 0.042 0.145 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.699 56.624 1250 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.31 % Allowed : 10.79 % Favored : 87.90 % 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: 1.15 (0.26), residues: 1126 helix: 1.74 (0.24), residues: 478 sheet: 0.13 (0.41), residues: 164 loop : 0.11 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.003 0.001 HIS C 32 PHE 0.009 0.001 PHE A 321 TYR 0.035 0.001 TYR C 145 ARG 0.008 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 426) hydrogen bonds : angle 4.21934 ( 1212) SS BOND : bond 0.01388 ( 1) SS BOND : angle 0.83438 ( 2) covalent geometry : bond 0.00328 ( 9140) covalent geometry : angle 0.48071 (12390) Misc. bond : bond 0.00007 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 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 85 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8460 (tp30) cc_final: 0.7988 (tp30) REVERT: A 32 MET cc_start: 0.8784 (mtp) cc_final: 0.8508 (mmm) REVERT: A 274 ASP cc_start: 0.8183 (t70) cc_final: 0.7375 (p0) REVERT: A 465 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8448 (t70) REVERT: A 596 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7563 (tttt) REVERT: A 668 MET cc_start: 0.8367 (tpp) cc_final: 0.8109 (mmm) REVERT: A 699 GLN cc_start: 0.8407 (mt0) cc_final: 0.7501 (mp10) REVERT: A 935 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 983 GLU cc_start: 0.8584 (mp0) cc_final: 0.8104 (mp0) REVERT: A 1005 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8019 (m) REVERT: C 59 ASP cc_start: 0.8293 (m-30) cc_final: 0.7672 (t70) REVERT: C 139 ARG cc_start: 0.6855 (ttm-80) cc_final: 0.6113 (mtm-85) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 1.3303 time to fit residues: 116.3142 Evaluate side-chains 82 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain C residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 0.6980 chunk 106 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.0970 chunk 105 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097346 restraints weight = 11652.690| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.02 r_work: 0.2968 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9143 Z= 0.112 Angle : 0.468 9.124 12392 Z= 0.243 Chirality : 0.041 0.146 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.654 56.362 1250 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.21 % Allowed : 11.09 % Favored : 87.70 % 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: 1.23 (0.26), residues: 1126 helix: 1.80 (0.24), residues: 478 sheet: 0.18 (0.41), residues: 164 loop : 0.15 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 PHE 0.009 0.001 PHE A 613 TYR 0.007 0.001 TYR A 736 ARG 0.008 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 426) hydrogen bonds : angle 4.15923 ( 1212) SS BOND : bond 0.01163 ( 1) SS BOND : angle 0.97198 ( 2) covalent geometry : bond 0.00267 ( 9140) covalent geometry : angle 0.46786 (12390) Misc. bond : bond 0.00022 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 6180.35 seconds wall clock time: 107 minutes 10.16 seconds (6430.16 seconds total)