Starting phenix.real_space_refine on Wed Sep 17 14:02:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5q_44221/09_2025/9b5q_44221.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5q_44221/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b5q_44221/09_2025/9b5q_44221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5q_44221/09_2025/9b5q_44221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5q_44221/09_2025/9b5q_44221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5q_44221/09_2025/9b5q_44221.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.80, per 1000 atoms: 0.20 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: 0.94 Conformation dependent library (CDL) restraints added in 345.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.54 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: 1.69 Time building geometry restraints manager: 1.17 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: 4.180 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 919 TYR 0.008 0.001 TYR A 732 PHE 0.010 0.001 PHE A 842 TRP 0.004 0.001 TRP A 608 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9140) covalent geometry : angle 0.46467 (12390) SS BOND : bond 0.86752 ( 1) SS BOND : angle 33.27292 ( 2) hydrogen bonds : bond 0.14919 ( 426) hydrogen bonds : angle 5.84327 ( 1212) 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 : 0.285 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: 0.6861 time to fit residues: 105.1116 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 : 0.371 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.133078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.093999 restraints weight = 11449.826| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.39 r_work: 0.2924 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9143 Z= 0.181 Angle : 0.523 8.098 12392 Z= 0.272 Chirality : 0.043 0.143 1374 Planarity : 0.004 0.040 1604 Dihedral : 6.218 67.767 1256 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.92 % Allowed : 6.35 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.25), residues: 1126 helix: 1.45 (0.24), residues: 486 sheet: 0.28 (0.41), residues: 174 loop : 0.11 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 139 TYR 0.010 0.001 TYR A 732 PHE 0.011 0.001 PHE A 842 TRP 0.005 0.001 TRP A 608 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9140) covalent geometry : angle 0.52127 (12390) SS BOND : bond 0.00416 ( 1) SS BOND : angle 3.03620 ( 2) hydrogen bonds : bond 0.04488 ( 426) hydrogen bonds : angle 4.73927 ( 1212) Misc. bond : bond 0.00120 ( 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 : 0.334 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8125 (t70) cc_final: 0.7141 (p0) REVERT: A 320 GLU cc_start: 0.7006 (tt0) cc_final: 0.6699 (tt0) REVERT: A 387 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8596 (p0) REVERT: A 442 MET cc_start: 0.8599 (tpp) cc_final: 0.8267 (mmm) REVERT: A 582 SER cc_start: 0.7751 (m) cc_final: 0.7513 (p) REVERT: A 596 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7266 (tttt) REVERT: A 668 MET cc_start: 0.7996 (tpp) cc_final: 0.7755 (mmm) REVERT: A 937 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 983 GLU cc_start: 0.8417 (mp0) cc_final: 0.7937 (mp0) REVERT: C 59 ASP cc_start: 0.8491 (m-30) cc_final: 0.7462 (t70) REVERT: C 72 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.7975 (mmm-85) outliers start: 19 outliers final: 10 residues processed: 101 average time/residue: 0.6543 time to fit residues: 70.2740 Evaluate side-chains 98 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 184 MET 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 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.134304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099403 restraints weight = 11590.859| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.86 r_work: 0.2978 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9143 Z= 0.158 Angle : 0.508 9.463 12392 Z= 0.262 Chirality : 0.043 0.153 1374 Planarity : 0.004 0.041 1604 Dihedral : 6.134 66.375 1255 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.62 % Allowed : 7.06 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.25), residues: 1126 helix: 1.50 (0.24), residues: 485 sheet: 0.24 (0.41), residues: 174 loop : 0.13 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 139 TYR 0.011 0.001 TYR C 145 PHE 0.010 0.001 PHE A 360 TRP 0.004 0.001 TRP A 608 HIS 0.006 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9140) covalent geometry : angle 0.50765 (12390) SS BOND : bond 0.01898 ( 1) SS BOND : angle 0.93009 ( 2) hydrogen bonds : bond 0.04047 ( 426) hydrogen bonds : angle 4.51227 ( 1212) Misc. bond : bond 0.00078 ( 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 107 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8181 (t70) cc_final: 0.7418 (p0) REVERT: A 320 GLU cc_start: 0.7402 (tt0) cc_final: 0.7176 (tt0) REVERT: A 582 SER cc_start: 0.8062 (m) cc_final: 0.7840 (p) REVERT: A 596 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7504 (tttt) REVERT: A 668 MET cc_start: 0.8366 (tpp) cc_final: 0.8086 (mmm) REVERT: A 937 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: A 983 GLU cc_start: 0.8605 (mp0) cc_final: 0.8182 (mp0) REVERT: C 59 ASP cc_start: 0.8373 (m-30) cc_final: 0.7610 (t70) outliers start: 26 outliers final: 17 residues processed: 98 average time/residue: 0.6690 time to fit residues: 69.6697 Evaluate side-chains 93 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 937 GLU 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 3 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.134327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099020 restraints weight = 11767.941| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.00 r_work: 0.2970 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9143 Z= 0.142 Angle : 0.488 10.559 12392 Z= 0.252 Chirality : 0.042 0.149 1374 Planarity : 0.004 0.042 1604 Dihedral : 6.027 62.571 1255 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.22 % Allowed : 9.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1126 helix: 1.54 (0.24), residues: 485 sheet: 0.19 (0.41), residues: 174 loop : 0.17 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 72 TYR 0.011 0.001 TYR C 145 PHE 0.009 0.001 PHE A 321 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9140) covalent geometry : angle 0.48730 (12390) SS BOND : bond 0.01538 ( 1) SS BOND : angle 1.25333 ( 2) hydrogen bonds : bond 0.03764 ( 426) hydrogen bonds : angle 4.37755 ( 1212) Misc. bond : bond 0.00010 ( 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: 22 poor density : 74 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8168 (t70) cc_final: 0.7377 (p0) REVERT: A 320 GLU cc_start: 0.7365 (tt0) cc_final: 0.7162 (tt0) REVERT: A 582 SER cc_start: 0.8056 (m) cc_final: 0.7831 (p) REVERT: A 596 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7480 (tttt) REVERT: A 699 GLN cc_start: 0.8424 (mt0) cc_final: 0.7547 (mp10) REVERT: A 983 GLU cc_start: 0.8554 (mp0) cc_final: 0.8090 (mp0) REVERT: C 59 ASP cc_start: 0.8356 (m-30) cc_final: 0.7629 (t70) REVERT: C 72 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8189 (mmm-85) outliers start: 22 outliers final: 11 residues processed: 91 average time/residue: 0.6255 time to fit residues: 60.7727 Evaluate side-chains 85 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 221 LEU 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 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 38 optimal weight: 0.0570 chunk 110 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.134884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099825 restraints weight = 11626.140| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.87 r_work: 0.2987 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1661 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= 0.130 Angle : 0.483 10.323 12392 Z= 0.250 Chirality : 0.041 0.150 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.803 61.398 1250 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.22 % Allowed : 9.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.26), residues: 1126 helix: 1.57 (0.24), residues: 486 sheet: 0.16 (0.41), residues: 174 loop : 0.21 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 72 TYR 0.012 0.001 TYR C 145 PHE 0.009 0.001 PHE A 321 TRP 0.003 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9140) covalent geometry : angle 0.48321 (12390) SS BOND : bond 0.01246 ( 1) SS BOND : angle 1.28844 ( 2) hydrogen bonds : bond 0.03636 ( 426) hydrogen bonds : angle 4.33448 ( 1212) Misc. bond : bond 0.00021 ( 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 97 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8436 (tp30) cc_final: 0.7994 (tp30) REVERT: A 274 ASP cc_start: 0.8164 (t70) cc_final: 0.7404 (p0) REVERT: A 465 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8387 (t0) REVERT: A 582 SER cc_start: 0.8085 (m) cc_final: 0.7862 (p) REVERT: A 596 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7544 (tttt) REVERT: A 699 GLN cc_start: 0.8418 (mt0) cc_final: 0.8150 (mp10) REVERT: A 983 GLU cc_start: 0.8558 (mp0) cc_final: 0.8100 (mp0) REVERT: C 59 ASP cc_start: 0.8318 (m-30) cc_final: 0.7643 (t70) REVERT: C 139 ARG cc_start: 0.6690 (ttm-80) cc_final: 0.6008 (mtm-85) outliers start: 22 outliers final: 12 residues processed: 88 average time/residue: 0.6594 time to fit residues: 61.7208 Evaluate side-chains 86 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 = 0.134321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099585 restraints weight = 11709.389| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.93 r_work: 0.2973 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9143 Z= 0.156 Angle : 0.488 10.500 12392 Z= 0.254 Chirality : 0.042 0.150 1374 Planarity : 0.004 0.048 1604 Dihedral : 5.848 61.387 1250 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.02 % Allowed : 9.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1126 helix: 1.56 (0.24), residues: 484 sheet: 0.10 (0.40), residues: 174 loop : 0.18 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 72 TYR 0.012 0.001 TYR C 145 PHE 0.009 0.001 PHE A 265 TRP 0.004 0.001 TRP A 608 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9140) covalent geometry : angle 0.48776 (12390) SS BOND : bond 0.01433 ( 1) SS BOND : angle 1.08452 ( 2) hydrogen bonds : bond 0.03817 ( 426) hydrogen bonds : angle 4.35200 ( 1212) Misc. bond : bond 0.00072 ( 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 94 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8443 (tp30) cc_final: 0.7992 (tp30) REVERT: A 274 ASP cc_start: 0.8187 (t70) cc_final: 0.7409 (p0) REVERT: A 465 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8402 (t70) REVERT: A 582 SER cc_start: 0.8092 (m) cc_final: 0.7870 (p) REVERT: A 596 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7530 (tttt) REVERT: A 668 MET cc_start: 0.8407 (tpp) cc_final: 0.8131 (mmm) REVERT: A 699 GLN cc_start: 0.8462 (mt0) cc_final: 0.7585 (mp10) REVERT: A 983 GLU cc_start: 0.8576 (mp0) cc_final: 0.8108 (mp0) REVERT: C 59 ASP cc_start: 0.8317 (m-30) cc_final: 0.7646 (t70) outliers start: 20 outliers final: 11 residues processed: 87 average time/residue: 0.6624 time to fit residues: 61.3682 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 : 0.368 ------------------------------------------------------------------------------- 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 979 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.134347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099155 restraints weight = 11696.013| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.89 r_work: 0.2972 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9143 Z= 0.149 Angle : 0.486 10.193 12392 Z= 0.252 Chirality : 0.042 0.150 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.825 60.191 1250 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.92 % Allowed : 10.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1126 helix: 1.59 (0.24), residues: 484 sheet: 0.05 (0.40), residues: 174 loop : 0.16 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 139 TYR 0.008 0.001 TYR A 736 PHE 0.009 0.001 PHE A 360 TRP 0.004 0.001 TRP A 917 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9140) covalent geometry : angle 0.48560 (12390) SS BOND : bond 0.01260 ( 1) SS BOND : angle 1.11852 ( 2) hydrogen bonds : bond 0.03749 ( 426) hydrogen bonds : angle 4.31621 ( 1212) Misc. bond : bond 0.00058 ( 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: 19 poor density : 75 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8451 (tp30) cc_final: 0.8004 (tp30) REVERT: A 274 ASP cc_start: 0.8191 (t70) cc_final: 0.7389 (p0) REVERT: A 465 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8406 (t70) REVERT: A 582 SER cc_start: 0.8095 (m) cc_final: 0.7874 (p) REVERT: A 596 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7520 (tttt) REVERT: A 668 MET cc_start: 0.8399 (tpp) cc_final: 0.8121 (mmm) REVERT: A 699 GLN cc_start: 0.8432 (mt0) cc_final: 0.7558 (mp10) REVERT: A 935 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7802 (tm130) REVERT: A 983 GLU cc_start: 0.8584 (mp0) cc_final: 0.8112 (mp0) REVERT: A 1005 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8090 (m) REVERT: C 59 ASP cc_start: 0.8316 (m-30) cc_final: 0.7633 (t70) REVERT: C 139 ARG cc_start: 0.6940 (ttm-80) cc_final: 0.6173 (mtm-85) outliers start: 19 outliers final: 10 residues processed: 89 average time/residue: 0.6457 time to fit residues: 61.2713 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 : 0.358 ------------------------------------------------------------------------------- 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 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 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 51 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.0270 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.135192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099193 restraints weight = 11675.617| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.97 r_work: 0.2970 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9143 Z= 0.123 Angle : 0.475 9.850 12392 Z= 0.247 Chirality : 0.042 0.167 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.742 57.931 1250 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.26), residues: 1126 helix: 1.67 (0.24), residues: 483 sheet: 0.08 (0.40), residues: 174 loop : 0.18 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 72 TYR 0.008 0.001 TYR A 736 PHE 0.009 0.001 PHE A 321 TRP 0.003 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9140) covalent geometry : angle 0.47530 (12390) SS BOND : bond 0.01488 ( 1) SS BOND : angle 0.62234 ( 2) hydrogen bonds : bond 0.03501 ( 426) hydrogen bonds : angle 4.26578 ( 1212) Misc. bond : bond 0.00006 ( 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 85 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8445 (tp30) cc_final: 0.7994 (tp30) REVERT: A 274 ASP cc_start: 0.8191 (t70) cc_final: 0.7361 (p0) REVERT: A 465 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8444 (t70) REVERT: A 582 SER cc_start: 0.8048 (m) cc_final: 0.7823 (p) REVERT: A 596 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7500 (tttt) REVERT: A 699 GLN cc_start: 0.8417 (mt0) cc_final: 0.7505 (mp10) REVERT: A 983 GLU cc_start: 0.8576 (mp0) cc_final: 0.8088 (mp0) REVERT: C 59 ASP cc_start: 0.8348 (m-30) cc_final: 0.7609 (t70) REVERT: C 139 ARG cc_start: 0.6906 (ttm-80) cc_final: 0.6150 (mtm-85) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.6485 time to fit residues: 57.2855 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 : 0.359 ------------------------------------------------------------------------------- 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 255 THR 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 C residue 91 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 overall best weight: 0.4018 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.135532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100010 restraints weight = 11619.341| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.96 r_work: 0.2990 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9143 Z= 0.111 Angle : 0.470 9.145 12392 Z= 0.243 Chirality : 0.041 0.144 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.651 56.011 1250 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.81 % Allowed : 10.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1126 helix: 1.72 (0.24), residues: 483 sheet: 0.24 (0.41), residues: 164 loop : 0.16 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.007 0.001 TYR A 736 PHE 0.009 0.001 PHE A 613 TRP 0.003 0.001 TRP A 917 HIS 0.002 0.000 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9140) covalent geometry : angle 0.47027 (12390) SS BOND : bond 0.01894 ( 1) SS BOND : angle 0.99951 ( 2) hydrogen bonds : bond 0.03318 ( 426) hydrogen bonds : angle 4.20210 ( 1212) Misc. bond : bond 0.00088 ( 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 91 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8440 (tp30) cc_final: 0.8003 (tp30) REVERT: A 32 MET cc_start: 0.8744 (mtp) cc_final: 0.8495 (mmm) REVERT: A 274 ASP cc_start: 0.8166 (t70) cc_final: 0.7341 (p0) REVERT: A 465 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8431 (t70) REVERT: A 582 SER cc_start: 0.8072 (m) cc_final: 0.7852 (p) REVERT: A 596 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7503 (tttt) REVERT: A 699 GLN cc_start: 0.8399 (mt0) cc_final: 0.7519 (mp10) REVERT: A 983 GLU cc_start: 0.8582 (mp0) cc_final: 0.8100 (mp0) REVERT: A 1005 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8102 (m) REVERT: C 59 ASP cc_start: 0.8304 (m-30) cc_final: 0.7604 (t70) REVERT: C 139 ARG cc_start: 0.6975 (ttm-80) cc_final: 0.6243 (mtm-85) outliers start: 18 outliers final: 9 residues processed: 85 average time/residue: 0.6647 time to fit residues: 60.0359 Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 86 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.134775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101291 restraints weight = 11568.935| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.73 r_work: 0.3026 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9143 Z= 0.118 Angle : 0.475 9.315 12392 Z= 0.246 Chirality : 0.041 0.144 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.637 55.947 1250 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.21 % Allowed : 11.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.26), residues: 1126 helix: 1.76 (0.24), residues: 477 sheet: 0.23 (0.41), residues: 164 loop : 0.17 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.007 0.001 TYR A 736 PHE 0.009 0.001 PHE A 321 TRP 0.003 0.001 TRP A 917 HIS 0.002 0.000 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9140) covalent geometry : angle 0.47464 (12390) SS BOND : bond 0.01261 ( 1) SS BOND : angle 1.00032 ( 2) hydrogen bonds : bond 0.03357 ( 426) hydrogen bonds : angle 4.19939 ( 1212) Misc. bond : bond 0.00022 ( 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 84 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8417 (tp30) cc_final: 0.8040 (tp30) REVERT: A 274 ASP cc_start: 0.8058 (t70) cc_final: 0.7480 (p0) REVERT: A 596 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7776 (tttt) REVERT: A 668 MET cc_start: 0.8437 (tpp) cc_final: 0.8183 (mmm) REVERT: A 699 GLN cc_start: 0.8329 (mt0) cc_final: 0.7584 (mp10) REVERT: A 983 GLU cc_start: 0.8587 (mp0) cc_final: 0.8222 (mp0) REVERT: A 1005 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8178 (m) REVERT: C 59 ASP cc_start: 0.8068 (m-30) cc_final: 0.7662 (t70) outliers start: 12 outliers final: 8 residues processed: 82 average time/residue: 0.6321 time to fit residues: 55.1873 Evaluate side-chains 81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.0170 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.134887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100369 restraints weight = 11520.245| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.78 r_work: 0.3013 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9143 Z= 0.125 Angle : 0.481 9.279 12392 Z= 0.250 Chirality : 0.041 0.144 1374 Planarity : 0.004 0.068 1604 Dihedral : 5.644 55.953 1250 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.11 % Allowed : 11.69 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.26), residues: 1126 helix: 1.71 (0.24), residues: 483 sheet: 0.20 (0.41), residues: 164 loop : 0.14 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 139 TYR 0.007 0.001 TYR A 736 PHE 0.008 0.001 PHE A 321 TRP 0.004 0.001 TRP A 917 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9140) covalent geometry : angle 0.48134 (12390) SS BOND : bond 0.01225 ( 1) SS BOND : angle 1.01096 ( 2) hydrogen bonds : bond 0.03416 ( 426) hydrogen bonds : angle 4.21316 ( 1212) Misc. bond : bond 0.00008 ( 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: 3121.89 seconds wall clock time: 53 minutes 42.59 seconds (3222.59 seconds total)