Starting phenix.real_space_refine on Sat Aug 23 04:18:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5x_44228/08_2025/9b5x_44228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5x_44228/08_2025/9b5x_44228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b5x_44228/08_2025/9b5x_44228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5x_44228/08_2025/9b5x_44228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5x_44228/08_2025/9b5x_44228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5x_44228/08_2025/9b5x_44228.map" } resolution = 4.16 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= 0.034 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 42 5.16 5 C 6074 2.51 5 N 1573 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9527 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: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} 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: 2.71, per 1000 atoms: 0.28 Number of scatterers: 9527 At special positions: 0 Unit cell: (94.696, 97.888, 119.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1833 8.00 N 1573 7.00 C 6074 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=2.92 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: 1.23 Conformation dependent library (CDL) restraints added in 429.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 11 sheets defined 46.1% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.825A 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: 3.686A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.958A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.221A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.682A 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: 3.705A 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: 4.220A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.950A pdb=" N GLN A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.705A 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: 4.465A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.864A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.662A 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 removed outlier: 3.601A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.899A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.511A 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 removed outlier: 3.528A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.766A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 736 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.928A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 4.112A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.532A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) 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 86 through 90 removed outlier: 3.530A pdb=" N LEU C 89 " --> pdb=" O LEU C 86 " (cutoff:3.500A) 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 helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.637A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.570A 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: 7.089A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.484A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.599A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 462 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.331A 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: 6.258A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP A 996 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL A 942 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.495A 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: 6.258A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.249A 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: 6.141A 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 Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16 removed outlier: 4.029A pdb=" N SER D 65 " --> pdb=" O GLN D 2 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1269 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: 1.61 Time building geometry restraints manager: 1.49 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: 1616 1.27 - 1.40: 2291 1.40 - 1.54: 5677 1.54 - 1.67: 90 1.67 - 1.81: 64 Bond restraints: 9738 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.526 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 9.05e-01 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 8.85e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.407 0.009 1.30e-02 5.92e+03 4.96e-01 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 12982 1.20 - 2.40: 134 2.40 - 3.59: 60 3.59 - 4.79: 14 4.79 - 5.99: 5 Bond angle restraints: 13195 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 121.70 127.69 -5.99 1.80e+00 3.09e-01 1.11e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.47 3.06 1.18e+00 7.24e-01 6.80e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.99 4.20 1.76e+00 3.23e-01 5.69e+00 angle pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.06 105.26 5.80 2.50e+00 1.60e-01 5.39e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 104.61 5.97 2.79e+00 1.28e-01 4.57e+00 ... (remaining 13190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 5626 15.21 - 30.42: 238 30.42 - 45.63: 46 45.63 - 60.84: 16 60.84 - 76.05: 3 Dihedral angle restraints: 5929 sinusoidal: 2424 harmonic: 3505 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 -162.05 76.05 1 1.00e+01 1.00e-02 7.29e+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 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" N GLU A 869 " pdb=" CA GLU A 869 " pdb=" CB GLU A 869 " pdb=" CG GLU A 869 " ideal model delta sinusoidal sigma weight residual -60.00 -118.79 58.79 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1287 0.055 - 0.111: 159 0.111 - 0.166: 22 0.166 - 0.221: 1 0.221 - 0.276: 2 Chirality restraints: 1471 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 -2.96 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.90 0.27 2.00e-01 2.50e+01 1.79e+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 -2.71 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1468 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 105 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C SER C 105 " -0.030 2.00e-02 2.50e+03 pdb=" O SER C 105 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE C 106 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 101 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C LYS C 101 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS C 101 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 102 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 543 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" C MET A 543 " -0.022 2.00e-02 2.50e+03 pdb=" O MET A 543 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR A 544 " 0.007 2.00e-02 2.50e+03 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 97 2.58 - 3.16: 8160 3.16 - 3.74: 14407 3.74 - 4.32: 20344 4.32 - 4.90: 34294 Nonbonded interactions: 77302 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2A ATP A1103 " model vdw 2.006 2.170 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.027 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.109 3.040 nonbonded pdb=" OD1 ASP A 154 " pdb=" NH1 ARG A 156 " model vdw 2.160 3.120 nonbonded pdb=" OG SER A 488 " pdb=" OE1 GLU A 489 " model vdw 2.184 3.040 ... (remaining 77297 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.730 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.009 0.885 9741 Z= 0.474 Angle : 0.698 61.862 13197 Z= 0.344 Chirality : 0.040 0.276 1471 Planarity : 0.003 0.023 1707 Dihedral : 9.372 73.529 3662 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.51 % Allowed : 2.83 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.97 (0.25), residues: 1199 helix: 1.52 (0.25), residues: 484 sheet: 0.11 (0.35), residues: 208 loop : 0.15 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 474 TYR 0.006 0.001 TYR A 277 PHE 0.008 0.001 PHE A 521 TRP 0.005 0.001 TRP C 93 HIS 0.002 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9738) covalent geometry : angle 0.44205 (13195) SS BOND : bond 0.88501 ( 1) SS BOND : angle 43.91215 ( 2) hydrogen bonds : bond 0.13970 ( 451) hydrogen bonds : angle 5.71452 ( 1269) Misc. bond : bond 0.07920 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9561 (ttp) cc_final: 0.9078 (tmm) REVERT: A 158 LEU cc_start: 0.9603 (mt) cc_final: 0.9380 (mp) REVERT: A 349 GLN cc_start: 0.8940 (mt0) cc_final: 0.8715 (pp30) REVERT: A 413 GLN cc_start: 0.9359 (tt0) cc_final: 0.9116 (mt0) REVERT: A 442 MET cc_start: 0.9785 (tpp) cc_final: 0.9224 (tpp) REVERT: A 448 MET cc_start: 0.9193 (mmp) cc_final: 0.8493 (mmm) REVERT: A 449 MET cc_start: 0.9468 (mtp) cc_final: 0.8874 (mmm) REVERT: A 533 THR cc_start: 0.9247 (m) cc_final: 0.8611 (p) REVERT: A 832 MET cc_start: 0.9308 (mtp) cc_final: 0.9008 (mtp) REVERT: A 869 GLU cc_start: 0.9529 (OUTLIER) cc_final: 0.9288 (mm-30) REVERT: A 941 GLU cc_start: 0.9373 (tt0) cc_final: 0.9049 (tm-30) REVERT: C 74 TYR cc_start: 0.9130 (t80) cc_final: 0.8067 (t80) REVERT: D 1 MET cc_start: 0.3807 (ptt) cc_final: 0.2537 (ptt) REVERT: D 18 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8098 (mm-30) outliers start: 16 outliers final: 6 residues processed: 180 average time/residue: 0.1179 time to fit residues: 28.7785 Evaluate side-chains 92 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.2958 r_free = 0.2958 target = 0.036234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.027787 restraints weight = 83100.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.028730 restraints weight = 56043.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.029359 restraints weight = 41600.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.029900 restraints weight = 33474.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030291 restraints weight = 27743.498| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9741 Z= 0.125 Angle : 0.529 7.903 13197 Z= 0.278 Chirality : 0.042 0.163 1471 Planarity : 0.004 0.065 1707 Dihedral : 5.137 55.666 1325 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.09 % Allowed : 1.70 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.21 (0.25), residues: 1199 helix: 1.50 (0.24), residues: 498 sheet: 0.65 (0.39), residues: 190 loop : 0.30 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 74 TYR 0.013 0.001 TYR A 81 PHE 0.011 0.001 PHE A 334 TRP 0.009 0.001 TRP C 93 HIS 0.004 0.001 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9738) covalent geometry : angle 0.52355 (13195) SS BOND : bond 0.01958 ( 1) SS BOND : angle 6.31124 ( 2) hydrogen bonds : bond 0.03548 ( 451) hydrogen bonds : angle 4.56774 ( 1269) Misc. bond : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9566 (ttp) cc_final: 0.9101 (tmm) REVERT: A 55 ASN cc_start: 0.9374 (m-40) cc_final: 0.8983 (m110) REVERT: A 413 GLN cc_start: 0.9299 (tt0) cc_final: 0.9028 (mt0) REVERT: A 442 MET cc_start: 0.9697 (tpp) cc_final: 0.9287 (tpp) REVERT: A 449 MET cc_start: 0.9377 (mtp) cc_final: 0.8762 (mmm) REVERT: A 464 MET cc_start: 0.9243 (pmm) cc_final: 0.8903 (pmm) REVERT: A 855 MET cc_start: 0.9281 (tpt) cc_final: 0.8802 (tpp) REVERT: A 941 GLU cc_start: 0.9410 (tt0) cc_final: 0.9055 (tm-30) REVERT: C 74 TYR cc_start: 0.8923 (t80) cc_final: 0.8434 (t80) REVERT: D 1 MET cc_start: 0.7948 (ptt) cc_final: 0.7471 (ptt) REVERT: D 23 ILE cc_start: 0.8998 (mm) cc_final: 0.8759 (mm) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.0769 time to fit residues: 13.0548 Evaluate side-chains 71 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 0.1980 chunk 34 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.2944 r_free = 0.2944 target = 0.035552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.026858 restraints weight = 83532.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.027777 restraints weight = 55977.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.028451 restraints weight = 41604.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.028964 restraints weight = 33009.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.029339 restraints weight = 27555.732| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9741 Z= 0.113 Angle : 0.496 6.671 13197 Z= 0.258 Chirality : 0.041 0.139 1471 Planarity : 0.004 0.066 1707 Dihedral : 5.047 58.205 1325 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.36 (0.26), residues: 1199 helix: 1.62 (0.24), residues: 498 sheet: 0.49 (0.40), residues: 197 loop : 0.51 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.018 0.001 TYR A 81 PHE 0.008 0.001 PHE A 678 TRP 0.010 0.001 TRP A 917 HIS 0.003 0.001 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9738) covalent geometry : angle 0.49162 (13195) SS BOND : bond 0.01491 ( 1) SS BOND : angle 5.05141 ( 2) hydrogen bonds : bond 0.03072 ( 451) hydrogen bonds : angle 4.35170 ( 1269) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9606 (ttp) cc_final: 0.9092 (tmm) REVERT: A 55 ASN cc_start: 0.9329 (m-40) cc_final: 0.8972 (m110) REVERT: A 334 PHE cc_start: 0.7231 (m-80) cc_final: 0.6913 (m-80) REVERT: A 413 GLN cc_start: 0.9338 (tt0) cc_final: 0.9024 (mt0) REVERT: A 442 MET cc_start: 0.9688 (tpp) cc_final: 0.9230 (tpp) REVERT: A 448 MET cc_start: 0.9125 (mmp) cc_final: 0.8849 (mmm) REVERT: A 464 MET cc_start: 0.9381 (pmm) cc_final: 0.8985 (pmm) REVERT: A 533 THR cc_start: 0.9286 (m) cc_final: 0.8668 (p) REVERT: A 832 MET cc_start: 0.9131 (mtm) cc_final: 0.8739 (ptm) REVERT: A 855 MET cc_start: 0.9240 (tpt) cc_final: 0.8754 (tpp) REVERT: C 13 LEU cc_start: 0.9119 (tt) cc_final: 0.8737 (pp) REVERT: C 30 LEU cc_start: 0.9784 (mm) cc_final: 0.9573 (mm) REVERT: D 1 MET cc_start: 0.8277 (ptt) cc_final: 0.7784 (ptt) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0896 time to fit residues: 11.6922 Evaluate side-chains 70 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 49 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- 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 = 0.2930 r_free = 0.2930 target = 0.035220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.026761 restraints weight = 86428.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.027677 restraints weight = 58015.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.028347 restraints weight = 42803.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.028835 restraints weight = 33974.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.029217 restraints weight = 28400.005| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9741 Z= 0.139 Angle : 0.514 5.998 13197 Z= 0.267 Chirality : 0.040 0.140 1471 Planarity : 0.004 0.056 1707 Dihedral : 5.239 59.864 1325 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.50 (0.26), residues: 1199 helix: 1.70 (0.24), residues: 497 sheet: 0.52 (0.40), residues: 193 loop : 0.63 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 74 TYR 0.014 0.001 TYR C 60 PHE 0.030 0.001 PHE C 50 TRP 0.010 0.001 TRP A 917 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9738) covalent geometry : angle 0.51064 (13195) SS BOND : bond 0.00768 ( 1) SS BOND : angle 4.49038 ( 2) hydrogen bonds : bond 0.02969 ( 451) hydrogen bonds : angle 4.31394 ( 1269) Misc. bond : bond 0.00011 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9604 (ttp) cc_final: 0.9369 (ppp) REVERT: A 55 ASN cc_start: 0.9295 (m-40) cc_final: 0.8962 (m110) REVERT: A 334 PHE cc_start: 0.7340 (m-80) cc_final: 0.7063 (m-80) REVERT: A 413 GLN cc_start: 0.9313 (tt0) cc_final: 0.8883 (mt0) REVERT: A 442 MET cc_start: 0.9641 (tpp) cc_final: 0.9203 (tpp) REVERT: A 449 MET cc_start: 0.9592 (mtp) cc_final: 0.8956 (mmt) REVERT: A 533 THR cc_start: 0.9236 (m) cc_final: 0.8673 (p) REVERT: A 832 MET cc_start: 0.9133 (mtm) cc_final: 0.8759 (ptm) REVERT: A 855 MET cc_start: 0.9312 (tpt) cc_final: 0.8959 (tpp) REVERT: A 941 GLU cc_start: 0.9393 (tt0) cc_final: 0.9049 (tm-30) REVERT: C 74 TYR cc_start: 0.8718 (t80) cc_final: 0.8301 (t80) REVERT: D 1 MET cc_start: 0.8282 (ptt) cc_final: 0.7836 (ptt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0818 time to fit residues: 9.9004 Evaluate side-chains 63 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.2923 r_free = 0.2923 target = 0.035110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.026997 restraints weight = 87123.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.027881 restraints weight = 58507.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.028545 restraints weight = 43376.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.029033 restraints weight = 34458.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.029403 restraints weight = 28885.993| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9741 Z= 0.125 Angle : 0.489 5.691 13197 Z= 0.253 Chirality : 0.040 0.133 1471 Planarity : 0.004 0.059 1707 Dihedral : 5.159 59.800 1325 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.55 (0.26), residues: 1199 helix: 1.74 (0.24), residues: 498 sheet: 0.51 (0.40), residues: 193 loop : 0.68 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 8 TYR 0.013 0.001 TYR C 60 PHE 0.018 0.001 PHE C 50 TRP 0.010 0.001 TRP A 917 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9738) covalent geometry : angle 0.48718 (13195) SS BOND : bond 0.00003 ( 1) SS BOND : angle 3.83256 ( 2) hydrogen bonds : bond 0.02792 ( 451) hydrogen bonds : angle 4.26839 ( 1269) Misc. bond : bond 0.00103 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9600 (ttp) cc_final: 0.9376 (ppp) REVERT: A 55 ASN cc_start: 0.9282 (m-40) cc_final: 0.8973 (m110) REVERT: A 184 MET cc_start: 0.8553 (tpt) cc_final: 0.8069 (tpt) REVERT: A 286 MET cc_start: 0.9174 (pmm) cc_final: 0.8958 (pmm) REVERT: A 413 GLN cc_start: 0.9307 (tt0) cc_final: 0.8968 (mt0) REVERT: A 442 MET cc_start: 0.9620 (tpp) cc_final: 0.9226 (tpp) REVERT: A 448 MET cc_start: 0.9180 (mmp) cc_final: 0.8840 (mmm) REVERT: A 449 MET cc_start: 0.9574 (mtp) cc_final: 0.8728 (mmm) REVERT: A 533 THR cc_start: 0.9211 (m) cc_final: 0.8681 (p) REVERT: A 832 MET cc_start: 0.9109 (mtm) cc_final: 0.8633 (ptp) REVERT: A 855 MET cc_start: 0.9324 (tpt) cc_final: 0.8840 (tpp) REVERT: A 865 LEU cc_start: 0.9662 (mt) cc_final: 0.9457 (mt) REVERT: A 866 VAL cc_start: 0.9599 (p) cc_final: 0.9121 (m) REVERT: A 869 GLU cc_start: 0.9154 (mp0) cc_final: 0.8706 (mp0) REVERT: C 13 LEU cc_start: 0.9138 (tt) cc_final: 0.8803 (pp) REVERT: C 74 TYR cc_start: 0.8534 (t80) cc_final: 0.8294 (t80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0774 time to fit residues: 9.1034 Evaluate side-chains 63 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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 = 0.2928 r_free = 0.2928 target = 0.035078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.026429 restraints weight = 85973.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.027327 restraints weight = 57272.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.027981 restraints weight = 42522.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.028470 restraints weight = 33986.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.028836 restraints weight = 28540.570| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9741 Z= 0.097 Angle : 0.490 6.636 13197 Z= 0.253 Chirality : 0.041 0.172 1471 Planarity : 0.004 0.068 1707 Dihedral : 5.139 59.982 1325 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.64 (0.26), residues: 1199 helix: 1.76 (0.24), residues: 497 sheet: 0.69 (0.40), residues: 192 loop : 0.74 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.011 0.001 TYR C 60 PHE 0.022 0.001 PHE A 526 TRP 0.008 0.001 TRP C 93 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9738) covalent geometry : angle 0.48930 (13195) SS BOND : bond 0.00437 ( 1) SS BOND : angle 2.69051 ( 2) hydrogen bonds : bond 0.02771 ( 451) hydrogen bonds : angle 4.19479 ( 1269) Misc. bond : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9578 (ttp) cc_final: 0.9367 (ppp) REVERT: A 55 ASN cc_start: 0.9299 (m-40) cc_final: 0.8981 (m110) REVERT: A 286 MET cc_start: 0.9223 (pmm) cc_final: 0.8989 (pmm) REVERT: A 413 GLN cc_start: 0.9340 (tt0) cc_final: 0.9020 (mt0) REVERT: A 442 MET cc_start: 0.9608 (tpp) cc_final: 0.9257 (tpp) REVERT: A 448 MET cc_start: 0.9105 (mmp) cc_final: 0.8830 (mmm) REVERT: A 449 MET cc_start: 0.9574 (mtp) cc_final: 0.8694 (mmm) REVERT: A 533 THR cc_start: 0.9170 (m) cc_final: 0.8581 (p) REVERT: A 832 MET cc_start: 0.9146 (mtm) cc_final: 0.8616 (ptp) REVERT: A 855 MET cc_start: 0.9331 (tpt) cc_final: 0.8950 (tpp) REVERT: C 74 TYR cc_start: 0.8693 (t80) cc_final: 0.8381 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0844 time to fit residues: 9.5783 Evaluate side-chains 62 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.2926 r_free = 0.2926 target = 0.034894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.026432 restraints weight = 85037.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.027311 restraints weight = 57777.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.027957 restraints weight = 43138.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.028447 restraints weight = 34522.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.028808 restraints weight = 29056.847| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9741 Z= 0.099 Angle : 0.476 5.530 13197 Z= 0.246 Chirality : 0.040 0.157 1471 Planarity : 0.004 0.067 1707 Dihedral : 5.060 59.878 1325 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.67 (0.26), residues: 1199 helix: 1.76 (0.24), residues: 498 sheet: 0.69 (0.40), residues: 193 loop : 0.79 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 8 TYR 0.011 0.001 TYR C 60 PHE 0.011 0.001 PHE C 50 TRP 0.007 0.001 TRP C 93 HIS 0.001 0.000 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9738) covalent geometry : angle 0.47357 (13195) SS BOND : bond 0.00234 ( 1) SS BOND : angle 3.82056 ( 2) hydrogen bonds : bond 0.02699 ( 451) hydrogen bonds : angle 4.14460 ( 1269) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9659 (ttp) cc_final: 0.9405 (ppp) REVERT: A 55 ASN cc_start: 0.9298 (m-40) cc_final: 0.8994 (m110) REVERT: A 286 MET cc_start: 0.9202 (pmm) cc_final: 0.8979 (pmm) REVERT: A 413 GLN cc_start: 0.9292 (tt0) cc_final: 0.9030 (mt0) REVERT: A 442 MET cc_start: 0.9610 (tpp) cc_final: 0.9224 (tpp) REVERT: A 533 THR cc_start: 0.9172 (m) cc_final: 0.8594 (p) REVERT: A 832 MET cc_start: 0.9138 (mtm) cc_final: 0.8618 (ptp) REVERT: A 855 MET cc_start: 0.9354 (tpt) cc_final: 0.8967 (tpp) REVERT: A 869 GLU cc_start: 0.9201 (mp0) cc_final: 0.8776 (mp0) REVERT: A 941 GLU cc_start: 0.9395 (tt0) cc_final: 0.9044 (tm-30) REVERT: C 74 TYR cc_start: 0.8663 (t80) cc_final: 0.8307 (t80) REVERT: C 126 VAL cc_start: 0.9588 (t) cc_final: 0.9232 (p) REVERT: D 1 MET cc_start: 0.8265 (ptt) cc_final: 0.7853 (ptp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0854 time to fit residues: 9.3603 Evaluate side-chains 63 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 63 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 68 optimal weight: 0.0050 chunk 39 optimal weight: 0.0470 chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5892 ------------------------------------------------------------------------------- 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 = 0.2926 r_free = 0.2926 target = 0.034913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.026436 restraints weight = 84344.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.027322 restraints weight = 57705.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.027972 restraints weight = 43109.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.028463 restraints weight = 34524.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.028826 restraints weight = 29080.472| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9741 Z= 0.093 Angle : 0.477 6.803 13197 Z= 0.244 Chirality : 0.040 0.154 1471 Planarity : 0.004 0.076 1707 Dihedral : 5.059 59.761 1325 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.72 (0.26), residues: 1199 helix: 1.78 (0.25), residues: 497 sheet: 0.77 (0.40), residues: 192 loop : 0.82 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 8 TYR 0.011 0.001 TYR C 60 PHE 0.021 0.001 PHE A 334 TRP 0.007 0.001 TRP C 93 HIS 0.001 0.000 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9738) covalent geometry : angle 0.47582 (13195) SS BOND : bond 0.00705 ( 1) SS BOND : angle 3.01238 ( 2) hydrogen bonds : bond 0.02667 ( 451) hydrogen bonds : angle 4.11384 ( 1269) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9621 (ttp) cc_final: 0.9403 (ppp) REVERT: A 55 ASN cc_start: 0.9289 (m-40) cc_final: 0.8987 (m110) REVERT: A 184 MET cc_start: 0.8828 (tpt) cc_final: 0.8269 (tpt) REVERT: A 286 MET cc_start: 0.9174 (pmm) cc_final: 0.8929 (pmm) REVERT: A 413 GLN cc_start: 0.9342 (tt0) cc_final: 0.8949 (mt0) REVERT: A 442 MET cc_start: 0.9591 (tpp) cc_final: 0.9223 (tpp) REVERT: A 448 MET cc_start: 0.9169 (mmp) cc_final: 0.8840 (mmm) REVERT: A 533 THR cc_start: 0.9166 (m) cc_final: 0.8600 (p) REVERT: A 832 MET cc_start: 0.9113 (mtm) cc_final: 0.8766 (ptm) REVERT: A 855 MET cc_start: 0.9341 (tpt) cc_final: 0.8970 (tpp) REVERT: A 869 GLU cc_start: 0.9156 (mp0) cc_final: 0.8880 (mp0) REVERT: A 906 MET cc_start: 0.8424 (pmm) cc_final: 0.8136 (pmm) REVERT: A 941 GLU cc_start: 0.9402 (tt0) cc_final: 0.9067 (tm-30) REVERT: C 69 PHE cc_start: 0.9343 (m-10) cc_final: 0.9140 (m-10) REVERT: C 74 TYR cc_start: 0.8613 (t80) cc_final: 0.8320 (t80) REVERT: C 101 LYS cc_start: 0.9400 (pttm) cc_final: 0.9155 (tptt) REVERT: C 126 VAL cc_start: 0.9576 (t) cc_final: 0.9218 (p) REVERT: D 1 MET cc_start: 0.8286 (ptt) cc_final: 0.7869 (ptp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0795 time to fit residues: 8.6895 Evaluate side-chains 64 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 95 optimal weight: 0.5980 chunk 30 optimal weight: 0.0370 chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 26 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.2930 r_free = 0.2930 target = 0.035066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.026560 restraints weight = 84415.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.027419 restraints weight = 56990.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.028058 restraints weight = 42714.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.028527 restraints weight = 34383.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.028894 restraints weight = 29056.160| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9741 Z= 0.093 Angle : 0.465 5.675 13197 Z= 0.239 Chirality : 0.040 0.152 1471 Planarity : 0.003 0.041 1707 Dihedral : 5.019 59.589 1325 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.74 (0.26), residues: 1199 helix: 1.80 (0.25), residues: 498 sheet: 0.71 (0.40), residues: 193 loop : 0.86 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 74 TYR 0.010 0.001 TYR C 134 PHE 0.013 0.001 PHE C 56 TRP 0.010 0.001 TRP C 33 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 9738) covalent geometry : angle 0.46367 (13195) SS BOND : bond 0.00904 ( 1) SS BOND : angle 2.65114 ( 2) hydrogen bonds : bond 0.02648 ( 451) hydrogen bonds : angle 4.08077 ( 1269) Misc. bond : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9623 (ttp) cc_final: 0.9402 (ppp) REVERT: A 55 ASN cc_start: 0.9282 (m-40) cc_final: 0.8971 (m110) REVERT: A 286 MET cc_start: 0.9166 (pmm) cc_final: 0.8911 (pmm) REVERT: A 413 GLN cc_start: 0.9316 (tt0) cc_final: 0.9057 (mt0) REVERT: A 442 MET cc_start: 0.9584 (tpp) cc_final: 0.9221 (tpp) REVERT: A 533 THR cc_start: 0.9168 (m) cc_final: 0.8585 (p) REVERT: A 832 MET cc_start: 0.9111 (mtm) cc_final: 0.8606 (ptp) REVERT: A 855 MET cc_start: 0.9333 (tpt) cc_final: 0.8972 (tpp) REVERT: A 865 LEU cc_start: 0.9660 (mt) cc_final: 0.9441 (mt) REVERT: A 869 GLU cc_start: 0.9142 (mp0) cc_final: 0.8695 (mp0) REVERT: A 906 MET cc_start: 0.8434 (pmm) cc_final: 0.8145 (pmm) REVERT: A 941 GLU cc_start: 0.9400 (tt0) cc_final: 0.9053 (tm-30) REVERT: C 74 TYR cc_start: 0.8634 (t80) cc_final: 0.8324 (t80) REVERT: C 101 LYS cc_start: 0.9395 (pttm) cc_final: 0.9162 (tptt) REVERT: C 126 VAL cc_start: 0.9580 (t) cc_final: 0.9225 (p) REVERT: D 1 MET cc_start: 0.8327 (ptt) cc_final: 0.7974 (ptp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0874 time to fit residues: 9.6938 Evaluate side-chains 64 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 1 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 0.0980 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 78 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.5140 ------------------------------------------------------------------------------- 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 = 0.2928 r_free = 0.2928 target = 0.034950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.026539 restraints weight = 85082.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.027418 restraints weight = 57911.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.028074 restraints weight = 43392.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.028580 restraints weight = 34664.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.028955 restraints weight = 29044.995| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9741 Z= 0.090 Angle : 0.475 6.485 13197 Z= 0.243 Chirality : 0.040 0.151 1471 Planarity : 0.004 0.071 1707 Dihedral : 5.021 59.336 1325 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.80 (0.26), residues: 1199 helix: 1.84 (0.24), residues: 497 sheet: 0.72 (0.38), residues: 204 loop : 0.92 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 8 TYR 0.010 0.001 TYR C 134 PHE 0.010 0.001 PHE A 633 TRP 0.009 0.001 TRP C 33 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 9738) covalent geometry : angle 0.47429 (13195) SS BOND : bond 0.00529 ( 1) SS BOND : angle 1.59281 ( 2) hydrogen bonds : bond 0.02595 ( 451) hydrogen bonds : angle 4.06297 ( 1269) Misc. bond : bond 0.00027 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9644 (ttp) cc_final: 0.9353 (ppp) REVERT: A 55 ASN cc_start: 0.9288 (m-40) cc_final: 0.8980 (m110) REVERT: A 413 GLN cc_start: 0.9334 (tt0) cc_final: 0.9108 (mt0) REVERT: A 442 MET cc_start: 0.9612 (tpp) cc_final: 0.9260 (tpp) REVERT: A 448 MET cc_start: 0.9157 (mmp) cc_final: 0.8928 (mmm) REVERT: A 533 THR cc_start: 0.9226 (m) cc_final: 0.8651 (p) REVERT: A 832 MET cc_start: 0.9153 (mtm) cc_final: 0.8766 (ptm) REVERT: A 855 MET cc_start: 0.9298 (tpt) cc_final: 0.8923 (tpp) REVERT: A 865 LEU cc_start: 0.9663 (mt) cc_final: 0.9448 (mt) REVERT: A 869 GLU cc_start: 0.9174 (mp0) cc_final: 0.8716 (mp0) REVERT: A 906 MET cc_start: 0.8447 (pmm) cc_final: 0.8178 (pmm) REVERT: A 941 GLU cc_start: 0.9397 (tt0) cc_final: 0.9055 (tm-30) REVERT: C 74 TYR cc_start: 0.8753 (t80) cc_final: 0.8367 (t80) REVERT: C 83 SER cc_start: 0.9512 (m) cc_final: 0.9136 (p) REVERT: C 101 LYS cc_start: 0.9396 (pttm) cc_final: 0.9184 (tptt) REVERT: C 126 VAL cc_start: 0.9588 (t) cc_final: 0.9240 (p) REVERT: D 1 MET cc_start: 0.8371 (ptt) cc_final: 0.7920 (ptp) REVERT: D 19 SER cc_start: 0.8743 (m) cc_final: 0.8348 (t) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0835 time to fit residues: 9.8452 Evaluate side-chains 67 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 16 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.2908 r_free = 0.2908 target = 0.034351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.026087 restraints weight = 88581.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.026943 restraints weight = 58942.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.027570 restraints weight = 44006.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.028041 restraints weight = 35109.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.028396 restraints weight = 29480.108| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9741 Z= 0.140 Angle : 0.511 7.023 13197 Z= 0.265 Chirality : 0.040 0.155 1471 Planarity : 0.003 0.042 1707 Dihedral : 5.076 59.596 1325 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.81 (0.26), residues: 1199 helix: 1.92 (0.24), residues: 498 sheet: 0.66 (0.38), residues: 202 loop : 0.87 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 74 TYR 0.015 0.001 TYR C 60 PHE 0.016 0.001 PHE C 50 TRP 0.012 0.001 TRP C 33 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9738) covalent geometry : angle 0.50991 (13195) SS BOND : bond 0.00811 ( 1) SS BOND : angle 2.52641 ( 2) hydrogen bonds : bond 0.02707 ( 451) hydrogen bonds : angle 4.19852 ( 1269) Misc. bond : bond 0.00015 ( 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: 1418.72 seconds wall clock time: 25 minutes 0.94 seconds (1500.94 seconds total)