Starting phenix.real_space_refine on Fri Mar 14 06:28:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5x_44228/03_2025/9b5x_44228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5x_44228/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5x_44228/03_2025/9b5x_44228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5x_44228/03_2025/9b5x_44228.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5x_44228/03_2025/9b5x_44228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5x_44228/03_2025/9b5x_44228.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.47, per 1000 atoms: 0.68 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: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.48 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: 3.61 Time building geometry restraints manager: 3.01 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: 3.360 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.850 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- 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 : 0.002 0.073 9738 Z= 0.133 Angle : 0.442 5.988 13195 Z= 0.228 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 : 2.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 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 TRP 0.005 0.001 TRP C 93 HIS 0.002 0.001 HIS D 68 PHE 0.008 0.001 PHE A 521 TYR 0.006 0.001 TYR A 277 ARG 0.002 0.000 ARG A 474 *********************** 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 : 1.108 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: 0.2372 time to fit residues: 57.7903 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 : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.0050 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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 = 0.2931 r_free = 0.2931 target = 0.035047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.026370 restraints weight = 83336.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.027276 restraints weight = 56040.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.027953 restraints weight = 41909.768| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9738 Z= 0.228 Angle : 0.543 6.102 13195 Z= 0.285 Chirality : 0.042 0.165 1471 Planarity : 0.004 0.064 1707 Dihedral : 5.206 56.390 1325 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1199 helix: 1.51 (0.24), residues: 499 sheet: 0.65 (0.39), residues: 194 loop : 0.39 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 93 HIS 0.004 0.001 HIS C 55 PHE 0.010 0.001 PHE A 170 TYR 0.012 0.001 TYR A 81 ARG 0.014 0.001 ARG D 74 *********************** 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 106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 1.021 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: symmetry clash REVERT: A 35 MET cc_start: 0.9634 (ttp) cc_final: 0.9104 (tmm) REVERT: A 55 ASN cc_start: 0.9374 (m-40) cc_final: 0.9005 (m110) REVERT: A 334 PHE cc_start: 0.6930 (m-80) cc_final: 0.6649 (m-80) REVERT: A 413 GLN cc_start: 0.9365 (tt0) cc_final: 0.9044 (mt0) REVERT: A 442 MET cc_start: 0.9723 (tpp) cc_final: 0.9283 (tpp) REVERT: A 449 MET cc_start: 0.9420 (mtp) cc_final: 0.8776 (mmm) REVERT: A 464 MET cc_start: 0.9344 (pmm) cc_final: 0.8972 (pmm) REVERT: A 855 MET cc_start: 0.9316 (tpt) cc_final: 0.8867 (tpp) REVERT: C 30 LEU cc_start: 0.9683 (mm) cc_final: 0.9400 (mm) REVERT: C 74 TYR cc_start: 0.9059 (t80) cc_final: 0.8499 (t80) REVERT: D 1 MET cc_start: 0.8270 (ptt) cc_final: 0.7930 (ptt) REVERT: D 23 ILE cc_start: 0.8953 (mm) cc_final: 0.8687 (mm) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.2045 time to fit residues: 31.4604 Evaluate side-chains 69 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 0.0040 chunk 5 optimal weight: 0.6980 chunk 92 optimal weight: 0.0470 chunk 18 optimal weight: 4.9990 overall best weight: 0.4892 ------------------------------------------------------------------------------- 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 = 0.2945 r_free = 0.2945 target = 0.035647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.026902 restraints weight = 84408.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.027822 restraints weight = 56403.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.028502 restraints weight = 42088.583| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9738 Z= 0.148 Angle : 0.481 5.810 13195 Z= 0.248 Chirality : 0.041 0.130 1471 Planarity : 0.003 0.043 1707 Dihedral : 5.068 58.197 1325 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1199 helix: 1.56 (0.24), residues: 499 sheet: 0.55 (0.40), residues: 193 loop : 0.53 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 93 HIS 0.001 0.000 HIS A 292 PHE 0.007 0.001 PHE C 50 TYR 0.010 0.001 TYR A 81 ARG 0.006 0.000 ARG D 74 *********************** 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 94 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9624 (ttp) cc_final: 0.9082 (tmm) REVERT: A 55 ASN cc_start: 0.9344 (m-40) cc_final: 0.8981 (m110) REVERT: A 334 PHE cc_start: 0.7063 (m-80) cc_final: 0.6841 (m-80) REVERT: A 413 GLN cc_start: 0.9334 (tt0) cc_final: 0.8972 (mt0) REVERT: A 442 MET cc_start: 0.9656 (tpp) cc_final: 0.9277 (tpp) REVERT: A 449 MET cc_start: 0.9481 (mtp) cc_final: 0.9232 (mtt) REVERT: A 464 MET cc_start: 0.9424 (pmm) cc_final: 0.9053 (pmm) REVERT: A 832 MET cc_start: 0.9152 (mtm) cc_final: 0.8756 (ptm) REVERT: A 855 MET cc_start: 0.9282 (tpt) cc_final: 0.8910 (tpp) REVERT: A 941 GLU cc_start: 0.9407 (tt0) cc_final: 0.9047 (tm-30) REVERT: C 30 LEU cc_start: 0.9735 (mm) cc_final: 0.9457 (mm) REVERT: D 1 MET cc_start: 0.8451 (ptt) cc_final: 0.8031 (ptt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2363 time to fit residues: 32.3239 Evaluate side-chains 68 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.2924 r_free = 0.2924 target = 0.034849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.026320 restraints weight = 86900.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.027258 restraints weight = 57953.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.027916 restraints weight = 42743.082| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9738 Z= 0.195 Angle : 0.501 5.835 13195 Z= 0.261 Chirality : 0.040 0.132 1471 Planarity : 0.004 0.054 1707 Dihedral : 5.169 58.984 1325 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1199 helix: 1.64 (0.24), residues: 497 sheet: 0.52 (0.40), residues: 193 loop : 0.57 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 93 HIS 0.002 0.001 HIS A 29 PHE 0.027 0.001 PHE C 50 TYR 0.014 0.001 TYR C 45 ARG 0.013 0.001 ARG D 74 *********************** 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 81 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9650 (ttp) cc_final: 0.9110 (tmm) REVERT: A 55 ASN cc_start: 0.9328 (m-40) cc_final: 0.8999 (m110) REVERT: A 184 MET cc_start: 0.9183 (mtp) cc_final: 0.8970 (tpt) REVERT: A 334 PHE cc_start: 0.7248 (m-80) cc_final: 0.6964 (m-80) REVERT: A 413 GLN cc_start: 0.9340 (tt0) cc_final: 0.9014 (mt0) REVERT: A 442 MET cc_start: 0.9655 (tpp) cc_final: 0.9194 (tpp) REVERT: A 449 MET cc_start: 0.9465 (mtp) cc_final: 0.9232 (mtt) REVERT: A 464 MET cc_start: 0.9367 (pmm) cc_final: 0.9125 (pmm) REVERT: A 533 THR cc_start: 0.9253 (m) cc_final: 0.8612 (p) REVERT: A 543 MET cc_start: 0.9614 (mtt) cc_final: 0.9303 (ptm) REVERT: A 832 MET cc_start: 0.9169 (mtm) cc_final: 0.8702 (ptp) REVERT: A 855 MET cc_start: 0.9298 (tpt) cc_final: 0.8899 (tpp) REVERT: A 941 GLU cc_start: 0.9407 (tt0) cc_final: 0.9054 (tm-30) REVERT: C 74 TYR cc_start: 0.8796 (t80) cc_final: 0.8270 (t80) REVERT: D 1 MET cc_start: 0.8485 (ptt) cc_final: 0.8126 (ptt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2120 time to fit residues: 25.7438 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 : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 104 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- 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 = 0.2919 r_free = 0.2919 target = 0.035090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.026849 restraints weight = 85648.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.027725 restraints weight = 56990.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.028407 restraints weight = 42601.855| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9738 Z= 0.175 Angle : 0.483 6.594 13195 Z= 0.248 Chirality : 0.040 0.197 1471 Planarity : 0.004 0.064 1707 Dihedral : 5.141 59.926 1325 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1199 helix: 1.68 (0.24), residues: 498 sheet: 0.51 (0.40), residues: 193 loop : 0.66 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 93 HIS 0.003 0.001 HIS A 29 PHE 0.018 0.001 PHE C 50 TYR 0.010 0.001 TYR C 60 ARG 0.006 0.000 ARG D 74 *********************** 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 82 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9643 (ttp) cc_final: 0.9380 (ppp) REVERT: A 55 ASN cc_start: 0.9318 (m-40) cc_final: 0.9014 (m110) REVERT: A 184 MET cc_start: 0.9176 (mtp) cc_final: 0.8850 (tpt) REVERT: A 286 MET cc_start: 0.9188 (pmm) cc_final: 0.8970 (pmm) REVERT: A 413 GLN cc_start: 0.9382 (tt0) cc_final: 0.9056 (mt0) REVERT: A 442 MET cc_start: 0.9636 (tpp) cc_final: 0.9233 (tpp) REVERT: A 448 MET cc_start: 0.9220 (mmp) cc_final: 0.8883 (mmm) REVERT: A 449 MET cc_start: 0.9480 (mtp) cc_final: 0.9235 (mtt) REVERT: A 464 MET cc_start: 0.9355 (pmm) cc_final: 0.9141 (pmm) REVERT: A 533 THR cc_start: 0.9272 (m) cc_final: 0.8647 (p) REVERT: A 556 LEU cc_start: 0.9630 (tp) cc_final: 0.9427 (tt) REVERT: A 832 MET cc_start: 0.9168 (mtm) cc_final: 0.8817 (ptm) REVERT: A 855 MET cc_start: 0.9337 (tpt) cc_final: 0.8939 (tpp) REVERT: A 865 LEU cc_start: 0.9691 (mt) cc_final: 0.9468 (mt) REVERT: A 866 VAL cc_start: 0.9642 (p) cc_final: 0.9156 (m) REVERT: A 869 GLU cc_start: 0.9252 (mp0) cc_final: 0.8800 (mp0) REVERT: A 941 GLU cc_start: 0.9399 (tt0) cc_final: 0.9034 (tm-30) REVERT: C 30 LEU cc_start: 0.9763 (mm) cc_final: 0.9540 (mm) REVERT: C 74 TYR cc_start: 0.8698 (t80) cc_final: 0.8350 (t80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2121 time to fit residues: 25.6507 Evaluate side-chains 65 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 0.0270 chunk 7 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.3044 ------------------------------------------------------------------------------- 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 = 0.2877 r_free = 0.2877 target = 0.033818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.025821 restraints weight = 87775.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.026676 restraints weight = 58443.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.027329 restraints weight = 43322.331| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9738 Z= 0.282 Angle : 0.565 7.547 13195 Z= 0.293 Chirality : 0.041 0.177 1471 Planarity : 0.004 0.067 1707 Dihedral : 5.317 59.841 1325 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1199 helix: 1.64 (0.24), residues: 497 sheet: 0.48 (0.39), residues: 192 loop : 0.71 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 33 HIS 0.004 0.001 HIS C 75 PHE 0.029 0.002 PHE A 526 TYR 0.015 0.001 TYR C 60 ARG 0.006 0.001 ARG C 8 *********************** 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 69 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9651 (ttp) cc_final: 0.9382 (ppp) REVERT: A 184 MET cc_start: 0.9180 (mtp) cc_final: 0.8819 (tpt) REVERT: A 286 MET cc_start: 0.9213 (pmm) cc_final: 0.8962 (pmm) REVERT: A 413 GLN cc_start: 0.9379 (tt0) cc_final: 0.9109 (mt0) REVERT: A 442 MET cc_start: 0.9699 (tpp) cc_final: 0.9263 (tpp) REVERT: A 448 MET cc_start: 0.9234 (mmp) cc_final: 0.9010 (mmm) REVERT: A 449 MET cc_start: 0.9520 (mtp) cc_final: 0.9235 (mtt) REVERT: A 533 THR cc_start: 0.9294 (m) cc_final: 0.8645 (p) REVERT: A 832 MET cc_start: 0.9204 (mtm) cc_final: 0.8845 (mtp) REVERT: A 855 MET cc_start: 0.9362 (tpt) cc_final: 0.8972 (tpp) REVERT: A 941 GLU cc_start: 0.9425 (tt0) cc_final: 0.9085 (tm-30) REVERT: C 74 TYR cc_start: 0.8820 (t80) cc_final: 0.8330 (t80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2103 time to fit residues: 21.5703 Evaluate side-chains 58 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 0.0870 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- 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 = 0.2893 r_free = 0.2893 target = 0.034171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.025731 restraints weight = 87235.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.026590 restraints weight = 59539.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.027221 restraints weight = 44392.612| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.003 0.035 9738 Z= 0.179 Angle : 0.496 5.689 13195 Z= 0.258 Chirality : 0.041 0.162 1471 Planarity : 0.004 0.082 1707 Dihedral : 5.285 59.664 1325 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1199 helix: 1.68 (0.24), residues: 498 sheet: 0.46 (0.39), residues: 191 loop : 0.76 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 33 HIS 0.003 0.001 HIS C 55 PHE 0.014 0.001 PHE A 334 TYR 0.012 0.001 TYR C 60 ARG 0.012 0.000 ARG C 8 *********************** 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 74 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.9305 (m-40) cc_final: 0.9000 (m-40) REVERT: A 184 MET cc_start: 0.9138 (mtp) cc_final: 0.8774 (tpt) REVERT: A 286 MET cc_start: 0.9179 (pmm) cc_final: 0.8928 (pmm) REVERT: A 413 GLN cc_start: 0.9372 (tt0) cc_final: 0.9108 (mt0) REVERT: A 442 MET cc_start: 0.9616 (tpp) cc_final: 0.9219 (tpp) REVERT: A 533 THR cc_start: 0.9272 (m) cc_final: 0.8632 (p) REVERT: A 832 MET cc_start: 0.9184 (mtm) cc_final: 0.8802 (mtp) REVERT: A 855 MET cc_start: 0.9334 (tpt) cc_final: 0.8981 (tpp) REVERT: A 869 GLU cc_start: 0.9226 (mp0) cc_final: 0.8843 (mp0) REVERT: A 941 GLU cc_start: 0.9448 (tt0) cc_final: 0.9234 (pt0) REVERT: A 944 MET cc_start: 0.9061 (mpp) cc_final: 0.8824 (mpp) REVERT: C 74 TYR cc_start: 0.8794 (t80) cc_final: 0.8363 (t80) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2152 time to fit residues: 23.6801 Evaluate side-chains 61 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.2883 r_free = 0.2883 target = 0.033713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.025408 restraints weight = 90883.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.026271 restraints weight = 60004.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.026907 restraints weight = 44581.668| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9738 Z= 0.212 Angle : 0.512 5.666 13195 Z= 0.267 Chirality : 0.041 0.163 1471 Planarity : 0.003 0.043 1707 Dihedral : 5.343 59.760 1325 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1199 helix: 1.68 (0.24), residues: 498 sheet: 0.35 (0.39), residues: 192 loop : 0.84 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 33 HIS 0.003 0.001 HIS C 75 PHE 0.022 0.001 PHE A 82 TYR 0.014 0.001 TYR C 60 ARG 0.003 0.000 ARG D 74 *********************** 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 69 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.9114 (mtp) cc_final: 0.8788 (tpt) REVERT: A 413 GLN cc_start: 0.9443 (tt0) cc_final: 0.9154 (mt0) REVERT: A 442 MET cc_start: 0.9647 (tpp) cc_final: 0.9235 (tpp) REVERT: A 448 MET cc_start: 0.9246 (mmp) cc_final: 0.8994 (mmm) REVERT: A 449 MET cc_start: 0.9571 (mtp) cc_final: 0.8681 (mmm) REVERT: A 533 THR cc_start: 0.9288 (m) cc_final: 0.8659 (p) REVERT: A 832 MET cc_start: 0.9180 (mtm) cc_final: 0.8789 (mtp) REVERT: A 855 MET cc_start: 0.9358 (tpt) cc_final: 0.9006 (tpp) REVERT: A 869 GLU cc_start: 0.9230 (mp0) cc_final: 0.8962 (mp0) REVERT: A 944 MET cc_start: 0.9088 (mpp) cc_final: 0.8855 (mpp) REVERT: C 74 TYR cc_start: 0.8794 (t80) cc_final: 0.8360 (t80) REVERT: C 101 LYS cc_start: 0.9582 (pttp) cc_final: 0.9257 (tptt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2464 time to fit residues: 24.8959 Evaluate side-chains 58 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.2898 r_free = 0.2898 target = 0.034256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.025926 restraints weight = 87787.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.026788 restraints weight = 58205.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.027417 restraints weight = 43336.367| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9738 Z= 0.154 Angle : 0.476 5.338 13195 Z= 0.247 Chirality : 0.041 0.155 1471 Planarity : 0.004 0.086 1707 Dihedral : 5.297 59.435 1325 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1199 helix: 1.74 (0.24), residues: 499 sheet: 0.43 (0.39), residues: 192 loop : 0.88 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 702 HIS 0.002 0.001 HIS A 292 PHE 0.023 0.001 PHE A 82 TYR 0.010 0.001 TYR C 60 ARG 0.013 0.000 ARG C 8 *********************** 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 74 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.9326 (m-40) cc_final: 0.9016 (m-40) REVERT: A 184 MET cc_start: 0.9092 (mtp) cc_final: 0.8758 (tpt) REVERT: A 413 GLN cc_start: 0.9420 (tt0) cc_final: 0.9123 (mt0) REVERT: A 442 MET cc_start: 0.9580 (tpp) cc_final: 0.9212 (tpp) REVERT: A 448 MET cc_start: 0.9176 (mmp) cc_final: 0.8966 (mmm) REVERT: A 449 MET cc_start: 0.9543 (mtp) cc_final: 0.8674 (mmm) REVERT: A 533 THR cc_start: 0.9252 (m) cc_final: 0.8608 (p) REVERT: A 832 MET cc_start: 0.9149 (mtm) cc_final: 0.8771 (mtp) REVERT: A 855 MET cc_start: 0.9350 (tpt) cc_final: 0.9005 (tpp) REVERT: A 869 GLU cc_start: 0.9157 (mp0) cc_final: 0.8886 (mp0) REVERT: C 74 TYR cc_start: 0.8726 (t80) cc_final: 0.8388 (t80) REVERT: D 1 MET cc_start: 0.8486 (ptt) cc_final: 0.8155 (ptp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2206 time to fit residues: 24.7322 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 : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 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 = 0.2897 r_free = 0.2897 target = 0.034098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.025724 restraints weight = 88472.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.026600 restraints weight = 58819.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.027249 restraints weight = 43606.805| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9738 Z= 0.162 Angle : 0.497 7.451 13195 Z= 0.261 Chirality : 0.041 0.157 1471 Planarity : 0.003 0.042 1707 Dihedral : 5.274 59.310 1325 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1199 helix: 1.66 (0.24), residues: 498 sheet: 0.45 (0.39), residues: 192 loop : 0.88 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 93 HIS 0.002 0.001 HIS A 819 PHE 0.021 0.001 PHE A 82 TYR 0.012 0.001 TYR C 60 ARG 0.004 0.000 ARG C 8 ********************** 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 72 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.9326 (m-40) cc_final: 0.9017 (m-40) REVERT: A 184 MET cc_start: 0.9054 (mtp) cc_final: 0.8738 (tpt) REVERT: A 413 GLN cc_start: 0.9442 (tt0) cc_final: 0.9150 (mt0) REVERT: A 442 MET cc_start: 0.9603 (tpp) cc_final: 0.9226 (tpp) REVERT: A 449 MET cc_start: 0.9546 (mtp) cc_final: 0.8677 (mmm) REVERT: A 533 THR cc_start: 0.9262 (m) cc_final: 0.8639 (p) REVERT: A 832 MET cc_start: 0.9154 (mtm) cc_final: 0.8774 (mtp) REVERT: A 855 MET cc_start: 0.9367 (tpt) cc_final: 0.9008 (tpp) REVERT: A 865 LEU cc_start: 0.9675 (mt) cc_final: 0.9469 (mt) REVERT: A 869 GLU cc_start: 0.9215 (mp0) cc_final: 0.8791 (mp0) REVERT: A 944 MET cc_start: 0.9051 (mpp) cc_final: 0.8712 (mpp) REVERT: C 74 TYR cc_start: 0.8779 (t80) cc_final: 0.8302 (t80) REVERT: C 101 LYS cc_start: 0.9526 (pttp) cc_final: 0.9231 (tptt) REVERT: C 126 VAL cc_start: 0.9624 (t) cc_final: 0.9313 (p) REVERT: D 1 MET cc_start: 0.8470 (ptt) cc_final: 0.8195 (ptp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2291 time to fit residues: 24.9560 Evaluate side-chains 65 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.0000 chunk 80 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.034491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.026065 restraints weight = 87243.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.026978 restraints weight = 58823.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.027630 restraints weight = 43280.916| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9738 Z= 0.141 Angle : 0.487 6.507 13195 Z= 0.254 Chirality : 0.041 0.156 1471 Planarity : 0.004 0.092 1707 Dihedral : 5.242 59.163 1325 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1199 helix: 1.63 (0.24), residues: 499 sheet: 0.53 (0.39), residues: 191 loop : 0.83 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 33 HIS 0.003 0.001 HIS A 292 PHE 0.020 0.001 PHE A 82 TYR 0.009 0.001 TYR C 60 ARG 0.016 0.000 ARG C 8 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2774.33 seconds wall clock time: 49 minutes 53.47 seconds (2993.47 seconds total)