Starting phenix.real_space_refine on Thu Jan 16 15:31:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5x_44228/01_2025/9b5x_44228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5x_44228/01_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_44228/01_2025/9b5x_44228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5x_44228/01_2025/9b5x_44228.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5x_44228/01_2025/9b5x_44228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5x_44228/01_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-5571/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: 6.30, per 1000 atoms: 0.66 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: 2.37 Conformation dependent library (CDL) restraints added in 1.2 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: 1.37 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: 3.15 Time building geometry restraints manager: 2.75 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: 2.680 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.880 ------------------------------------------------------------------------------- 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 : 1.187 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: 0.2614 time to fit residues: 63.4552 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 : 1.186 ------------------------------------------------------------------------------- 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 = 0.026369 restraints weight = 83336.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.027306 restraints weight = 56048.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.027971 restraints weight = 41408.051| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- 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 : 0.941 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: 0.9635 (ttp) cc_final: 0.9105 (tmm) REVERT: A 55 ASN cc_start: 0.9374 (m-40) cc_final: 0.9004 (m110) REVERT: A 334 PHE cc_start: 0.6928 (m-80) cc_final: 0.6650 (m-80) REVERT: A 413 GLN cc_start: 0.9365 (tt0) cc_final: 0.9043 (mt0) REVERT: A 442 MET cc_start: 0.9722 (tpp) cc_final: 0.9283 (tpp) REVERT: A 449 MET cc_start: 0.9421 (mtp) cc_final: 0.8775 (mmm) REVERT: A 464 MET cc_start: 0.9344 (pmm) cc_final: 0.8972 (pmm) REVERT: A 855 MET cc_start: 0.9314 (tpt) cc_final: 0.8865 (tpp) REVERT: C 30 LEU cc_start: 0.9682 (mm) cc_final: 0.9399 (mm) REVERT: C 74 TYR cc_start: 0.9059 (t80) cc_final: 0.8500 (t80) REVERT: D 1 MET cc_start: 0.8272 (ptt) cc_final: 0.7931 (ptt) REVERT: D 23 ILE cc_start: 0.8952 (mm) cc_final: 0.8686 (mm) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.2087 time to fit residues: 32.0156 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 : 1.232 ------------------------------------------------------------------------------- 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: 1.9990 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.2936 r_free = 0.2936 target = 0.035401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.026764 restraints weight = 85591.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.027679 restraints weight = 56912.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.028355 restraints weight = 42396.519| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9738 Z= 0.162 Angle : 0.477 5.864 13195 Z= 0.248 Chirality : 0.041 0.139 1471 Planarity : 0.003 0.048 1707 Dihedral : 5.071 58.375 1325 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: 1.39 (0.26), residues: 1199 helix: 1.59 (0.24), residues: 499 sheet: 0.55 (0.40), residues: 193 loop : 0.56 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 93 HIS 0.002 0.000 HIS D 68 PHE 0.008 0.001 PHE A 888 TYR 0.009 0.001 TYR C 134 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 88 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.094 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: 0.9628 (ttp) cc_final: 0.9084 (tmm) REVERT: A 55 ASN cc_start: 0.9339 (m-40) cc_final: 0.8988 (m110) REVERT: A 334 PHE cc_start: 0.7077 (m-80) cc_final: 0.6862 (m-80) REVERT: A 413 GLN cc_start: 0.9337 (tt0) cc_final: 0.8941 (mt0) REVERT: A 442 MET cc_start: 0.9657 (tpp) cc_final: 0.9244 (tpp) REVERT: A 448 MET cc_start: 0.9140 (mmp) cc_final: 0.8830 (mmm) REVERT: A 464 MET cc_start: 0.9433 (pmm) cc_final: 0.9066 (pmm) REVERT: A 832 MET cc_start: 0.9151 (mtm) cc_final: 0.8759 (ptm) REVERT: A 855 MET cc_start: 0.9263 (tpt) cc_final: 0.8882 (tpp) REVERT: C 30 LEU cc_start: 0.9735 (mm) cc_final: 0.9461 (mm) REVERT: C 126 VAL cc_start: 0.9591 (t) cc_final: 0.9379 (p) REVERT: D 1 MET cc_start: 0.8493 (ptt) cc_final: 0.8084 (ptt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2095 time to fit residues: 27.3377 Evaluate side-chains 66 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 0.0770 chunk 82 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 95 optimal weight: 0.0980 overall best weight: 1.6344 ------------------------------------------------------------------------------- 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 = 0.2912 r_free = 0.2912 target = 0.034806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.026621 restraints weight = 86447.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.027523 restraints weight = 57530.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.028185 restraints weight = 42454.190| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9738 Z= 0.225 Angle : 0.523 5.868 13195 Z= 0.273 Chirality : 0.040 0.129 1471 Planarity : 0.004 0.053 1707 Dihedral : 5.271 59.963 1325 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 0.49 (0.40), residues: 193 loop : 0.60 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 93 HIS 0.003 0.001 HIS A 29 PHE 0.030 0.001 PHE C 50 TYR 0.014 0.001 TYR C 45 ARG 0.014 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 77 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9639 (ttp) cc_final: 0.9118 (tmm) REVERT: A 55 ASN cc_start: 0.9312 (m-40) cc_final: 0.9006 (m110) REVERT: A 334 PHE cc_start: 0.7244 (m-80) cc_final: 0.6998 (m-80) REVERT: A 413 GLN cc_start: 0.9361 (tt0) cc_final: 0.8923 (mt0) REVERT: A 442 MET cc_start: 0.9668 (tpp) cc_final: 0.9178 (tpp) REVERT: A 449 MET cc_start: 0.9599 (mtp) cc_final: 0.8969 (mmt) REVERT: A 533 THR cc_start: 0.9248 (m) cc_final: 0.8630 (p) REVERT: A 832 MET cc_start: 0.9169 (mtm) cc_final: 0.8852 (ptm) REVERT: A 855 MET cc_start: 0.9335 (tpt) cc_final: 0.8947 (tpp) REVERT: A 941 GLU cc_start: 0.9384 (tt0) cc_final: 0.9025 (tm-30) REVERT: C 74 TYR cc_start: 0.8729 (t80) cc_final: 0.8292 (t80) REVERT: D 1 MET cc_start: 0.8441 (ptt) cc_final: 0.7999 (ptt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2102 time to fit residues: 24.0295 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 : 1.100 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.035278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.026983 restraints weight = 85446.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.027906 restraints weight = 56964.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.028561 restraints weight = 41974.519| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3099 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= 0.161 Angle : 0.480 5.664 13195 Z= 0.247 Chirality : 0.040 0.131 1471 Planarity : 0.004 0.061 1707 Dihedral : 5.336 59.816 1325 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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 (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: 1.45 (0.25), residues: 1199 helix: 1.65 (0.24), residues: 498 sheet: 0.53 (0.40), residues: 193 loop : 0.61 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 93 HIS 0.002 0.001 HIS A 292 PHE 0.016 0.001 PHE C 50 TYR 0.010 0.001 TYR C 134 ARG 0.009 0.000 ARG C 8 *********************** 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 79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9647 (ttp) cc_final: 0.9386 (ppp) REVERT: A 55 ASN cc_start: 0.9329 (m-40) cc_final: 0.9023 (m110) REVERT: A 286 MET cc_start: 0.9180 (pmm) cc_final: 0.8957 (pmm) REVERT: A 413 GLN cc_start: 0.9364 (tt0) cc_final: 0.8998 (mt0) REVERT: A 442 MET cc_start: 0.9629 (tpp) cc_final: 0.9245 (tpp) REVERT: A 448 MET cc_start: 0.9194 (mmp) cc_final: 0.8832 (mmm) REVERT: A 449 MET cc_start: 0.9591 (mtp) cc_final: 0.8764 (mmm) REVERT: A 533 THR cc_start: 0.9253 (m) cc_final: 0.8597 (p) REVERT: A 832 MET cc_start: 0.9164 (mtm) cc_final: 0.8732 (ptp) REVERT: A 855 MET cc_start: 0.9337 (tpt) cc_final: 0.8945 (tpp) REVERT: A 866 VAL cc_start: 0.9613 (p) cc_final: 0.9198 (m) REVERT: A 869 GLU cc_start: 0.9167 (mp0) cc_final: 0.8741 (mp0) REVERT: A 941 GLU cc_start: 0.9395 (tt0) cc_final: 0.9033 (tm-30) REVERT: C 74 TYR cc_start: 0.8634 (t80) cc_final: 0.8310 (t80) REVERT: D 1 MET cc_start: 0.8355 (ptt) cc_final: 0.7967 (ptt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2035 time to fit residues: 23.8166 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 : 1.138 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 0.0020 chunk 102 optimal weight: 5.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- 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 = 0.2911 r_free = 0.2911 target = 0.034947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.026650 restraints weight = 86418.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.027558 restraints weight = 57797.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.028217 restraints weight = 42727.277| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9738 Z= 0.178 Angle : 0.495 6.114 13195 Z= 0.256 Chirality : 0.040 0.171 1471 Planarity : 0.004 0.064 1707 Dihedral : 5.188 59.999 1325 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 1.54 (0.25), residues: 1199 helix: 1.70 (0.24), residues: 497 sheet: 0.54 (0.39), residues: 193 loop : 0.71 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 93 HIS 0.002 0.001 HIS C 75 PHE 0.022 0.001 PHE A 526 TYR 0.010 0.001 TYR C 60 ARG 0.007 0.000 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 74 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9596 (ttp) cc_final: 0.9370 (ppp) REVERT: A 55 ASN cc_start: 0.9316 (m-40) cc_final: 0.9023 (m110) REVERT: A 286 MET cc_start: 0.9178 (pmm) cc_final: 0.8962 (pmm) REVERT: A 413 GLN cc_start: 0.9368 (tt0) cc_final: 0.8998 (mt0) REVERT: A 442 MET cc_start: 0.9642 (tpp) cc_final: 0.9238 (tpp) REVERT: A 448 MET cc_start: 0.9165 (mmp) cc_final: 0.8902 (mmm) REVERT: A 449 MET cc_start: 0.9583 (mtp) cc_final: 0.8709 (mmm) REVERT: A 533 THR cc_start: 0.9250 (m) cc_final: 0.8615 (p) REVERT: A 832 MET cc_start: 0.9180 (mtm) cc_final: 0.8808 (mtp) REVERT: A 855 MET cc_start: 0.9348 (tpt) cc_final: 0.8946 (tpp) REVERT: A 941 GLU cc_start: 0.9409 (tt0) cc_final: 0.9042 (tm-30) REVERT: C 74 TYR cc_start: 0.8658 (t80) cc_final: 0.8317 (t80) REVERT: C 101 LYS cc_start: 0.9544 (pttt) cc_final: 0.9301 (pttm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2116 time to fit residues: 23.4046 Evaluate side-chains 60 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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: 0.6980 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.2894 r_free = 0.2894 target = 0.034454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.026338 restraints weight = 88254.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.027201 restraints weight = 58934.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.027836 restraints weight = 43801.561| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9738 Z= 0.204 Angle : 0.502 5.444 13195 Z= 0.262 Chirality : 0.041 0.163 1471 Planarity : 0.004 0.066 1707 Dihedral : 5.228 59.694 1325 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 1.58 (0.25), residues: 1199 helix: 1.73 (0.24), residues: 498 sheet: 0.46 (0.39), residues: 193 loop : 0.77 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 93 HIS 0.003 0.001 HIS C 55 PHE 0.015 0.001 PHE C 50 TYR 0.012 0.001 TYR C 60 ARG 0.006 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 72 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9651 (ttp) cc_final: 0.9410 (ppp) REVERT: A 55 ASN cc_start: 0.9342 (m-40) cc_final: 0.9063 (m110) REVERT: A 286 MET cc_start: 0.9150 (pmm) cc_final: 0.8891 (pmm) REVERT: A 413 GLN cc_start: 0.9384 (tt0) cc_final: 0.9030 (mt0) REVERT: A 442 MET cc_start: 0.9659 (tpp) cc_final: 0.9238 (tpp) REVERT: A 449 MET cc_start: 0.9586 (mtp) cc_final: 0.8687 (mmm) REVERT: A 533 THR cc_start: 0.9234 (m) cc_final: 0.8599 (p) REVERT: A 832 MET cc_start: 0.9182 (mtm) cc_final: 0.8816 (mtp) REVERT: A 855 MET cc_start: 0.9344 (tpt) cc_final: 0.8960 (tpp) REVERT: A 869 GLU cc_start: 0.9294 (mp0) cc_final: 0.8904 (mp0) REVERT: A 941 GLU cc_start: 0.9408 (tt0) cc_final: 0.9055 (tm-30) REVERT: C 74 TYR cc_start: 0.8737 (t80) cc_final: 0.8329 (t80) REVERT: C 101 LYS cc_start: 0.9494 (pttt) cc_final: 0.9251 (pttm) REVERT: D 1 MET cc_start: 0.8290 (ptt) cc_final: 0.8082 (ptp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2095 time to fit residues: 22.5788 Evaluate side-chains 60 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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: 0.4980 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.034415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.025917 restraints weight = 88450.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.026799 restraints weight = 58738.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.027468 restraints weight = 43795.368| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9738 Z= 0.144 Angle : 0.470 5.288 13195 Z= 0.244 Chirality : 0.041 0.160 1471 Planarity : 0.004 0.060 1707 Dihedral : 5.175 59.609 1325 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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 (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: 1.66 (0.26), residues: 1199 helix: 1.80 (0.24), residues: 497 sheet: 0.51 (0.39), residues: 191 loop : 0.81 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 33 HIS 0.002 0.000 HIS A 292 PHE 0.026 0.001 PHE A 82 TYR 0.015 0.001 TYR A 81 ARG 0.012 0.000 ARG C 8 *********************** 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 76 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.9659 (ttp) cc_final: 0.9404 (ppp) REVERT: A 55 ASN cc_start: 0.9333 (m-40) cc_final: 0.9035 (m110) REVERT: A 413 GLN cc_start: 0.9358 (tt0) cc_final: 0.9075 (mt0) REVERT: A 442 MET cc_start: 0.9615 (tpp) cc_final: 0.9260 (tpp) REVERT: A 448 MET cc_start: 0.9267 (mmp) cc_final: 0.8967 (mmm) REVERT: A 449 MET cc_start: 0.9588 (mtp) cc_final: 0.8693 (mmm) REVERT: A 533 THR cc_start: 0.9218 (m) cc_final: 0.8604 (p) REVERT: A 832 MET cc_start: 0.9190 (mtm) cc_final: 0.8795 (mtp) REVERT: A 855 MET cc_start: 0.9355 (tpt) cc_final: 0.8975 (tpp) REVERT: A 869 GLU cc_start: 0.9221 (mp0) cc_final: 0.8947 (mp0) REVERT: A 941 GLU cc_start: 0.9419 (tt0) cc_final: 0.9074 (tm-30) REVERT: C 74 TYR cc_start: 0.8748 (t80) cc_final: 0.8295 (t80) REVERT: C 101 LYS cc_start: 0.9518 (pttt) cc_final: 0.9273 (pttm) REVERT: C 126 VAL cc_start: 0.9638 (t) cc_final: 0.9324 (p) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2099 time to fit residues: 23.6484 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 : 1.187 ------------------------------------------------------------------------------- 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: 0.8980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 0.0570 chunk 30 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.2912 r_free = 0.2912 target = 0.034552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.026085 restraints weight = 84804.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.026936 restraints weight = 57122.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.027585 restraints weight = 42978.939| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3669 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= 0.146 Angle : 0.467 5.263 13195 Z= 0.240 Chirality : 0.040 0.154 1471 Planarity : 0.003 0.043 1707 Dihedral : 5.150 59.320 1325 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 1.64 (0.26), residues: 1199 helix: 1.77 (0.24), residues: 498 sheet: 0.49 (0.39), residues: 192 loop : 0.81 (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 0.023 0.001 PHE A 82 TYR 0.009 0.001 TYR C 60 ARG 0.005 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 : 1.069 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.9646 (ttp) cc_final: 0.9403 (ppp) REVERT: A 55 ASN cc_start: 0.9329 (m-40) cc_final: 0.9037 (m110) REVERT: A 413 GLN cc_start: 0.9346 (tt0) cc_final: 0.9088 (mt0) REVERT: A 442 MET cc_start: 0.9605 (tpp) cc_final: 0.9240 (tpp) REVERT: A 448 MET cc_start: 0.9244 (mmp) cc_final: 0.8977 (mmm) REVERT: A 449 MET cc_start: 0.9581 (mtp) cc_final: 0.8687 (mmm) REVERT: A 533 THR cc_start: 0.9252 (m) cc_final: 0.8622 (p) REVERT: A 832 MET cc_start: 0.9175 (mtm) cc_final: 0.8781 (mtp) REVERT: A 855 MET cc_start: 0.9335 (tpt) cc_final: 0.8972 (tpp) REVERT: A 869 GLU cc_start: 0.9199 (mp0) cc_final: 0.8776 (mp0) REVERT: A 941 GLU cc_start: 0.9425 (tt0) cc_final: 0.9066 (tm-30) REVERT: C 74 TYR cc_start: 0.8729 (t80) cc_final: 0.8357 (t80) REVERT: C 101 LYS cc_start: 0.9490 (pttt) cc_final: 0.9227 (pttm) REVERT: C 126 VAL cc_start: 0.9627 (t) cc_final: 0.9310 (p) REVERT: D 1 MET cc_start: 0.8367 (ptt) cc_final: 0.8112 (ptp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2063 time to fit residues: 22.8347 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 : 1.093 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.2894 r_free = 0.2894 target = 0.034053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.025792 restraints weight = 87574.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.026677 restraints weight = 59212.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.027328 restraints weight = 43968.923| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9738 Z= 0.167 Angle : 0.473 5.618 13195 Z= 0.245 Chirality : 0.040 0.154 1471 Planarity : 0.004 0.087 1707 Dihedral : 5.098 59.149 1325 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.80 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: 1.66 (0.25), residues: 1199 helix: 1.80 (0.24), residues: 498 sheet: 0.49 (0.39), residues: 192 loop : 0.82 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 33 HIS 0.002 0.001 HIS A 292 PHE 0.019 0.001 PHE A 82 TYR 0.011 0.001 TYR C 60 ARG 0.013 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 : 1.073 Fit side-chains REVERT: A 35 MET cc_start: 0.9658 (ttp) cc_final: 0.9405 (ppp) REVERT: A 55 ASN cc_start: 0.9336 (m-40) cc_final: 0.9028 (m-40) REVERT: A 413 GLN cc_start: 0.9406 (tt0) cc_final: 0.9109 (mt0) REVERT: A 442 MET cc_start: 0.9638 (tpp) cc_final: 0.9227 (tpp) REVERT: A 448 MET cc_start: 0.9272 (mmp) cc_final: 0.9048 (mmm) REVERT: A 449 MET cc_start: 0.9598 (mtp) cc_final: 0.8697 (mmm) REVERT: A 533 THR cc_start: 0.9263 (m) cc_final: 0.8661 (p) REVERT: A 832 MET cc_start: 0.9202 (mtm) cc_final: 0.8798 (mtp) REVERT: A 855 MET cc_start: 0.9339 (tpt) cc_final: 0.8963 (tpp) REVERT: A 865 LEU cc_start: 0.9683 (mt) cc_final: 0.9481 (mt) REVERT: A 869 GLU cc_start: 0.9225 (mp0) cc_final: 0.8804 (mp0) REVERT: A 941 GLU cc_start: 0.9420 (tt0) cc_final: 0.9070 (tm-30) REVERT: C 74 TYR cc_start: 0.8772 (t80) cc_final: 0.8343 (t80) REVERT: C 101 LYS cc_start: 0.9492 (pttt) cc_final: 0.9223 (pttm) REVERT: C 126 VAL cc_start: 0.9637 (t) cc_final: 0.9312 (p) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2030 time to fit residues: 21.8769 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 : 1.056 ------------------------------------------------------------------------------- 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: 6.9990 chunk 89 optimal weight: 0.0770 chunk 78 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.2911 r_free = 0.2911 target = 0.034578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.026132 restraints weight = 86906.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.027023 restraints weight = 57841.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.027666 restraints weight = 42911.165| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3782 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= 0.142 Angle : 0.475 7.326 13195 Z= 0.246 Chirality : 0.040 0.153 1471 Planarity : 0.003 0.043 1707 Dihedral : 5.141 59.060 1325 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.68 (0.25), residues: 1199 helix: 1.79 (0.24), residues: 497 sheet: 0.59 (0.39), residues: 191 loop : 0.82 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.003 0.001 HIS A 292 PHE 0.019 0.001 PHE A 82 TYR 0.009 0.001 TYR C 60 ARG 0.003 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: 2676.49 seconds wall clock time: 48 minutes 50.74 seconds (2930.74 seconds total)