Starting phenix.real_space_refine on Tue Jan 14 23:24:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r4b_18884/01_2025/8r4b_18884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r4b_18884/01_2025/8r4b_18884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r4b_18884/01_2025/8r4b_18884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r4b_18884/01_2025/8r4b_18884.map" model { file = "/net/cci-nas-00/data/ceres_data/8r4b_18884/01_2025/8r4b_18884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r4b_18884/01_2025/8r4b_18884_neut.cif" } resolution = 3.88 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= 0.002 sd= 0.063 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 24 5.16 5 C 4806 2.51 5 N 1277 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 7600 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 5956 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 34, 'TRANS': 773} Chain breaks: 8 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 499 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 209 Chain: "B" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 769 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 843 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 112} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.15, per 1000 atoms: 0.68 Number of scatterers: 7600 At special positions: 0 Unit cell: (70.97, 80.03, 182.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 3 15.00 O 1490 8.00 N 1277 7.00 C 4806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 929.8 milliseconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 24.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 51 through 62 removed outlier: 3.736A pdb=" N ILE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 3.617A pdb=" N LEU A 62 " --> pdb=" O PRO A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.089A pdb=" N SER A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.522A pdb=" N SER A 149 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 211 through 216 removed outlier: 4.089A pdb=" N GLU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.904A pdb=" N SER A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.740A pdb=" N LEU A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 419 through 426 removed outlier: 3.790A pdb=" N GLY A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 439 Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.834A pdb=" N LEU A 506 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 507 " --> pdb=" O ASP A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 507' Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.631A pdb=" N ASP A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 removed outlier: 3.626A pdb=" N LEU A 552 " --> pdb=" O LYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 588 Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.512A pdb=" N LEU A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 647 removed outlier: 3.629A pdb=" N ILE A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 661 removed outlier: 4.040A pdb=" N SER A 661 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 678 Processing helix chain 'A' and resid 697 through 710 removed outlier: 3.551A pdb=" N THR A 702 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 705 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.687A pdb=" N ILE A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 872 through 881 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.849A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.298A pdb=" N GLU A 19 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 30 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 41 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 222 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.842A pdb=" N LEU A 310 " --> pdb=" O TRP A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 377 removed outlier: 6.411A pdb=" N GLU A 396 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 490 through 493 removed outlier: 8.611A pdb=" N VAL A 535 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS A 454 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N MET A 537 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS A 456 " --> pdb=" O MET A 537 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU A 539 " --> pdb=" O HIS A 456 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 458 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ILE A 565 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR A 536 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 567 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 538 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 596 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 830 through 834 removed outlier: 3.622A pdb=" N LYS A 844 " --> pdb=" O ALA A 857 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 800 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 23 Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.839A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.184A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL C 33 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.184A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLY C 99 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN C 107 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE C 101 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYR C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 597 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: 2.57 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2494 1.34 - 1.46: 1166 1.46 - 1.57: 4028 1.57 - 1.69: 5 1.69 - 1.81: 38 Bond restraints: 7731 Sorted by residual: bond pdb=" N GLU A 769 " pdb=" CA GLU A 769 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.67e+00 bond pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta sigma weight residual 1.469 1.485 -0.016 1.28e-02 6.10e+03 1.57e+00 bond pdb=" C ALA B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.340 1.373 -0.033 2.76e-02 1.31e+03 1.46e+00 bond pdb=" CB ILE A 144 " pdb=" CG1 ILE A 144 " ideal model delta sigma weight residual 1.530 1.554 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" CA ILE A 144 " pdb=" CB ILE A 144 " ideal model delta sigma weight residual 1.540 1.556 -0.016 1.36e-02 5.41e+03 1.36e+00 ... (remaining 7726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 10144 1.54 - 3.08: 321 3.08 - 4.62: 65 4.62 - 6.16: 18 6.16 - 7.70: 6 Bond angle restraints: 10554 Sorted by residual: angle pdb=" N ILE A 166 " pdb=" CA ILE A 166 " pdb=" C ILE A 166 " ideal model delta sigma weight residual 113.20 109.25 3.95 9.60e-01 1.09e+00 1.69e+01 angle pdb=" CB ILE A 144 " pdb=" CG1 ILE A 144 " pdb=" CD1 ILE A 144 " ideal model delta sigma weight residual 113.80 121.50 -7.70 2.10e+00 2.27e-01 1.34e+01 angle pdb=" CA ILE A 144 " pdb=" CB ILE A 144 " pdb=" CG1 ILE A 144 " ideal model delta sigma weight residual 110.40 116.37 -5.97 1.70e+00 3.46e-01 1.23e+01 angle pdb=" CA GLN A 12 " pdb=" CB GLN A 12 " pdb=" CG GLN A 12 " ideal model delta sigma weight residual 114.10 120.43 -6.33 2.00e+00 2.50e-01 1.00e+01 angle pdb=" N ALA C 91 " pdb=" CA ALA C 91 " pdb=" C ALA C 91 " ideal model delta sigma weight residual 108.34 112.10 -3.76 1.31e+00 5.83e-01 8.24e+00 ... (remaining 10549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.03: 4185 22.03 - 44.05: 394 44.05 - 66.08: 46 66.08 - 88.11: 12 88.11 - 110.14: 2 Dihedral angle restraints: 4639 sinusoidal: 1637 harmonic: 3002 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual 93.00 167.81 -74.81 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 141.71 -48.71 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" O3B GSP A1201 " pdb=" O3A GSP A1201 " pdb=" PB GSP A1201 " pdb=" PA GSP A1201 " ideal model delta sinusoidal sigma weight residual 93.55 -156.31 -110.14 1 2.00e+01 2.50e-03 3.23e+01 ... (remaining 4636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 768 0.033 - 0.067: 354 0.067 - 0.100: 105 0.100 - 0.133: 40 0.133 - 0.167: 4 Chirality restraints: 1271 Sorted by residual: chirality pdb=" CA ILE A 821 " pdb=" N ILE A 821 " pdb=" C ILE A 821 " pdb=" CB ILE A 821 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CA ILE A 408 " pdb=" N ILE A 408 " pdb=" C ILE A 408 " pdb=" CB ILE A 408 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE A 565 " pdb=" N ILE A 565 " pdb=" C ILE A 565 " pdb=" CB ILE A 565 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1268 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 413 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO A 414 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 414 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 414 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 189 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 190 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 190 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 190 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 803 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" CG ASP A 803 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP A 803 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 803 " -0.010 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 701 2.75 - 3.28: 7503 3.28 - 3.82: 12321 3.82 - 4.36: 14678 4.36 - 4.90: 24858 Nonbonded interactions: 60061 Sorted by model distance: nonbonded pdb=" OH TYR A 45 " pdb=" OD1 ASN C 32 " model vdw 2.206 3.040 nonbonded pdb=" O SER A 417 " pdb=" OH TYR A 433 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR A 154 " pdb=" OE1 GLU A 155 " model vdw 2.283 3.040 nonbonded pdb=" O SER A 352 " pdb=" OG1 THR A 374 " model vdw 2.285 3.040 nonbonded pdb=" N GLU A 686 " pdb=" OE1 GLU A 686 " model vdw 2.289 3.120 ... (remaining 60056 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.200 Find NCS groups from input model: 0.080 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 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 : 0.003 0.041 7731 Z= 0.214 Angle : 0.686 7.697 10554 Z= 0.365 Chirality : 0.044 0.167 1271 Planarity : 0.005 0.047 1346 Dihedral : 16.622 110.136 2681 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.51 % Favored : 90.19 % Rotamer: Outliers : 0.52 % Allowed : 20.63 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.78 (0.25), residues: 1009 helix: -1.10 (0.34), residues: 233 sheet: -1.20 (0.32), residues: 250 loop : -2.57 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 36 HIS 0.004 0.001 HIS A 549 PHE 0.014 0.001 PHE A 410 TYR 0.011 0.001 TYR C 37 ARG 0.007 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7587 (tt0) REVERT: A 252 THR cc_start: 0.7969 (p) cc_final: 0.7747 (m) REVERT: A 275 ASP cc_start: 0.6974 (t0) cc_final: 0.6558 (t0) REVERT: A 323 LEU cc_start: 0.7940 (tp) cc_final: 0.7739 (mm) REVERT: A 351 LEU cc_start: 0.8182 (mt) cc_final: 0.7940 (mt) REVERT: A 402 PHE cc_start: 0.6348 (t80) cc_final: 0.6051 (t80) REVERT: A 409 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7958 (p) REVERT: A 427 LYS cc_start: 0.7390 (tmtt) cc_final: 0.6904 (tttp) REVERT: A 432 GLN cc_start: 0.8751 (mt0) cc_final: 0.8031 (mm-40) REVERT: A 706 TYR cc_start: 0.3964 (t80) cc_final: 0.2587 (t80) REVERT: A 715 LYS cc_start: 0.8547 (tttt) cc_final: 0.8291 (tptt) REVERT: A 753 GLN cc_start: 0.6659 (tt0) cc_final: 0.6411 (tt0) REVERT: B 86 MET cc_start: 0.7352 (mmm) cc_final: 0.6425 (mmp) REVERT: C 12 VAL cc_start: 0.7922 (t) cc_final: 0.7583 (p) REVERT: C 45 ARG cc_start: 0.7138 (mtm-85) cc_final: 0.6855 (mtt180) REVERT: C 56 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7201 (mtm180) REVERT: C 80 LEU cc_start: 0.8706 (tp) cc_final: 0.8222 (tp) REVERT: C 114 THR cc_start: 0.8573 (m) cc_final: 0.8340 (p) outliers start: 4 outliers final: 1 residues processed: 230 average time/residue: 0.1863 time to fit residues: 58.1324 Evaluate side-chains 188 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 577 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS A 819 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098334 restraints weight = 16062.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100279 restraints weight = 10424.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.101712 restraints weight = 7590.815| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7731 Z= 0.256 Angle : 0.680 10.089 10554 Z= 0.349 Chirality : 0.045 0.247 1271 Planarity : 0.005 0.040 1346 Dihedral : 7.659 107.106 1094 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.81 % Favored : 89.89 % Rotamer: Outliers : 6.14 % Allowed : 20.63 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.75 (0.25), residues: 1009 helix: -1.10 (0.34), residues: 231 sheet: -1.21 (0.32), residues: 237 loop : -2.50 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 36 HIS 0.012 0.002 HIS A 449 PHE 0.026 0.002 PHE A 410 TYR 0.019 0.002 TYR C 94 ARG 0.006 0.001 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8076 (p0) cc_final: 0.7787 (p0) REVERT: A 131 LEU cc_start: 0.8118 (tp) cc_final: 0.7772 (tt) REVERT: A 147 LEU cc_start: 0.8803 (mp) cc_final: 0.8548 (mm) REVERT: A 184 GLN cc_start: 0.7786 (mp10) cc_final: 0.7570 (mp10) REVERT: A 252 THR cc_start: 0.8170 (p) cc_final: 0.7941 (m) REVERT: A 275 ASP cc_start: 0.7118 (t0) cc_final: 0.6880 (t0) REVERT: A 323 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7749 (mm) REVERT: A 402 PHE cc_start: 0.6342 (t80) cc_final: 0.6069 (t80) REVERT: A 409 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7706 (p) REVERT: A 427 LYS cc_start: 0.7293 (tmtt) cc_final: 0.6890 (tttp) REVERT: A 432 GLN cc_start: 0.8814 (mt0) cc_final: 0.8215 (mm110) REVERT: A 547 ASN cc_start: 0.6252 (t0) cc_final: 0.5995 (t0) REVERT: A 574 ASN cc_start: 0.7933 (t0) cc_final: 0.7654 (t0) REVERT: A 696 LEU cc_start: 0.5150 (OUTLIER) cc_final: 0.4826 (pt) REVERT: A 715 LYS cc_start: 0.8810 (tttt) cc_final: 0.8425 (tptt) REVERT: B 86 MET cc_start: 0.7117 (mmm) cc_final: 0.6599 (mmm) REVERT: C 45 ARG cc_start: 0.6760 (mtm-85) cc_final: 0.6372 (mtt180) REVERT: C 56 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7264 (mtm180) REVERT: C 66 ARG cc_start: 0.7080 (mtm-85) cc_final: 0.6846 (mtp-110) REVERT: C 80 LEU cc_start: 0.8591 (tp) cc_final: 0.8237 (tp) REVERT: C 114 THR cc_start: 0.8490 (m) cc_final: 0.8198 (p) outliers start: 47 outliers final: 23 residues processed: 220 average time/residue: 0.1807 time to fit residues: 54.8995 Evaluate side-chains 201 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 62 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 578 ASN A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.096700 restraints weight = 16323.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098845 restraints weight = 10400.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100359 restraints weight = 7425.249| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7731 Z= 0.249 Angle : 0.664 7.758 10554 Z= 0.339 Chirality : 0.045 0.257 1271 Planarity : 0.004 0.041 1346 Dihedral : 7.661 108.132 1094 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.72 % Favored : 90.88 % Rotamer: Outliers : 5.61 % Allowed : 22.72 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.65 (0.25), residues: 1009 helix: -1.11 (0.34), residues: 241 sheet: -1.10 (0.33), residues: 237 loop : -2.43 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 36 HIS 0.010 0.001 HIS A 523 PHE 0.018 0.002 PHE A 410 TYR 0.013 0.001 TYR C 94 ARG 0.003 0.001 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.5922 (p0) cc_final: 0.5187 (p0) REVERT: A 38 ARG cc_start: 0.6857 (mpt-90) cc_final: 0.6652 (mmt90) REVERT: A 54 ARG cc_start: 0.7810 (ptp90) cc_final: 0.7132 (ptt-90) REVERT: A 85 ASN cc_start: 0.7965 (p0) cc_final: 0.7707 (p0) REVERT: A 86 SER cc_start: 0.8014 (p) cc_final: 0.7384 (p) REVERT: A 184 GLN cc_start: 0.7756 (mp10) cc_final: 0.7515 (mp10) REVERT: A 254 ILE cc_start: 0.7211 (tp) cc_final: 0.6845 (tp) REVERT: A 282 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7307 (mp) REVERT: A 378 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7031 (p) REVERT: A 402 PHE cc_start: 0.6327 (t80) cc_final: 0.6126 (t80) REVERT: A 405 SER cc_start: 0.8446 (p) cc_final: 0.8171 (m) REVERT: A 409 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7719 (p) REVERT: A 427 LYS cc_start: 0.7279 (tmtt) cc_final: 0.6808 (tttp) REVERT: A 432 GLN cc_start: 0.8828 (mt0) cc_final: 0.8569 (mm-40) REVERT: A 514 TRP cc_start: 0.6388 (m-10) cc_final: 0.5865 (m-10) REVERT: A 547 ASN cc_start: 0.6690 (t0) cc_final: 0.6426 (t0) REVERT: A 556 GLU cc_start: 0.6903 (tp30) cc_final: 0.6512 (tp30) REVERT: A 574 ASN cc_start: 0.8033 (t0) cc_final: 0.7700 (t0) REVERT: A 696 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.5140 (pt) REVERT: A 715 LYS cc_start: 0.8876 (tttt) cc_final: 0.8449 (tptt) REVERT: A 768 ASP cc_start: 0.6350 (p0) cc_final: 0.6145 (p0) REVERT: B 86 MET cc_start: 0.7092 (mmm) cc_final: 0.6277 (mmm) REVERT: C 45 ARG cc_start: 0.6713 (mtm-85) cc_final: 0.6205 (mtt180) REVERT: C 80 LEU cc_start: 0.8660 (tp) cc_final: 0.8167 (tp) REVERT: C 114 THR cc_start: 0.8344 (m) cc_final: 0.8072 (p) outliers start: 43 outliers final: 24 residues processed: 223 average time/residue: 0.1952 time to fit residues: 58.9877 Evaluate side-chains 219 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.109802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095277 restraints weight = 16292.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097303 restraints weight = 10465.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098749 restraints weight = 7534.684| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7731 Z= 0.312 Angle : 0.702 8.110 10554 Z= 0.358 Chirality : 0.046 0.270 1271 Planarity : 0.005 0.055 1346 Dihedral : 8.052 114.625 1094 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.80 % Favored : 88.80 % Rotamer: Outliers : 6.53 % Allowed : 23.50 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.71 (0.25), residues: 1009 helix: -1.23 (0.34), residues: 245 sheet: -1.03 (0.33), residues: 238 loop : -2.49 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 53 HIS 0.007 0.001 HIS A 523 PHE 0.019 0.002 PHE A 410 TYR 0.011 0.002 TYR C 94 ARG 0.007 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.6206 (p0) cc_final: 0.5323 (p0) REVERT: A 38 ARG cc_start: 0.6887 (mpt-90) cc_final: 0.6590 (mmt90) REVERT: A 74 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8199 (mm-40) REVERT: A 85 ASN cc_start: 0.7918 (p0) cc_final: 0.7703 (p0) REVERT: A 86 SER cc_start: 0.8071 (p) cc_final: 0.7477 (p) REVERT: A 254 ILE cc_start: 0.7275 (tp) cc_final: 0.6924 (tp) REVERT: A 282 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 316 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7773 (mm-40) REVERT: A 338 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7457 (mm110) REVERT: A 378 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7246 (p) REVERT: A 402 PHE cc_start: 0.6285 (t80) cc_final: 0.6074 (t80) REVERT: A 405 SER cc_start: 0.8479 (p) cc_final: 0.8192 (m) REVERT: A 427 LYS cc_start: 0.7340 (tmtt) cc_final: 0.6767 (tptp) REVERT: A 432 GLN cc_start: 0.8753 (mt0) cc_final: 0.8517 (mm-40) REVERT: A 547 ASN cc_start: 0.7254 (t0) cc_final: 0.7046 (t0) REVERT: A 556 GLU cc_start: 0.6984 (tp30) cc_final: 0.6550 (tp30) REVERT: A 574 ASN cc_start: 0.8060 (t0) cc_final: 0.7648 (t0) REVERT: A 696 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5223 (pt) REVERT: A 715 LYS cc_start: 0.8770 (tttt) cc_final: 0.8438 (tptt) REVERT: B 51 ILE cc_start: 0.7523 (mm) cc_final: 0.7268 (mm) REVERT: B 86 MET cc_start: 0.7073 (mmm) cc_final: 0.6165 (mmm) REVERT: C 80 LEU cc_start: 0.8512 (tp) cc_final: 0.7978 (tp) REVERT: C 86 LYS cc_start: 0.8362 (mtmm) cc_final: 0.7954 (mttp) REVERT: C 114 THR cc_start: 0.8298 (m) cc_final: 0.8076 (p) outliers start: 50 outliers final: 39 residues processed: 229 average time/residue: 0.1829 time to fit residues: 57.2574 Evaluate side-chains 236 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.109439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095119 restraints weight = 16319.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097110 restraints weight = 10487.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.098540 restraints weight = 7603.068| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7731 Z= 0.298 Angle : 0.692 10.804 10554 Z= 0.353 Chirality : 0.045 0.277 1271 Planarity : 0.005 0.055 1346 Dihedral : 8.124 116.042 1094 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.21 % Favored : 89.40 % Rotamer: Outliers : 6.14 % Allowed : 25.07 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.70 (0.25), residues: 1009 helix: -1.35 (0.33), residues: 254 sheet: -0.97 (0.34), residues: 237 loop : -2.46 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 53 HIS 0.005 0.001 HIS A 526 PHE 0.016 0.002 PHE A 410 TYR 0.013 0.002 TYR B 60 ARG 0.005 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7686 (ptp90) cc_final: 0.7321 (ptt180) REVERT: A 85 ASN cc_start: 0.7845 (p0) cc_final: 0.7309 (p0) REVERT: A 86 SER cc_start: 0.8073 (p) cc_final: 0.7411 (p) REVERT: A 165 ASP cc_start: 0.7144 (t0) cc_final: 0.6879 (t0) REVERT: A 184 GLN cc_start: 0.7627 (mp10) cc_final: 0.7299 (mp10) REVERT: A 254 ILE cc_start: 0.7308 (tp) cc_final: 0.6941 (tp) REVERT: A 316 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7728 (mm-40) REVERT: A 338 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7357 (mm110) REVERT: A 378 VAL cc_start: 0.7854 (OUTLIER) cc_final: 0.7398 (p) REVERT: A 427 LYS cc_start: 0.7323 (tmtt) cc_final: 0.7017 (tptp) REVERT: A 556 GLU cc_start: 0.7008 (tp30) cc_final: 0.6572 (tp30) REVERT: A 574 ASN cc_start: 0.8107 (t0) cc_final: 0.7659 (t0) REVERT: A 715 LYS cc_start: 0.8770 (tttt) cc_final: 0.8408 (tptt) REVERT: B 51 ILE cc_start: 0.7497 (mm) cc_final: 0.7138 (mt) REVERT: B 86 MET cc_start: 0.6971 (mmm) cc_final: 0.6086 (mmm) REVERT: C 80 LEU cc_start: 0.8538 (tp) cc_final: 0.7994 (tp) REVERT: C 86 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7897 (mttp) outliers start: 47 outliers final: 41 residues processed: 217 average time/residue: 0.1854 time to fit residues: 54.7704 Evaluate side-chains 225 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.095635 restraints weight = 16501.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097754 restraints weight = 10624.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.099217 restraints weight = 7612.678| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7731 Z= 0.249 Angle : 0.666 7.745 10554 Z= 0.339 Chirality : 0.045 0.266 1271 Planarity : 0.005 0.055 1346 Dihedral : 7.970 117.756 1094 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.71 % Favored : 89.89 % Rotamer: Outliers : 6.40 % Allowed : 25.72 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.63 (0.26), residues: 1009 helix: -1.32 (0.33), residues: 252 sheet: -0.89 (0.34), residues: 237 loop : -2.42 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.003 0.001 HIS A 526 PHE 0.015 0.002 PHE A 410 TYR 0.012 0.002 TYR C 94 ARG 0.005 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7721 (ptp90) cc_final: 0.7476 (ptt180) REVERT: A 85 ASN cc_start: 0.7777 (p0) cc_final: 0.7538 (p0) REVERT: A 86 SER cc_start: 0.7984 (p) cc_final: 0.7338 (p) REVERT: A 165 ASP cc_start: 0.7147 (t0) cc_final: 0.6945 (t0) REVERT: A 184 GLN cc_start: 0.7633 (mp10) cc_final: 0.7333 (mp10) REVERT: A 254 ILE cc_start: 0.7252 (tp) cc_final: 0.6936 (tp) REVERT: A 316 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7916 (mm-40) REVERT: A 338 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7389 (mm110) REVERT: A 378 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7492 (p) REVERT: A 427 LYS cc_start: 0.7325 (tmtt) cc_final: 0.7059 (tptp) REVERT: A 556 GLU cc_start: 0.6914 (tp30) cc_final: 0.6482 (tp30) REVERT: A 715 LYS cc_start: 0.8759 (tttt) cc_final: 0.8411 (tptt) REVERT: B 51 ILE cc_start: 0.7450 (mm) cc_final: 0.7066 (mt) REVERT: B 86 MET cc_start: 0.7062 (mmm) cc_final: 0.6204 (mmm) REVERT: C 80 LEU cc_start: 0.8393 (tp) cc_final: 0.7904 (tp) outliers start: 49 outliers final: 37 residues processed: 217 average time/residue: 0.1927 time to fit residues: 57.1942 Evaluate side-chains 215 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094411 restraints weight = 16402.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096429 restraints weight = 10555.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097840 restraints weight = 7626.049| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7731 Z= 0.328 Angle : 0.723 10.596 10554 Z= 0.369 Chirality : 0.046 0.229 1271 Planarity : 0.005 0.057 1346 Dihedral : 8.205 122.704 1094 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.20 % Favored : 88.40 % Rotamer: Outliers : 6.66 % Allowed : 25.85 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.70 (0.25), residues: 1009 helix: -1.39 (0.33), residues: 238 sheet: -0.91 (0.34), residues: 237 loop : -2.45 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 333 HIS 0.004 0.001 HIS A 718 PHE 0.015 0.002 PHE A 115 TYR 0.013 0.002 TYR A 767 ARG 0.005 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7772 (ptp90) cc_final: 0.7435 (ptt180) REVERT: A 86 SER cc_start: 0.7993 (p) cc_final: 0.7540 (p) REVERT: A 184 GLN cc_start: 0.7669 (mp10) cc_final: 0.7402 (mp10) REVERT: A 254 ILE cc_start: 0.7238 (tp) cc_final: 0.6953 (tp) REVERT: A 338 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7525 (mm110) REVERT: A 378 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7750 (m) REVERT: A 427 LYS cc_start: 0.7375 (tmtt) cc_final: 0.7163 (tptp) REVERT: A 556 GLU cc_start: 0.6704 (tp30) cc_final: 0.6271 (tp30) REVERT: A 574 ASN cc_start: 0.7834 (t0) cc_final: 0.7494 (t0) REVERT: A 715 LYS cc_start: 0.8726 (tttt) cc_final: 0.8381 (tptt) REVERT: B 51 ILE cc_start: 0.7464 (mm) cc_final: 0.7122 (mt) REVERT: B 86 MET cc_start: 0.7059 (mmm) cc_final: 0.6212 (mmm) REVERT: C 80 LEU cc_start: 0.8602 (tp) cc_final: 0.8097 (tp) outliers start: 51 outliers final: 42 residues processed: 213 average time/residue: 0.1819 time to fit residues: 53.6548 Evaluate side-chains 222 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 51 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.109991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095558 restraints weight = 16442.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097656 restraints weight = 10471.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098907 restraints weight = 7464.821| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7731 Z= 0.266 Angle : 0.689 9.026 10554 Z= 0.352 Chirality : 0.045 0.188 1271 Planarity : 0.005 0.058 1346 Dihedral : 8.020 124.841 1094 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.12 % Favored : 90.49 % Rotamer: Outliers : 6.79 % Allowed : 27.42 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.65 (0.25), residues: 1009 helix: -1.37 (0.33), residues: 244 sheet: -0.92 (0.34), residues: 237 loop : -2.39 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 53 HIS 0.005 0.001 HIS A 526 PHE 0.015 0.002 PHE A 115 TYR 0.016 0.002 TYR A 684 ARG 0.007 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.6326 (p0) cc_final: 0.5449 (p0) REVERT: A 54 ARG cc_start: 0.7763 (ptp90) cc_final: 0.7442 (ptt180) REVERT: A 74 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: A 86 SER cc_start: 0.7955 (p) cc_final: 0.7294 (p) REVERT: A 184 GLN cc_start: 0.7672 (mp10) cc_final: 0.7465 (mp10) REVERT: A 254 ILE cc_start: 0.7332 (tp) cc_final: 0.7031 (tp) REVERT: A 338 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7537 (mm110) REVERT: A 378 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7712 (m) REVERT: A 427 LYS cc_start: 0.7355 (tmtt) cc_final: 0.6817 (tptp) REVERT: A 556 GLU cc_start: 0.6574 (tp30) cc_final: 0.6171 (tp30) REVERT: A 574 ASN cc_start: 0.7893 (t0) cc_final: 0.7518 (t0) REVERT: A 715 LYS cc_start: 0.8722 (tttt) cc_final: 0.8365 (tptt) REVERT: B 51 ILE cc_start: 0.7465 (mm) cc_final: 0.7098 (mt) REVERT: B 86 MET cc_start: 0.7062 (mmm) cc_final: 0.6235 (mmm) REVERT: C 80 LEU cc_start: 0.8553 (tp) cc_final: 0.8025 (tp) outliers start: 52 outliers final: 44 residues processed: 218 average time/residue: 0.1844 time to fit residues: 55.3109 Evaluate side-chains 227 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094708 restraints weight = 16608.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096644 restraints weight = 10847.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097748 restraints weight = 7905.840| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7731 Z= 0.343 Angle : 0.742 9.794 10554 Z= 0.377 Chirality : 0.046 0.190 1271 Planarity : 0.005 0.059 1346 Dihedral : 8.359 128.734 1094 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.00 % Favored : 88.60 % Rotamer: Outliers : 6.14 % Allowed : 27.55 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.72 (0.25), residues: 1009 helix: -1.35 (0.34), residues: 232 sheet: -1.06 (0.33), residues: 237 loop : -2.41 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 53 HIS 0.005 0.002 HIS A 718 PHE 0.015 0.002 PHE A 115 TYR 0.013 0.002 TYR A 536 ARG 0.007 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.6134 (p0) cc_final: 0.5777 (p0) REVERT: A 38 ARG cc_start: 0.6705 (mmt90) cc_final: 0.6419 (mmt90) REVERT: A 54 ARG cc_start: 0.7787 (ptp90) cc_final: 0.7455 (ptt180) REVERT: A 74 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: A 86 SER cc_start: 0.7958 (p) cc_final: 0.7337 (p) REVERT: A 184 GLN cc_start: 0.7713 (mp10) cc_final: 0.7476 (mp10) REVERT: A 254 ILE cc_start: 0.7267 (tp) cc_final: 0.6999 (tp) REVERT: A 338 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7591 (mm110) REVERT: A 378 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7726 (m) REVERT: A 432 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8151 (mm-40) REVERT: A 556 GLU cc_start: 0.6532 (tp30) cc_final: 0.6132 (tp30) REVERT: A 574 ASN cc_start: 0.7877 (t0) cc_final: 0.7474 (t0) REVERT: A 715 LYS cc_start: 0.8684 (tttt) cc_final: 0.8365 (tptt) REVERT: B 51 ILE cc_start: 0.7461 (mm) cc_final: 0.7115 (mt) REVERT: B 86 MET cc_start: 0.7032 (mmm) cc_final: 0.6162 (mmm) REVERT: C 80 LEU cc_start: 0.8592 (tp) cc_final: 0.8084 (tp) outliers start: 47 outliers final: 44 residues processed: 217 average time/residue: 0.1785 time to fit residues: 53.5870 Evaluate side-chains 231 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 0.0050 chunk 46 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.0270 chunk 47 optimal weight: 0.0670 overall best weight: 0.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 HIS A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.099507 restraints weight = 16441.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.101663 restraints weight = 10389.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103158 restraints weight = 7373.777| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7731 Z= 0.184 Angle : 0.687 9.577 10554 Z= 0.348 Chirality : 0.044 0.177 1271 Planarity : 0.005 0.056 1346 Dihedral : 7.560 127.560 1094 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.93 % Favored : 91.77 % Rotamer: Outliers : 3.66 % Allowed : 30.55 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.47 (0.26), residues: 1009 helix: -1.14 (0.34), residues: 243 sheet: -0.95 (0.34), residues: 238 loop : -2.24 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 827 HIS 0.005 0.001 HIS A 549 PHE 0.018 0.001 PHE A 410 TYR 0.017 0.001 TYR A 684 ARG 0.008 0.001 ARG C 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8254 (mm-40) REVERT: A 86 SER cc_start: 0.7716 (p) cc_final: 0.7032 (p) REVERT: A 254 ILE cc_start: 0.7183 (tp) cc_final: 0.6927 (tp) REVERT: A 291 ASN cc_start: 0.7830 (p0) cc_final: 0.7562 (p0) REVERT: A 338 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7595 (mm110) REVERT: A 378 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7640 (m) REVERT: A 432 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8184 (mm-40) REVERT: A 547 ASN cc_start: 0.7516 (p0) cc_final: 0.6874 (t0) REVERT: A 556 GLU cc_start: 0.6697 (tp30) cc_final: 0.6339 (tp30) REVERT: A 574 ASN cc_start: 0.7838 (t0) cc_final: 0.7472 (t0) REVERT: A 715 LYS cc_start: 0.8718 (tttt) cc_final: 0.8340 (tptt) REVERT: A 802 TYR cc_start: 0.5619 (m-80) cc_final: 0.5417 (m-80) REVERT: B 51 ILE cc_start: 0.7471 (mm) cc_final: 0.7034 (mt) REVERT: B 86 MET cc_start: 0.7112 (mmm) cc_final: 0.6192 (mmm) REVERT: C 80 LEU cc_start: 0.8532 (tp) cc_final: 0.8053 (tp) outliers start: 28 outliers final: 22 residues processed: 201 average time/residue: 0.1722 time to fit residues: 48.1297 Evaluate side-chains 202 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 3 optimal weight: 0.0030 chunk 56 optimal weight: 0.0030 chunk 23 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097895 restraints weight = 16305.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.100013 restraints weight = 10352.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101504 restraints weight = 7388.531| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7731 Z= 0.231 Angle : 0.694 8.566 10554 Z= 0.352 Chirality : 0.044 0.179 1271 Planarity : 0.005 0.056 1346 Dihedral : 7.573 129.016 1093 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.92 % Favored : 90.78 % Rotamer: Outliers : 3.13 % Allowed : 31.07 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.44 (0.26), residues: 1009 helix: -1.10 (0.35), residues: 237 sheet: -0.93 (0.33), residues: 242 loop : -2.22 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 53 HIS 0.003 0.001 HIS A 549 PHE 0.017 0.002 PHE A 410 TYR 0.043 0.002 TYR A 767 ARG 0.007 0.001 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2512.76 seconds wall clock time: 45 minutes 55.09 seconds (2755.09 seconds total)