Starting phenix.real_space_refine on Wed Mar 12 08:36:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r4b_18884/03_2025/8r4b_18884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r4b_18884/03_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_18884/03_2025/8r4b_18884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r4b_18884/03_2025/8r4b_18884.map" model { file = "/net/cci-nas-00/data/ceres_data/8r4b_18884/03_2025/8r4b_18884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r4b_18884/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.03, per 1000 atoms: 0.66 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: 2.15 Conformation dependent library (CDL) restraints added in 859.1 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: 1.31 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: 2.64 Time building geometry restraints manager: 2.48 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.860 Find NCS groups from input model: 0.060 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.170 ------------------------------------------------------------------------------- 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 : 1.107 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: 0.1874 time to fit residues: 58.8670 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 : 0.829 ------------------------------------------------------------------------------- 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 = 49)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098291 restraints weight = 16062.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100289 restraints weight = 10458.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.101699 restraints weight = 7584.370| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 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 10.090 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 : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8080 (p0) cc_final: 0.7791 (p0) REVERT: A 131 LEU cc_start: 0.8117 (tp) cc_final: 0.7770 (tt) REVERT: A 147 LEU cc_start: 0.8797 (mp) cc_final: 0.8542 (mm) REVERT: A 184 GLN cc_start: 0.7789 (mp10) cc_final: 0.7565 (mp10) REVERT: A 252 THR cc_start: 0.8175 (p) cc_final: 0.7944 (m) REVERT: A 275 ASP cc_start: 0.7121 (t0) cc_final: 0.6878 (t0) REVERT: A 323 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7748 (mm) REVERT: A 402 PHE cc_start: 0.6345 (t80) cc_final: 0.6075 (t80) REVERT: A 409 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7702 (p) REVERT: A 427 LYS cc_start: 0.7295 (tmtt) cc_final: 0.6888 (tttp) REVERT: A 432 GLN cc_start: 0.8808 (mt0) cc_final: 0.8211 (mm110) REVERT: A 547 ASN cc_start: 0.6262 (t0) cc_final: 0.6003 (t0) REVERT: A 574 ASN cc_start: 0.7950 (t0) cc_final: 0.7668 (t0) REVERT: A 696 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4827 (pt) REVERT: A 715 LYS cc_start: 0.8810 (tttt) cc_final: 0.8426 (tptt) REVERT: B 86 MET cc_start: 0.7119 (mmm) cc_final: 0.6600 (mmm) REVERT: C 45 ARG cc_start: 0.6755 (mtm-85) cc_final: 0.6366 (mtt180) REVERT: C 56 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7266 (mtm180) REVERT: C 66 ARG cc_start: 0.7088 (mtm-85) cc_final: 0.6854 (mtp-110) REVERT: C 80 LEU cc_start: 0.8587 (tp) cc_final: 0.8232 (tp) REVERT: C 114 THR cc_start: 0.8486 (m) cc_final: 0.8187 (p) outliers start: 47 outliers final: 23 residues processed: 220 average time/residue: 0.1702 time to fit residues: 51.6266 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 : 0.871 ------------------------------------------------------------------------------- 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: 0.6980 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 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 = 0.3508 r_free = 0.3508 target = 0.110686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.095913 restraints weight = 16317.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.097978 restraints weight = 10454.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099505 restraints weight = 7499.251| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7731 Z= 0.279 Angle : 0.683 7.954 10554 Z= 0.349 Chirality : 0.045 0.274 1271 Planarity : 0.005 0.042 1346 Dihedral : 7.840 109.383 1094 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.32 % Favored : 90.29 % Rotamer: Outliers : 5.61 % Allowed : 23.24 % Favored : 71.15 % 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: -1.16 (0.34), residues: 250 sheet: -1.14 (0.33), residues: 237 loop : -2.54 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 36 HIS 0.011 0.001 HIS A 523 PHE 0.020 0.002 PHE A 410 TYR 0.013 0.001 TYR C 94 ARG 0.004 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 245 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.6049 (p0) cc_final: 0.5290 (p0) REVERT: A 54 ARG cc_start: 0.7778 (ptp90) cc_final: 0.7105 (ptt-90) REVERT: A 85 ASN cc_start: 0.7972 (p0) cc_final: 0.7722 (p0) REVERT: A 86 SER cc_start: 0.8023 (p) cc_final: 0.7393 (p) REVERT: A 184 GLN cc_start: 0.7661 (mp10) cc_final: 0.7452 (mp10) REVERT: A 254 ILE cc_start: 0.7234 (tp) cc_final: 0.6896 (tp) REVERT: A 275 ASP cc_start: 0.7174 (t0) cc_final: 0.6972 (t0) REVERT: A 282 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7304 (mp) REVERT: A 338 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7481 (mm110) REVERT: A 378 VAL cc_start: 0.7607 (OUTLIER) cc_final: 0.7109 (p) REVERT: A 402 PHE cc_start: 0.6340 (t80) cc_final: 0.6124 (t80) REVERT: A 405 SER cc_start: 0.8446 (p) cc_final: 0.8184 (m) REVERT: A 409 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7713 (p) REVERT: A 427 LYS cc_start: 0.7381 (tmtt) cc_final: 0.6906 (tttp) REVERT: A 432 GLN cc_start: 0.8796 (mt0) cc_final: 0.8537 (mm-40) REVERT: A 514 TRP cc_start: 0.6395 (m-10) cc_final: 0.5866 (m-10) REVERT: A 547 ASN cc_start: 0.6728 (t0) cc_final: 0.6467 (t0) REVERT: A 556 GLU cc_start: 0.6888 (tp30) cc_final: 0.6470 (tp30) REVERT: A 574 ASN cc_start: 0.8030 (t0) cc_final: 0.7693 (t0) REVERT: A 696 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.5121 (pt) REVERT: A 715 LYS cc_start: 0.8852 (tttt) cc_final: 0.8450 (tptt) REVERT: A 768 ASP cc_start: 0.6283 (p0) cc_final: 0.6059 (p0) REVERT: B 86 MET cc_start: 0.7105 (mmm) cc_final: 0.6285 (mmm) REVERT: C 45 ARG cc_start: 0.6740 (mtm-85) cc_final: 0.6244 (mtt180) REVERT: C 80 LEU cc_start: 0.8615 (tp) cc_final: 0.7943 (tp) REVERT: C 114 THR cc_start: 0.8351 (m) cc_final: 0.8089 (p) outliers start: 43 outliers final: 26 residues processed: 226 average time/residue: 0.1881 time to fit residues: 57.7470 Evaluate side-chains 218 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 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 B residue 102 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: 0.8980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 762 GLN 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 = 0.3498 r_free = 0.3498 target = 0.109670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095132 restraints weight = 16322.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097186 restraints weight = 10516.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098636 restraints weight = 7571.778| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7731 Z= 0.311 Angle : 0.699 8.279 10554 Z= 0.357 Chirality : 0.046 0.269 1271 Planarity : 0.005 0.057 1346 Dihedral : 8.072 114.739 1094 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.60 % Favored : 89.00 % Rotamer: Outliers : 6.40 % Allowed : 23.63 % 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: -2.77 (0.25), residues: 1009 helix: -1.19 (0.34), residues: 239 sheet: -1.07 (0.33), residues: 237 loop : -2.57 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 333 HIS 0.006 0.001 HIS A 523 PHE 0.018 0.002 PHE A 410 TYR 0.014 0.002 TYR A 767 ARG 0.006 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 246 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6622 (mmt90) cc_final: 0.5958 (mmt90) REVERT: A 74 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8406 (mm-40) REVERT: A 85 ASN cc_start: 0.7936 (p0) cc_final: 0.7722 (p0) REVERT: A 86 SER cc_start: 0.8065 (p) cc_final: 0.7464 (p) REVERT: A 133 GLU cc_start: 0.8024 (tt0) cc_final: 0.7824 (tt0) REVERT: A 254 ILE cc_start: 0.7294 (tp) cc_final: 0.6914 (tp) REVERT: A 275 ASP cc_start: 0.7379 (t0) cc_final: 0.7125 (t0) REVERT: A 282 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7321 (mp) REVERT: A 316 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7775 (mm-40) REVERT: A 338 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7418 (mm110) REVERT: A 378 VAL cc_start: 0.7714 (OUTLIER) cc_final: 0.7263 (p) REVERT: A 402 PHE cc_start: 0.6279 (t80) cc_final: 0.6056 (t80) REVERT: A 405 SER cc_start: 0.8481 (p) cc_final: 0.8200 (m) REVERT: A 427 LYS cc_start: 0.7347 (tmtt) cc_final: 0.6781 (tptp) REVERT: A 432 GLN cc_start: 0.8793 (mt0) cc_final: 0.8537 (mm-40) REVERT: A 514 TRP cc_start: 0.6396 (m-10) cc_final: 0.5900 (m-10) REVERT: A 547 ASN cc_start: 0.7248 (t0) cc_final: 0.7035 (t0) REVERT: A 556 GLU cc_start: 0.6980 (tp30) cc_final: 0.6538 (tp30) REVERT: A 574 ASN cc_start: 0.8061 (t0) cc_final: 0.7646 (t0) REVERT: A 696 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.5246 (pt) REVERT: A 715 LYS cc_start: 0.8780 (tttt) cc_final: 0.8435 (tptt) REVERT: B 86 MET cc_start: 0.7088 (mmm) cc_final: 0.6168 (mmm) REVERT: C 80 LEU cc_start: 0.8512 (tp) cc_final: 0.7974 (tp) REVERT: C 86 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7958 (mttp) REVERT: C 114 THR cc_start: 0.8302 (m) cc_final: 0.8074 (p) outliers start: 49 outliers final: 38 residues processed: 225 average time/residue: 0.1783 time to fit residues: 54.8371 Evaluate side-chains 234 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 58 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 471 GLN 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 = 0.3477 r_free = 0.3477 target = 0.108388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094335 restraints weight = 16348.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096160 restraints weight = 10719.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097617 restraints weight = 7884.582| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 7731 Z= 0.361 Angle : 0.729 10.557 10554 Z= 0.374 Chirality : 0.047 0.273 1271 Planarity : 0.005 0.057 1346 Dihedral : 8.433 117.464 1094 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.60 % Favored : 89.00 % Rotamer: Outliers : 7.18 % Allowed : 24.28 % Favored : 68.54 % 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: -2.85 (0.25), residues: 1009 helix: -1.33 (0.33), residues: 239 sheet: -1.03 (0.34), residues: 237 loop : -2.63 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 333 HIS 0.004 0.001 HIS A 526 PHE 0.016 0.002 PHE A 115 TYR 0.015 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 248 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6609 (mmt90) cc_final: 0.6244 (mmt90) REVERT: A 54 ARG cc_start: 0.7685 (ptp90) cc_final: 0.7335 (ptt180) REVERT: A 85 ASN cc_start: 0.7838 (p0) cc_final: 0.7364 (p0) REVERT: A 86 SER cc_start: 0.8090 (p) cc_final: 0.7513 (p) REVERT: A 111 MET cc_start: 0.7429 (ttp) cc_final: 0.7176 (tmm) REVERT: A 133 GLU cc_start: 0.8027 (tt0) cc_final: 0.7814 (tt0) REVERT: A 184 GLN cc_start: 0.7622 (mp10) cc_final: 0.7313 (mp10) REVERT: A 254 ILE cc_start: 0.7416 (tp) cc_final: 0.6986 (tp) REVERT: A 275 ASP cc_start: 0.7391 (t0) cc_final: 0.7172 (t0) REVERT: A 282 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7344 (mp) REVERT: A 316 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7879 (mm-40) REVERT: A 338 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7414 (mm110) REVERT: A 378 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7457 (p) REVERT: A 405 SER cc_start: 0.8457 (p) cc_final: 0.8204 (m) REVERT: A 427 LYS cc_start: 0.7336 (tmtt) cc_final: 0.7035 (tptp) REVERT: A 471 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: A 556 GLU cc_start: 0.6620 (tp30) cc_final: 0.6204 (tp30) REVERT: A 715 LYS cc_start: 0.8751 (tttt) cc_final: 0.8409 (tptt) REVERT: B 86 MET cc_start: 0.6990 (mmm) cc_final: 0.6137 (mmm) REVERT: C 80 LEU cc_start: 0.8532 (tp) cc_final: 0.7980 (tp) REVERT: C 86 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7870 (mttp) REVERT: C 114 THR cc_start: 0.8309 (m) cc_final: 0.8068 (p) outliers start: 55 outliers final: 44 residues processed: 226 average time/residue: 0.1829 time to fit residues: 56.9166 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 : 0.916 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain A residue 110 SER 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 177 GLU Chi-restraints excluded: chain A residue 185 ILE 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 282 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 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 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 471 GLN 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 58 THR 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: 0.5980 chunk 39 optimal weight: 0.0980 chunk 34 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN 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 = 0.3510 r_free = 0.3510 target = 0.110189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.095769 restraints weight = 16518.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.097847 restraints weight = 10519.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099314 restraints weight = 7520.022| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7731 Z= 0.230 Angle : 0.668 8.724 10554 Z= 0.340 Chirality : 0.045 0.277 1271 Planarity : 0.005 0.057 1346 Dihedral : 7.999 118.430 1094 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.52 % Favored : 91.08 % Rotamer: Outliers : 6.40 % Allowed : 26.11 % 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: -2.71 (0.26), residues: 1009 helix: -1.23 (0.34), residues: 239 sheet: -0.93 (0.34), residues: 238 loop : -2.55 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 333 HIS 0.004 0.001 HIS A 526 PHE 0.015 0.002 PHE A 115 TYR 0.012 0.001 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 237 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6611 (mmt90) cc_final: 0.6273 (mmt90) REVERT: A 54 ARG cc_start: 0.7722 (ptp90) cc_final: 0.7466 (ptt180) REVERT: A 74 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8380 (mm-40) REVERT: A 85 ASN cc_start: 0.7674 (p0) cc_final: 0.7138 (p0) REVERT: A 86 SER cc_start: 0.7981 (p) cc_final: 0.7272 (p) REVERT: A 111 MET cc_start: 0.7443 (ttp) cc_final: 0.7196 (tmm) REVERT: A 184 GLN cc_start: 0.7636 (mp10) cc_final: 0.7332 (mp10) REVERT: A 254 ILE cc_start: 0.7288 (tp) cc_final: 0.6896 (tp) REVERT: A 338 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7524 (mm110) REVERT: A 432 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8053 (mm110) REVERT: A 471 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7895 (pp30) REVERT: A 556 GLU cc_start: 0.6546 (tp30) cc_final: 0.6147 (tp30) REVERT: A 574 ASN cc_start: 0.7852 (t0) cc_final: 0.7433 (t0) REVERT: A 715 LYS cc_start: 0.8732 (tttt) cc_final: 0.8371 (tptt) REVERT: B 86 MET cc_start: 0.7126 (mmm) cc_final: 0.6209 (mmm) REVERT: C 80 LEU cc_start: 0.8653 (tp) cc_final: 0.8058 (tp) REVERT: C 114 THR cc_start: 0.8414 (m) cc_final: 0.8181 (p) outliers start: 49 outliers final: 38 residues processed: 221 average time/residue: 0.1768 time to fit residues: 53.4991 Evaluate side-chains 215 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 81 LEU Chi-restraints excluded: chain A residue 84 LEU 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 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 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 471 GLN 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 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: 0.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 15 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 471 GLN A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.110055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.095590 restraints weight = 16326.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.097711 restraints weight = 10453.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099155 restraints weight = 7479.174| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4154 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= 0.259 Angle : 0.686 7.834 10554 Z= 0.352 Chirality : 0.045 0.255 1271 Planarity : 0.005 0.056 1346 Dihedral : 7.944 119.816 1094 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.51 % Favored : 90.09 % 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: -2.69 (0.25), residues: 1009 helix: -1.33 (0.33), residues: 244 sheet: -0.93 (0.34), residues: 237 loop : -2.47 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.003 0.001 HIS A 526 PHE 0.016 0.002 PHE A 115 TYR 0.015 0.002 TYR A 684 ARG 0.006 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 230 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6752 (mmt90) cc_final: 0.6525 (mmt90) REVERT: A 54 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7418 (ptt180) REVERT: A 74 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8406 (mm-40) REVERT: A 86 SER cc_start: 0.7982 (p) cc_final: 0.7399 (p) REVERT: A 254 ILE cc_start: 0.7297 (tp) cc_final: 0.6943 (tp) REVERT: A 338 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7565 (mm110) REVERT: A 432 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8048 (mm110) REVERT: A 471 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7785 (pp30) REVERT: A 556 GLU cc_start: 0.6577 (tp30) cc_final: 0.6169 (tp30) REVERT: A 574 ASN cc_start: 0.7891 (t0) cc_final: 0.7451 (t0) REVERT: A 715 LYS cc_start: 0.8724 (tttt) cc_final: 0.8366 (tptt) REVERT: B 51 ILE cc_start: 0.7589 (mm) cc_final: 0.7077 (mt) REVERT: B 86 MET cc_start: 0.7089 (mmm) cc_final: 0.6214 (mmm) REVERT: C 80 LEU cc_start: 0.8558 (tp) cc_final: 0.8043 (tp) REVERT: C 114 THR cc_start: 0.8376 (m) cc_final: 0.8066 (p) outliers start: 47 outliers final: 41 residues processed: 211 average time/residue: 0.1807 time to fit residues: 52.9143 Evaluate side-chains 221 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 81 LEU 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 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 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 330 SER 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 386 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 526 HIS 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 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: 0.9990 chunk 81 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094823 restraints weight = 16490.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.096952 restraints weight = 10468.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098371 restraints weight = 7468.010| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7731 Z= 0.304 Angle : 0.721 9.161 10554 Z= 0.368 Chirality : 0.045 0.228 1271 Planarity : 0.005 0.059 1346 Dihedral : 8.082 122.389 1094 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.91 % Favored : 89.69 % Rotamer: Outliers : 6.01 % Allowed : 28.07 % Favored : 65.93 % 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: -1.38 (0.34), residues: 238 sheet: -0.98 (0.34), residues: 237 loop : -2.43 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 53 HIS 0.003 0.001 HIS A 718 PHE 0.016 0.002 PHE A 115 TYR 0.016 0.002 TYR A 684 ARG 0.006 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: 46 poor density : 193 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6795 (mmt90) cc_final: 0.6567 (mmt90) REVERT: A 54 ARG cc_start: 0.7781 (ptp90) cc_final: 0.7456 (ptt180) REVERT: A 74 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: A 86 SER cc_start: 0.8006 (p) cc_final: 0.7410 (p) REVERT: A 184 GLN cc_start: 0.7659 (mp-120) cc_final: 0.7190 (mp10) REVERT: A 254 ILE cc_start: 0.7358 (tp) cc_final: 0.7001 (tp) REVERT: A 338 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7560 (mm110) REVERT: A 432 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8222 (mm110) REVERT: A 556 GLU cc_start: 0.6559 (tp30) cc_final: 0.6155 (tp30) REVERT: A 574 ASN cc_start: 0.7926 (t0) cc_final: 0.7470 (t0) REVERT: A 715 LYS cc_start: 0.8736 (tttt) cc_final: 0.8376 (tptt) REVERT: B 51 ILE cc_start: 0.7604 (mm) cc_final: 0.7093 (mt) REVERT: B 86 MET cc_start: 0.7042 (mmm) cc_final: 0.6133 (mmm) REVERT: C 80 LEU cc_start: 0.8551 (tp) cc_final: 0.8014 (tp) REVERT: C 114 THR cc_start: 0.8365 (m) cc_final: 0.8044 (p) outliers start: 46 outliers final: 42 residues processed: 218 average time/residue: 0.1763 time to fit residues: 53.2441 Evaluate side-chains 232 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 93 ASP 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 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 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 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: 0.3980 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.096759 restraints weight = 16490.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098852 restraints weight = 10439.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100350 restraints weight = 7436.247| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7731 Z= 0.224 Angle : 0.687 9.313 10554 Z= 0.347 Chirality : 0.044 0.184 1271 Planarity : 0.005 0.059 1346 Dihedral : 7.800 123.656 1094 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.22 % Favored : 90.49 % Rotamer: Outliers : 6.40 % Allowed : 28.20 % Favored : 65.40 % 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: -2.59 (0.26), residues: 1009 helix: -1.29 (0.34), residues: 250 sheet: -0.98 (0.34), residues: 238 loop : -2.32 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.004 0.001 HIS A 526 PHE 0.015 0.002 PHE A 115 TYR 0.013 0.001 TYR A 684 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: 49 poor density : 186 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6772 (mmt90) cc_final: 0.6554 (mmt90) REVERT: A 54 ARG cc_start: 0.7767 (ptp90) cc_final: 0.7438 (ptt180) REVERT: A 74 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8402 (mm-40) REVERT: A 86 SER cc_start: 0.7883 (p) cc_final: 0.7231 (p) REVERT: A 184 GLN cc_start: 0.7595 (mp-120) cc_final: 0.7229 (mp10) REVERT: A 254 ILE cc_start: 0.7325 (tp) cc_final: 0.7019 (tp) REVERT: A 338 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7555 (mm110) REVERT: A 432 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8230 (mm110) REVERT: A 471 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: A 547 ASN cc_start: 0.7260 (t0) cc_final: 0.6979 (p0) REVERT: A 556 GLU cc_start: 0.6606 (tp30) cc_final: 0.6239 (tp30) REVERT: A 574 ASN cc_start: 0.7899 (t0) cc_final: 0.7449 (t0) REVERT: A 706 TYR cc_start: 0.3826 (t80) cc_final: 0.2504 (t80) REVERT: A 715 LYS cc_start: 0.8717 (tttt) cc_final: 0.8349 (tptt) REVERT: B 51 ILE cc_start: 0.7581 (mm) cc_final: 0.7036 (mt) REVERT: B 83 TYR cc_start: 0.6596 (m-80) cc_final: 0.6050 (m-80) REVERT: B 86 MET cc_start: 0.7077 (mmm) cc_final: 0.6154 (mmm) REVERT: C 80 LEU cc_start: 0.8552 (tp) cc_final: 0.8042 (tp) REVERT: C 114 THR cc_start: 0.8376 (m) cc_final: 0.8048 (p) outliers start: 49 outliers final: 43 residues processed: 215 average time/residue: 0.1860 time to fit residues: 54.8067 Evaluate side-chains 227 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 105 SER 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 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 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 248 SER 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 365 SER 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 471 GLN 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 48 VAL 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 92 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 chunk 12 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 overall best weight: 0.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3532 r_free = 0.3532 target = 0.111686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097126 restraints weight = 16473.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099220 restraints weight = 10441.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100687 restraints weight = 7427.612| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7731 Z= 0.215 Angle : 0.679 9.153 10554 Z= 0.343 Chirality : 0.044 0.184 1271 Planarity : 0.005 0.059 1346 Dihedral : 7.673 123.922 1094 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.12 % Favored : 90.58 % Rotamer: Outliers : 5.87 % Allowed : 29.24 % Favored : 64.88 % 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: -2.56 (0.25), residues: 1009 helix: -1.25 (0.34), residues: 244 sheet: -0.94 (0.34), residues: 237 loop : -2.32 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.004 0.001 HIS A 526 PHE 0.015 0.002 PHE A 883 TYR 0.013 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 230 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.6121 (p0) cc_final: 0.5738 (p0) REVERT: A 54 ARG cc_start: 0.7767 (ptp90) cc_final: 0.7436 (ptt180) REVERT: A 74 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8402 (mm-40) REVERT: A 86 SER cc_start: 0.7846 (p) cc_final: 0.7152 (p) REVERT: A 254 ILE cc_start: 0.7292 (tp) cc_final: 0.7002 (tp) REVERT: A 338 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7580 (mm110) REVERT: A 432 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8196 (mm110) REVERT: A 547 ASN cc_start: 0.7236 (t0) cc_final: 0.6956 (p0) REVERT: A 556 GLU cc_start: 0.6649 (tp30) cc_final: 0.6291 (tp30) REVERT: A 574 ASN cc_start: 0.7899 (t0) cc_final: 0.7430 (t0) REVERT: A 715 LYS cc_start: 0.8720 (tttt) cc_final: 0.8360 (tptt) REVERT: B 51 ILE cc_start: 0.7573 (mm) cc_final: 0.7021 (mt) REVERT: B 83 TYR cc_start: 0.6600 (m-80) cc_final: 0.5982 (m-80) REVERT: B 86 MET cc_start: 0.7072 (mmm) cc_final: 0.6166 (mmm) REVERT: C 80 LEU cc_start: 0.8559 (tp) cc_final: 0.8052 (tp) REVERT: C 114 THR cc_start: 0.8373 (m) cc_final: 0.8050 (p) outliers start: 45 outliers final: 41 residues processed: 211 average time/residue: 0.1744 time to fit residues: 50.9582 Evaluate side-chains 223 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 105 SER 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 147 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 185 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 248 SER 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 364 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 383 ILE 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 48 VAL 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: 1.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 4 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 471 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3519 r_free = 0.3519 target = 0.110917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096340 restraints weight = 16351.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.098452 restraints weight = 10405.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099848 restraints weight = 7423.142| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.4482 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= 0.250 Angle : 0.694 8.897 10554 Z= 0.350 Chirality : 0.044 0.186 1271 Planarity : 0.005 0.057 1346 Dihedral : 7.746 126.098 1093 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.32 % Favored : 90.39 % Rotamer: Outliers : 6.14 % Allowed : 28.98 % Favored : 64.88 % 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: -2.54 (0.26), residues: 1009 helix: -1.27 (0.34), residues: 244 sheet: -0.91 (0.34), residues: 237 loop : -2.29 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.003 0.001 HIS A 526 PHE 0.015 0.002 PHE A 115 TYR 0.015 0.002 TYR A 684 ARG 0.008 0.001 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.33 seconds wall clock time: 45 minutes 55.05 seconds (2755.05 seconds total)