Starting phenix.real_space_refine on Fri Aug 22 20:14:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r4b_18884/08_2025/8r4b_18884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r4b_18884/08_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_18884/08_2025/8r4b_18884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r4b_18884/08_2025/8r4b_18884.map" model { file = "/net/cci-nas-00/data/ceres_data/8r4b_18884/08_2025/8r4b_18884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r4b_18884/08_2025/8r4b_18884_neut.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 8, 'GLN:plan1': 7, 'GLU:plan': 19, 'ASP:plan': 7, 'ASN:plan1': 6, 'TYR:plan': 2, 'PHE:plan': 2} 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, 'ASP:plan': 2, 'GLU:plan': 1} 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: 1.78, per 1000 atoms: 0.23 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: 0.61 Conformation dependent library (CDL) restraints added in 521.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.33 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: 1.37 Time building geometry restraints manager: 0.84 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.680 ------------------------------------------------------------------------------- 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 7733 Z= 0.145 Angle : 0.686 7.697 10558 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.007 0.001 ARG A 270 TYR 0.011 0.001 TYR C 37 PHE 0.014 0.001 PHE A 410 TRP 0.027 0.001 TRP C 36 HIS 0.004 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7731) covalent geometry : angle 0.68603 (10554) SS BOND : bond 0.00372 ( 2) SS BOND : angle 1.42580 ( 4) hydrogen bonds : bond 0.14884 ( 233) hydrogen bonds : angle 6.61955 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.353 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: 0.0900 time to fit residues: 28.2610 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 : 0.292 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 578 ASN A 819 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.113305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098789 restraints weight = 16173.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.100791 restraints weight = 10536.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.102217 restraints weight = 7633.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.103217 restraints weight = 6000.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.103917 restraints weight = 5008.255| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7733 Z= 0.164 Angle : 0.676 10.197 10558 Z= 0.347 Chirality : 0.045 0.241 1271 Planarity : 0.005 0.040 1346 Dihedral : 7.595 107.147 1094 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.51 % Favored : 90.19 % Rotamer: Outliers : 5.61 % Allowed : 21.28 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.25), residues: 1009 helix: -1.07 (0.35), residues: 231 sheet: -1.18 (0.32), residues: 240 loop : -2.51 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 226 TYR 0.018 0.002 TYR C 94 PHE 0.023 0.002 PHE A 410 TRP 0.011 0.001 TRP C 36 HIS 0.012 0.002 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7731) covalent geometry : angle 0.67528 (10554) SS BOND : bond 0.00467 ( 2) SS BOND : angle 1.50384 ( 4) hydrogen bonds : bond 0.04043 ( 233) hydrogen bonds : angle 5.31416 ( 597) *********************** 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 241 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7893 (ptp-170) cc_final: 0.7668 (ptp90) REVERT: A 85 ASN cc_start: 0.8068 (p0) cc_final: 0.7792 (p0) REVERT: A 131 LEU cc_start: 0.8104 (tp) cc_final: 0.7783 (tt) REVERT: A 147 LEU cc_start: 0.8811 (mp) cc_final: 0.8559 (mm) REVERT: A 184 GLN cc_start: 0.7786 (mp10) cc_final: 0.7548 (mp10) REVERT: A 252 THR cc_start: 0.8147 (p) cc_final: 0.7928 (m) REVERT: A 275 ASP cc_start: 0.7098 (t0) cc_final: 0.6873 (t0) REVERT: A 323 LEU cc_start: 0.7957 (tp) cc_final: 0.7742 (mm) REVERT: A 402 PHE cc_start: 0.6350 (t80) cc_final: 0.6068 (t80) REVERT: A 409 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7724 (p) REVERT: A 427 LYS cc_start: 0.7291 (tmtt) cc_final: 0.6884 (tttp) REVERT: A 432 GLN cc_start: 0.8750 (mt0) cc_final: 0.8433 (mm-40) REVERT: A 547 ASN cc_start: 0.6167 (t0) cc_final: 0.5914 (t0) REVERT: A 696 LEU cc_start: 0.5229 (OUTLIER) cc_final: 0.4920 (pt) REVERT: A 715 LYS cc_start: 0.8769 (tttt) cc_final: 0.8394 (tptt) REVERT: A 758 ASP cc_start: 0.7785 (m-30) cc_final: 0.7421 (m-30) REVERT: B 86 MET cc_start: 0.7037 (mmm) cc_final: 0.6480 (mmm) REVERT: C 45 ARG cc_start: 0.6766 (mtm-85) cc_final: 0.6403 (mtt180) REVERT: C 56 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7241 (mtm180) REVERT: C 66 ARG cc_start: 0.7035 (mtm-85) cc_final: 0.6802 (mtp-110) REVERT: C 80 LEU cc_start: 0.8696 (tp) cc_final: 0.8274 (tp) REVERT: C 114 THR cc_start: 0.8473 (m) cc_final: 0.8164 (p) outliers start: 43 outliers final: 23 residues processed: 218 average time/residue: 0.0817 time to fit residues: 24.7906 Evaluate side-chains 201 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 75 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN A 316 GLN A 338 GLN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.093440 restraints weight = 16274.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095250 restraints weight = 10792.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096639 restraints weight = 7967.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097504 restraints weight = 6328.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098202 restraints weight = 5405.893| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 7733 Z= 0.290 Angle : 0.803 8.992 10558 Z= 0.413 Chirality : 0.049 0.325 1271 Planarity : 0.005 0.046 1346 Dihedral : 8.722 118.805 1094 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.20 % Favored : 88.40 % Rotamer: Outliers : 6.79 % Allowed : 22.32 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.24), residues: 1009 helix: -1.46 (0.32), residues: 238 sheet: -1.26 (0.32), residues: 236 loop : -2.69 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 226 TYR 0.014 0.002 TYR A 536 PHE 0.023 0.003 PHE A 410 TRP 0.017 0.002 TRP B 36 HIS 0.014 0.002 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00675 ( 7731) covalent geometry : angle 0.80262 (10554) SS BOND : bond 0.00781 ( 2) SS BOND : angle 2.08435 ( 4) hydrogen bonds : bond 0.05375 ( 233) hydrogen bonds : angle 5.91847 ( 597) *********************** 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 250 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 36 ASP cc_start: 0.6071 (p0) cc_final: 0.5288 (p0) REVERT: A 85 ASN cc_start: 0.7963 (p0) cc_final: 0.7675 (p0) REVERT: A 86 SER cc_start: 0.8067 (p) cc_final: 0.7550 (p) REVERT: A 254 ILE cc_start: 0.7442 (tp) cc_final: 0.7048 (tp) REVERT: A 282 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7333 (mp) REVERT: A 338 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7448 (mm110) REVERT: A 378 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7280 (p) REVERT: A 402 PHE cc_start: 0.6313 (t80) cc_final: 0.6066 (t80) REVERT: A 405 SER cc_start: 0.8431 (p) cc_final: 0.8207 (m) REVERT: A 427 LYS cc_start: 0.7359 (tmtt) cc_final: 0.6992 (tptp) REVERT: A 432 GLN cc_start: 0.8632 (mt0) cc_final: 0.8384 (mm-40) REVERT: A 471 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: A 526 HIS cc_start: 0.6365 (OUTLIER) cc_final: 0.6121 (m90) REVERT: A 556 GLU cc_start: 0.6848 (tp30) cc_final: 0.6472 (tp30) REVERT: A 715 LYS cc_start: 0.8724 (tttt) cc_final: 0.8425 (tptt) REVERT: B 86 MET cc_start: 0.7066 (mmm) cc_final: 0.6244 (mmm) REVERT: C 80 LEU cc_start: 0.8620 (tp) cc_final: 0.7921 (tp) REVERT: C 86 LYS cc_start: 0.8429 (mtmm) cc_final: 0.8049 (mttp) REVERT: C 114 THR cc_start: 0.8302 (m) cc_final: 0.8038 (p) outliers start: 52 outliers final: 36 residues processed: 226 average time/residue: 0.0765 time to fit residues: 23.5472 Evaluate side-chains 228 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 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 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 229 ILE 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 338 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 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 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 72 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.109225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095244 restraints weight = 16513.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097172 restraints weight = 10789.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098448 restraints weight = 7862.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099466 restraints weight = 6263.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100117 restraints weight = 5256.446| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7733 Z= 0.183 Angle : 0.704 8.459 10558 Z= 0.358 Chirality : 0.045 0.264 1271 Planarity : 0.005 0.043 1346 Dihedral : 8.303 118.718 1094 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.81 % Favored : 89.79 % Rotamer: Outliers : 6.79 % Allowed : 24.54 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.25), residues: 1009 helix: -1.33 (0.33), residues: 247 sheet: -1.10 (0.33), residues: 235 loop : -2.61 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 66 TYR 0.013 0.002 TYR C 94 PHE 0.018 0.002 PHE A 410 TRP 0.013 0.002 TRP A 91 HIS 0.002 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 7731) covalent geometry : angle 0.70371 (10554) SS BOND : bond 0.00492 ( 2) SS BOND : angle 1.61489 ( 4) hydrogen bonds : bond 0.04311 ( 233) hydrogen bonds : angle 5.55365 ( 597) *********************** 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 244 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6538 (mmt90) cc_final: 0.6175 (mmt90) REVERT: A 54 ARG cc_start: 0.7741 (ptp90) cc_final: 0.7023 (ptt-90) REVERT: A 74 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8414 (mm-40) REVERT: A 85 ASN cc_start: 0.7851 (p0) cc_final: 0.7610 (p0) REVERT: A 86 SER cc_start: 0.8024 (p) cc_final: 0.7367 (p) REVERT: A 254 ILE cc_start: 0.7334 (tp) cc_final: 0.7006 (tp) REVERT: A 282 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7304 (mp) REVERT: A 338 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7674 (mm110) REVERT: A 378 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7412 (p) REVERT: A 402 PHE cc_start: 0.6249 (t80) cc_final: 0.6033 (t80) REVERT: A 405 SER cc_start: 0.8467 (p) cc_final: 0.8188 (m) REVERT: A 427 LYS cc_start: 0.7303 (tmtt) cc_final: 0.6788 (tptp) REVERT: A 432 GLN cc_start: 0.8638 (mt0) cc_final: 0.8428 (mm-40) REVERT: A 471 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: A 556 GLU cc_start: 0.6609 (tp30) cc_final: 0.6210 (tp30) REVERT: A 574 ASN cc_start: 0.7730 (t0) cc_final: 0.7521 (t0) REVERT: A 715 LYS cc_start: 0.8664 (tttt) cc_final: 0.8346 (tptt) REVERT: B 86 MET cc_start: 0.7168 (mmm) cc_final: 0.6342 (mmm) REVERT: C 66 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7429 (ttm110) REVERT: C 80 LEU cc_start: 0.8556 (tp) cc_final: 0.8021 (tp) REVERT: C 86 LYS cc_start: 0.8359 (mtmm) cc_final: 0.7897 (mttp) REVERT: C 114 THR cc_start: 0.8294 (m) cc_final: 0.8039 (p) outliers start: 52 outliers final: 38 residues processed: 220 average time/residue: 0.0760 time to fit residues: 23.0926 Evaluate side-chains 230 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 84 LEU 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 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 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 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 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 98 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 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 316 GLN ** 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 = 0.3465 r_free = 0.3465 target = 0.107960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.093978 restraints weight = 16324.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.095919 restraints weight = 10750.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097262 restraints weight = 7822.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098149 restraints weight = 6206.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.098875 restraints weight = 5248.856| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7733 Z= 0.231 Angle : 0.741 8.253 10558 Z= 0.379 Chirality : 0.047 0.275 1271 Planarity : 0.005 0.059 1346 Dihedral : 8.583 121.662 1094 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.60 % Favored : 89.00 % Rotamer: Outliers : 7.57 % Allowed : 24.41 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.25), residues: 1009 helix: -1.45 (0.33), residues: 246 sheet: -1.09 (0.34), residues: 237 loop : -2.61 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 38 TYR 0.014 0.002 TYR B 60 PHE 0.016 0.002 PHE A 115 TRP 0.020 0.002 TRP B 53 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 7731) covalent geometry : angle 0.73990 (10554) SS BOND : bond 0.00615 ( 2) SS BOND : angle 1.84705 ( 4) hydrogen bonds : bond 0.04736 ( 233) hydrogen bonds : angle 5.71742 ( 597) *********************** 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 253 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6445 (mmt90) cc_final: 0.6113 (mmt90) REVERT: A 54 ARG cc_start: 0.7807 (ptp90) cc_final: 0.7131 (ptt-90) REVERT: A 74 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: A 85 ASN cc_start: 0.7862 (p0) cc_final: 0.7385 (p0) REVERT: A 86 SER cc_start: 0.8124 (p) cc_final: 0.7569 (p) REVERT: A 184 GLN cc_start: 0.7568 (mp10) cc_final: 0.7305 (mp10) REVERT: A 254 ILE cc_start: 0.7265 (tp) cc_final: 0.6940 (tp) REVERT: A 338 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7579 (mm110) REVERT: A 405 SER cc_start: 0.8407 (p) cc_final: 0.8158 (m) REVERT: A 427 LYS cc_start: 0.7312 (tmtt) cc_final: 0.6822 (tptp) REVERT: A 471 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: A 547 ASN cc_start: 0.7293 (t0) cc_final: 0.6975 (p0) REVERT: A 556 GLU cc_start: 0.6578 (tp30) cc_final: 0.6162 (tp30) REVERT: A 574 ASN cc_start: 0.7871 (t0) cc_final: 0.7591 (t0) REVERT: A 672 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6324 (tp) REVERT: A 715 LYS cc_start: 0.8821 (tttt) cc_final: 0.8439 (tptt) REVERT: B 86 MET cc_start: 0.7162 (mmm) cc_final: 0.6314 (mmm) REVERT: C 80 LEU cc_start: 0.8618 (tp) cc_final: 0.7982 (tp) REVERT: C 114 THR cc_start: 0.8295 (m) cc_final: 0.8011 (p) outliers start: 58 outliers final: 44 residues processed: 230 average time/residue: 0.0686 time to fit residues: 21.9900 Evaluate side-chains 234 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 84 LEU 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 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 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 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 672 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.108997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.094526 restraints weight = 16446.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096599 restraints weight = 10482.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098064 restraints weight = 7500.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099129 restraints weight = 5849.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099755 restraints weight = 4886.009| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7733 Z= 0.186 Angle : 0.703 9.141 10558 Z= 0.359 Chirality : 0.045 0.236 1271 Planarity : 0.005 0.059 1346 Dihedral : 8.306 125.206 1094 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.51 % Favored : 90.09 % Rotamer: Outliers : 6.92 % Allowed : 26.24 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.83 (0.25), residues: 1009 helix: -1.40 (0.33), residues: 246 sheet: -1.08 (0.34), residues: 238 loop : -2.55 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.013 0.002 TYR B 60 PHE 0.016 0.002 PHE A 115 TRP 0.014 0.001 TRP B 53 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 7731) covalent geometry : angle 0.70244 (10554) SS BOND : bond 0.00515 ( 2) SS BOND : angle 1.66298 ( 4) hydrogen bonds : bond 0.04376 ( 233) hydrogen bonds : angle 5.55280 ( 597) *********************** 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 246 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6574 (mmt90) cc_final: 0.6230 (mmt90) REVERT: A 54 ARG cc_start: 0.7750 (ptp90) cc_final: 0.7282 (ptt180) REVERT: A 74 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: A 85 ASN cc_start: 0.7727 (p0) cc_final: 0.7299 (p0) REVERT: A 86 SER cc_start: 0.8052 (p) cc_final: 0.7440 (p) REVERT: A 132 THR cc_start: 0.8240 (p) cc_final: 0.7692 (t) REVERT: A 184 GLN cc_start: 0.7566 (mp10) cc_final: 0.7301 (mp10) REVERT: A 254 ILE cc_start: 0.7361 (tp) cc_final: 0.7027 (tp) REVERT: A 338 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7556 (mm110) REVERT: A 405 SER cc_start: 0.8441 (p) cc_final: 0.8182 (m) REVERT: A 427 LYS cc_start: 0.7316 (tmtt) cc_final: 0.6736 (tptp) REVERT: A 432 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8015 (mm110) REVERT: A 471 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: A 556 GLU cc_start: 0.6470 (tp30) cc_final: 0.6095 (tp30) REVERT: A 574 ASN cc_start: 0.7886 (t0) cc_final: 0.7560 (t0) REVERT: A 672 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6235 (tp) REVERT: A 715 LYS cc_start: 0.8803 (tttt) cc_final: 0.8392 (tptt) REVERT: B 86 MET cc_start: 0.7182 (mmm) cc_final: 0.6299 (mmm) REVERT: C 80 LEU cc_start: 0.8580 (tp) cc_final: 0.8082 (tp) REVERT: C 114 THR cc_start: 0.8297 (m) cc_final: 0.7964 (p) outliers start: 53 outliers final: 41 residues processed: 223 average time/residue: 0.0730 time to fit residues: 22.6912 Evaluate side-chains 229 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 79 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP 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 204 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 325 SER Chi-restraints excluded: chain A residue 330 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 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 672 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 73 optimal weight: 0.0270 chunk 57 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 8 optimal weight: 0.0570 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.109805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095243 restraints weight = 16373.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097326 restraints weight = 10316.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098773 restraints weight = 7336.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099886 restraints weight = 5761.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100690 restraints weight = 4752.847| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7733 Z= 0.158 Angle : 0.682 8.031 10558 Z= 0.350 Chirality : 0.044 0.208 1271 Planarity : 0.005 0.059 1346 Dihedral : 8.092 126.013 1094 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.71 % Favored : 89.89 % Rotamer: Outliers : 6.53 % Allowed : 27.42 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.25), residues: 1009 helix: -1.36 (0.33), residues: 244 sheet: -1.02 (0.34), residues: 238 loop : -2.52 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 66 TYR 0.012 0.002 TYR B 60 PHE 0.015 0.002 PHE A 115 TRP 0.014 0.001 TRP B 53 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7731) covalent geometry : angle 0.68163 (10554) SS BOND : bond 0.00372 ( 2) SS BOND : angle 1.41548 ( 4) hydrogen bonds : bond 0.04054 ( 233) hydrogen bonds : angle 5.39031 ( 597) *********************** 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 242 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6651 (mmt90) cc_final: 0.6435 (mmt90) REVERT: A 54 ARG cc_start: 0.7804 (ptp90) cc_final: 0.7440 (ptt180) REVERT: A 86 SER cc_start: 0.7943 (p) cc_final: 0.7343 (p) REVERT: A 254 ILE cc_start: 0.7341 (tp) cc_final: 0.7023 (tp) REVERT: A 338 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7514 (mm110) REVERT: A 380 ARG cc_start: 0.7077 (mpt180) cc_final: 0.6660 (mmt90) REVERT: A 432 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8002 (mm110) REVERT: A 556 GLU cc_start: 0.6559 (tp30) cc_final: 0.6201 (tp30) REVERT: A 574 ASN cc_start: 0.7893 (t0) cc_final: 0.7552 (t0) REVERT: A 715 LYS cc_start: 0.8797 (tttt) cc_final: 0.8367 (tptt) REVERT: B 86 MET cc_start: 0.7176 (mmm) cc_final: 0.6273 (mmm) REVERT: C 80 LEU cc_start: 0.8684 (tp) cc_final: 0.8143 (tp) REVERT: C 114 THR cc_start: 0.8296 (m) cc_final: 0.7984 (p) outliers start: 50 outliers final: 45 residues processed: 220 average time/residue: 0.0719 time to fit residues: 21.8592 Evaluate side-chains 232 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 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 185 ILE 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 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 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 753 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN ** 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 = 0.3482 r_free = 0.3482 target = 0.108531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094618 restraints weight = 16515.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096546 restraints weight = 10853.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097875 restraints weight = 7909.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098803 restraints weight = 6316.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.099229 restraints weight = 5340.722| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7733 Z= 0.208 Angle : 0.733 9.089 10558 Z= 0.376 Chirality : 0.046 0.286 1271 Planarity : 0.005 0.059 1346 Dihedral : 8.369 129.592 1094 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.31 % Favored : 89.30 % Rotamer: Outliers : 7.05 % Allowed : 27.42 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.25), residues: 1009 helix: -1.38 (0.34), residues: 237 sheet: -1.12 (0.33), residues: 237 loop : -2.47 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 66 TYR 0.014 0.002 TYR B 60 PHE 0.015 0.002 PHE A 115 TRP 0.015 0.001 TRP B 53 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 7731) covalent geometry : angle 0.73247 (10554) SS BOND : bond 0.00546 ( 2) SS BOND : angle 1.69715 ( 4) hydrogen bonds : bond 0.04487 ( 233) hydrogen bonds : angle 5.61135 ( 597) *********************** 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 247 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7738 (ptp90) cc_final: 0.7389 (ptt180) REVERT: A 74 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8201 (mm-40) REVERT: A 86 SER cc_start: 0.7986 (p) cc_final: 0.7327 (p) REVERT: A 132 THR cc_start: 0.8203 (p) cc_final: 0.7697 (t) REVERT: A 254 ILE cc_start: 0.7282 (tp) cc_final: 0.7012 (tp) REVERT: A 338 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7581 (mm110) REVERT: A 380 ARG cc_start: 0.7198 (mpt180) cc_final: 0.6947 (mtt90) REVERT: A 432 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8160 (mm-40) REVERT: A 556 GLU cc_start: 0.6541 (tp30) cc_final: 0.6185 (tp30) REVERT: A 574 ASN cc_start: 0.7836 (t0) cc_final: 0.7485 (t0) REVERT: A 672 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6327 (tp) REVERT: A 715 LYS cc_start: 0.8643 (tttt) cc_final: 0.8303 (tptt) REVERT: B 86 MET cc_start: 0.7153 (mmm) cc_final: 0.6128 (mmm) REVERT: C 80 LEU cc_start: 0.8594 (tp) cc_final: 0.8118 (tp) REVERT: C 114 THR cc_start: 0.8355 (m) cc_final: 0.8031 (p) outliers start: 54 outliers final: 47 residues processed: 225 average time/residue: 0.0673 time to fit residues: 21.0635 Evaluate side-chains 240 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 79 SER 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 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 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 383 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 450 LEU 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 672 LEU Chi-restraints excluded: chain A residue 676 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 758 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 619 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 = 0.3511 r_free = 0.3511 target = 0.110246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096472 restraints weight = 16455.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.098395 restraints weight = 10812.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099736 restraints weight = 7890.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.100697 restraints weight = 6238.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101319 restraints weight = 5258.702| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7733 Z= 0.151 Angle : 0.702 8.686 10558 Z= 0.358 Chirality : 0.045 0.238 1271 Planarity : 0.005 0.059 1346 Dihedral : 8.075 131.180 1094 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.32 % Favored : 90.39 % Rotamer: Outliers : 6.14 % Allowed : 28.85 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.25), residues: 1009 helix: -1.27 (0.34), residues: 238 sheet: -1.13 (0.33), residues: 238 loop : -2.41 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 66 TYR 0.013 0.002 TYR A 802 PHE 0.015 0.002 PHE A 115 TRP 0.013 0.001 TRP B 53 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7731) covalent geometry : angle 0.70208 (10554) SS BOND : bond 0.00340 ( 2) SS BOND : angle 1.35916 ( 4) hydrogen bonds : bond 0.03919 ( 233) hydrogen bonds : angle 5.34573 ( 597) *********************** 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 237 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7352 (ptt180) REVERT: A 74 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8192 (mm-40) REVERT: A 86 SER cc_start: 0.7846 (p) cc_final: 0.7164 (p) REVERT: A 254 ILE cc_start: 0.7320 (tp) cc_final: 0.7031 (tp) REVERT: A 338 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7566 (mm110) REVERT: A 432 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8179 (mm110) REVERT: A 556 GLU cc_start: 0.6633 (tp30) cc_final: 0.6348 (tp30) REVERT: A 574 ASN cc_start: 0.7813 (t0) cc_final: 0.7464 (t0) REVERT: A 715 LYS cc_start: 0.8615 (tttt) cc_final: 0.8260 (tptt) REVERT: B 86 MET cc_start: 0.7179 (mmm) cc_final: 0.6233 (mmm) REVERT: C 80 LEU cc_start: 0.8704 (tp) cc_final: 0.8174 (tp) REVERT: C 114 THR cc_start: 0.8352 (m) cc_final: 0.8015 (p) outliers start: 47 outliers final: 46 residues processed: 216 average time/residue: 0.0642 time to fit residues: 19.5126 Evaluate side-chains 232 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 79 SER 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 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 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 364 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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** ** 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 = 0.3504 r_free = 0.3504 target = 0.109797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.095917 restraints weight = 16431.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097685 restraints weight = 10817.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099056 restraints weight = 8000.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100099 restraints weight = 6396.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100794 restraints weight = 5341.219| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7733 Z= 0.170 Angle : 0.716 8.554 10558 Z= 0.364 Chirality : 0.045 0.187 1271 Planarity : 0.005 0.059 1346 Dihedral : 8.101 133.002 1093 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.51 % Favored : 90.19 % Rotamer: Outliers : 6.40 % Allowed : 28.98 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.25), residues: 1009 helix: -1.24 (0.34), residues: 238 sheet: -1.13 (0.33), residues: 237 loop : -2.41 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 66 TYR 0.014 0.002 TYR A 684 PHE 0.014 0.002 PHE A 115 TRP 0.012 0.001 TRP B 53 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7731) covalent geometry : angle 0.71583 (10554) SS BOND : bond 0.00446 ( 2) SS BOND : angle 1.50819 ( 4) hydrogen bonds : bond 0.04047 ( 233) hydrogen bonds : angle 5.42237 ( 597) ********************** 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 233 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6786 (mmt90) cc_final: 0.6476 (mmt90) REVERT: A 54 ARG cc_start: 0.7740 (ptp90) cc_final: 0.7396 (ptt180) REVERT: A 74 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8203 (mm-40) REVERT: A 86 SER cc_start: 0.7873 (p) cc_final: 0.7222 (p) REVERT: A 254 ILE cc_start: 0.7348 (tp) cc_final: 0.7013 (tp) REVERT: A 338 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7628 (mm110) REVERT: A 432 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8302 (mm110) REVERT: A 556 GLU cc_start: 0.6649 (tp30) cc_final: 0.6373 (tp30) REVERT: A 574 ASN cc_start: 0.7838 (t0) cc_final: 0.7469 (t0) REVERT: A 706 TYR cc_start: 0.3905 (t80) cc_final: 0.2516 (t80) REVERT: A 715 LYS cc_start: 0.8626 (tttt) cc_final: 0.8271 (tptt) REVERT: B 86 MET cc_start: 0.7182 (mmm) cc_final: 0.6235 (mmm) REVERT: C 80 LEU cc_start: 0.8679 (tp) cc_final: 0.8155 (tp) REVERT: C 114 THR cc_start: 0.8355 (m) cc_final: 0.8025 (p) outliers start: 49 outliers final: 47 residues processed: 214 average time/residue: 0.0667 time to fit residues: 19.9877 Evaluate side-chains 232 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 79 SER 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 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 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 364 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** 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 = 0.3498 r_free = 0.3498 target = 0.109426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.095375 restraints weight = 16425.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097325 restraints weight = 10720.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098735 restraints weight = 7804.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099748 restraints weight = 6159.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100448 restraints weight = 5145.781| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7733 Z= 0.184 Angle : 0.727 8.427 10558 Z= 0.370 Chirality : 0.045 0.189 1271 Planarity : 0.005 0.067 1346 Dihedral : 8.212 136.211 1093 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.71 % Favored : 89.99 % Rotamer: Outliers : 6.79 % Allowed : 29.11 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.25), residues: 1009 helix: -1.25 (0.34), residues: 238 sheet: -1.14 (0.33), residues: 237 loop : -2.39 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 66 TYR 0.014 0.002 TYR A 684 PHE 0.014 0.002 PHE A 115 TRP 0.014 0.001 TRP B 53 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 7731) covalent geometry : angle 0.72680 (10554) SS BOND : bond 0.00476 ( 2) SS BOND : angle 1.58440 ( 4) hydrogen bonds : bond 0.04089 ( 233) hydrogen bonds : angle 5.49360 ( 597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1260.08 seconds wall clock time: 22 minutes 29.18 seconds (1349.18 seconds total)