Starting phenix.real_space_refine on Fri Jul 19 10:43:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/07_2024/8r4b_18884_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/07_2024/8r4b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/07_2024/8r4b_18884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/07_2024/8r4b_18884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/07_2024/8r4b_18884_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/07_2024/8r4b_18884_neut.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 24 5.16 5 C 4806 2.51 5 N 1277 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 504": "OD1" <-> "OD2" Residue "A ASP 545": "OD1" <-> "OD2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 621": "OD1" <-> "OD2" Residue "A TYR 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 803": "OD1" <-> "OD2" Residue "A TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7600 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 5956 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 34, 'TRANS': 773} Chain breaks: 8 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 499 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 209 Chain: "B" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 769 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 843 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 112} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.03, per 1000 atoms: 0.66 Number of scatterers: 7600 At special positions: 0 Unit cell: (70.97, 80.03, 182.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 3 15.00 O 1490 8.00 N 1277 7.00 C 4806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 24.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 51 through 62 removed outlier: 3.736A pdb=" N ILE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 3.617A pdb=" N LEU A 62 " --> pdb=" O PRO A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.089A pdb=" N SER A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.522A pdb=" N SER A 149 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 211 through 216 removed outlier: 4.089A pdb=" N GLU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.904A pdb=" N SER A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.740A pdb=" N LEU A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 419 through 426 removed outlier: 3.790A pdb=" N GLY A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 439 Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.834A pdb=" N LEU A 506 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 507 " --> pdb=" O ASP A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 507' Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.631A pdb=" N ASP A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 removed outlier: 3.626A pdb=" N LEU A 552 " --> pdb=" O LYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 588 Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.512A pdb=" N LEU A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 647 removed outlier: 3.629A pdb=" N ILE A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 661 removed outlier: 4.040A pdb=" N SER A 661 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 678 Processing helix chain 'A' and resid 697 through 710 removed outlier: 3.551A pdb=" N THR A 702 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 705 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.687A pdb=" N ILE A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 872 through 881 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.849A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.298A pdb=" N GLU A 19 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 30 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 41 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 222 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.842A pdb=" N LEU A 310 " --> pdb=" O TRP A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 377 removed outlier: 6.411A pdb=" N GLU A 396 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 490 through 493 removed outlier: 8.611A pdb=" N VAL A 535 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS A 454 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N MET A 537 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS A 456 " --> pdb=" O MET A 537 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU A 539 " --> pdb=" O HIS A 456 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 458 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ILE A 565 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR A 536 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 567 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 538 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 596 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 830 through 834 removed outlier: 3.622A pdb=" N LYS A 844 " --> pdb=" O ALA A 857 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 800 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 23 Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.839A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.184A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL C 33 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.184A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLY C 99 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN C 107 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE C 101 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYR C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 3.33 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: 99.21 - 106.17: 178 106.17 - 113.13: 4310 113.13 - 120.09: 2573 120.09 - 127.06: 3405 127.06 - 134.02: 88 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 2.440 nonbonded pdb=" O SER A 417 " pdb=" OH TYR A 433 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR A 154 " pdb=" OE1 GLU A 155 " model vdw 2.283 2.440 nonbonded pdb=" O SER A 352 " pdb=" OG1 THR A 374 " model vdw 2.285 2.440 nonbonded pdb=" N GLU A 686 " pdb=" OE1 GLU A 686 " model vdw 2.289 2.520 ... (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 ========== 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.670 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7731 Z= 0.214 Angle : 0.686 7.697 10554 Z= 0.365 Chirality : 0.044 0.167 1271 Planarity : 0.005 0.047 1346 Dihedral : 16.622 110.136 2681 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.51 % Favored : 90.19 % Rotamer: Outliers : 0.52 % Allowed : 20.63 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.25), residues: 1009 helix: -1.10 (0.34), residues: 233 sheet: -1.20 (0.32), residues: 250 loop : -2.57 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 36 HIS 0.004 0.001 HIS A 549 PHE 0.014 0.001 PHE A 410 TYR 0.011 0.001 TYR C 37 ARG 0.007 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 228 time to evaluate : 0.881 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: 0.1819 time to fit residues: 56.5802 Evaluate side-chains 188 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 577 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7162 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7731 Z= 0.316 Angle : 0.705 10.653 10554 Z= 0.361 Chirality : 0.046 0.273 1271 Planarity : 0.005 0.042 1346 Dihedral : 7.849 108.012 1094 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.40 % Favored : 88.21 % Rotamer: Outliers : 6.01 % Allowed : 21.80 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.25), residues: 1009 helix: -1.16 (0.34), residues: 237 sheet: -1.22 (0.32), residues: 237 loop : -2.61 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 36 HIS 0.013 0.002 HIS A 449 PHE 0.025 0.002 PHE A 410 TYR 0.020 0.002 TYR A 767 ARG 0.006 0.001 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 206 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.8218 (tp) cc_final: 0.7909 (tt) REVERT: A 147 LEU cc_start: 0.8846 (mp) cc_final: 0.8586 (mm) REVERT: A 275 ASP cc_start: 0.7007 (t0) cc_final: 0.6697 (t0) REVERT: A 323 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7757 (mm) REVERT: A 402 PHE cc_start: 0.6329 (t80) cc_final: 0.6000 (t80) REVERT: A 427 LYS cc_start: 0.7342 (tmtt) cc_final: 0.6851 (tttp) REVERT: A 432 GLN cc_start: 0.8741 (mt0) cc_final: 0.8410 (mm-40) REVERT: A 696 LEU cc_start: 0.5416 (OUTLIER) cc_final: 0.5105 (pt) REVERT: A 715 LYS cc_start: 0.8605 (tttt) cc_final: 0.8342 (tptt) REVERT: B 86 MET cc_start: 0.7266 (mmm) cc_final: 0.6664 (mmm) REVERT: C 45 ARG cc_start: 0.6775 (mtm-85) cc_final: 0.6389 (mtt180) REVERT: C 64 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8829 (pttt) REVERT: C 66 ARG cc_start: 0.7098 (mtm-85) cc_final: 0.6828 (mtp-110) REVERT: C 80 LEU cc_start: 0.8635 (tp) cc_final: 0.8274 (tp) REVERT: C 86 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7941 (mttp) REVERT: C 114 THR cc_start: 0.8362 (m) cc_final: 0.8110 (p) outliers start: 46 outliers final: 25 residues processed: 228 average time/residue: 0.1789 time to fit residues: 55.6268 Evaluate side-chains 214 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 177 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 238 LEU 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 577 TYR Chi-restraints excluded: chain A residue 609 ILE 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 57 ILE Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN A 451 GLN A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7731 Z= 0.344 Angle : 0.722 8.344 10554 Z= 0.368 Chirality : 0.046 0.282 1271 Planarity : 0.005 0.045 1346 Dihedral : 8.149 117.042 1093 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.90 % Favored : 88.70 % Rotamer: Outliers : 6.92 % Allowed : 23.50 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.25), residues: 1009 helix: -1.30 (0.33), residues: 238 sheet: -1.18 (0.33), residues: 236 loop : -2.63 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 36 HIS 0.012 0.002 HIS A 523 PHE 0.021 0.002 PHE A 410 TYR 0.014 0.002 TYR C 94 ARG 0.004 0.001 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 198 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7720 (ptp90) cc_final: 0.6993 (ptt-90) REVERT: A 184 GLN cc_start: 0.7599 (mp10) cc_final: 0.7240 (mp10) REVERT: A 254 ILE cc_start: 0.7354 (tp) cc_final: 0.7008 (tp) REVERT: A 275 ASP cc_start: 0.7044 (t0) cc_final: 0.6640 (t0) REVERT: A 282 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7255 (mp) REVERT: A 338 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7423 (mm110) REVERT: A 377 ASP cc_start: 0.6484 (t0) cc_final: 0.6195 (t0) REVERT: A 378 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7294 (p) REVERT: A 402 PHE cc_start: 0.6260 (t80) cc_final: 0.5926 (t80) REVERT: A 409 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7922 (p) REVERT: A 427 LYS cc_start: 0.7369 (tmtt) cc_final: 0.6989 (tptp) REVERT: A 432 GLN cc_start: 0.8711 (mt0) cc_final: 0.8462 (mm-40) REVERT: A 556 GLU cc_start: 0.6888 (tp30) cc_final: 0.6500 (tp30) REVERT: A 696 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.5185 (pt) REVERT: B 86 MET cc_start: 0.7137 (mmm) cc_final: 0.6219 (mmm) REVERT: C 80 LEU cc_start: 0.8584 (tp) cc_final: 0.8068 (tp) REVERT: C 86 LYS cc_start: 0.8407 (mtmm) cc_final: 0.8024 (mttp) REVERT: C 114 THR cc_start: 0.8308 (m) cc_final: 0.8080 (p) outliers start: 53 outliers final: 34 residues processed: 228 average time/residue: 0.1863 time to fit residues: 57.3653 Evaluate side-chains 225 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 141 ILE 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 282 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.0170 chunk 26 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 471 GLN A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7731 Z= 0.264 Angle : 0.672 8.624 10554 Z= 0.340 Chirality : 0.045 0.267 1271 Planarity : 0.005 0.042 1346 Dihedral : 7.873 119.449 1093 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.80 % Favored : 88.80 % Rotamer: Outliers : 7.18 % Allowed : 25.46 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.25), residues: 1009 helix: -1.23 (0.33), residues: 247 sheet: -1.08 (0.33), residues: 236 loop : -2.51 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 700 HIS 0.003 0.001 HIS A 526 PHE 0.018 0.002 PHE A 410 TYR 0.013 0.001 TYR C 94 ARG 0.004 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 195 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.6244 (p0) cc_final: 0.5427 (p0) REVERT: A 133 GLU cc_start: 0.8018 (tt0) cc_final: 0.7790 (tt0) REVERT: A 254 ILE cc_start: 0.7318 (tp) cc_final: 0.6929 (tp) REVERT: A 275 ASP cc_start: 0.7075 (t0) cc_final: 0.6676 (t0) REVERT: A 338 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7440 (mm110) REVERT: A 378 VAL cc_start: 0.7868 (OUTLIER) cc_final: 0.7301 (p) REVERT: A 402 PHE cc_start: 0.6281 (t80) cc_final: 0.5965 (t80) REVERT: A 409 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7911 (p) REVERT: A 427 LYS cc_start: 0.7270 (tmtt) cc_final: 0.7000 (tptp) REVERT: A 432 GLN cc_start: 0.8697 (mt0) cc_final: 0.8496 (mm-40) REVERT: A 471 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: A 547 ASN cc_start: 0.7055 (t0) cc_final: 0.6850 (p0) REVERT: A 556 GLU cc_start: 0.6920 (tp30) cc_final: 0.6504 (tp30) REVERT: B 33 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.7006 (p) REVERT: B 86 MET cc_start: 0.7170 (mmm) cc_final: 0.6220 (mmm) REVERT: C 38 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6820 (ptt180) REVERT: C 80 LEU cc_start: 0.8589 (tp) cc_final: 0.8106 (tp) REVERT: C 86 LYS cc_start: 0.8389 (mtmm) cc_final: 0.8008 (mttp) outliers start: 55 outliers final: 41 residues processed: 230 average time/residue: 0.1851 time to fit residues: 58.2181 Evaluate side-chains 232 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 LEU 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 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 ILE 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 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER 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 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 33 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 0.0770 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7731 Z= 0.282 Angle : 0.677 7.474 10554 Z= 0.347 Chirality : 0.045 0.275 1271 Planarity : 0.005 0.040 1346 Dihedral : 7.903 121.824 1093 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.51 % Favored : 89.10 % Rotamer: Outliers : 6.79 % Allowed : 27.02 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.25), residues: 1009 helix: -1.36 (0.32), residues: 250 sheet: -0.95 (0.34), residues: 236 loop : -2.47 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 53 HIS 0.003 0.001 HIS A 456 PHE 0.017 0.002 PHE A 115 TYR 0.016 0.002 TYR A 767 ARG 0.005 0.001 ARG C 66 *********************** 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 241 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 189 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7912 (tt0) cc_final: 0.7710 (tt0) REVERT: A 184 GLN cc_start: 0.7511 (mp10) cc_final: 0.7147 (mp10) REVERT: A 235 LEU cc_start: 0.7392 (mt) cc_final: 0.7169 (mt) REVERT: A 254 ILE cc_start: 0.7337 (tp) cc_final: 0.7006 (tp) REVERT: A 338 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7468 (mm110) REVERT: A 378 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7386 (p) REVERT: A 402 PHE cc_start: 0.6266 (t80) cc_final: 0.5966 (t80) REVERT: A 409 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7944 (p) REVERT: A 427 LYS cc_start: 0.7250 (tmtt) cc_final: 0.6715 (tptp) REVERT: A 556 GLU cc_start: 0.6921 (tp30) cc_final: 0.6480 (tp30) REVERT: B 86 MET cc_start: 0.7026 (mmm) cc_final: 0.6199 (mmm) REVERT: C 38 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6875 (ptt180) REVERT: C 80 LEU cc_start: 0.8585 (tp) cc_final: 0.8118 (tp) REVERT: C 86 LYS cc_start: 0.8353 (mtmm) cc_final: 0.8012 (mttp) outliers start: 52 outliers final: 41 residues processed: 216 average time/residue: 0.1739 time to fit residues: 51.5609 Evaluate side-chains 229 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 185 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 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 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 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER 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 A residue 708 ILE Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 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 87 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.0270 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7731 Z= 0.217 Angle : 0.648 8.190 10554 Z= 0.331 Chirality : 0.044 0.274 1271 Planarity : 0.005 0.045 1346 Dihedral : 7.585 122.492 1093 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.61 % Favored : 89.99 % Rotamer: Outliers : 7.44 % Allowed : 26.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.26), residues: 1009 helix: -1.27 (0.33), residues: 246 sheet: -0.82 (0.34), residues: 237 loop : -2.46 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.003 0.001 HIS A 526 PHE 0.015 0.002 PHE A 115 TYR 0.011 0.001 TYR C 94 ARG 0.005 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 189 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7952 (mm-40) REVERT: A 133 GLU cc_start: 0.7917 (tt0) cc_final: 0.7710 (tt0) REVERT: A 184 GLN cc_start: 0.7499 (mp10) cc_final: 0.7112 (mp10) REVERT: A 235 LEU cc_start: 0.7333 (mt) cc_final: 0.6979 (mt) REVERT: A 254 ILE cc_start: 0.7302 (tp) cc_final: 0.7035 (tp) REVERT: A 338 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7524 (mm110) REVERT: A 378 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7382 (p) REVERT: A 402 PHE cc_start: 0.6227 (t80) cc_final: 0.5954 (t80) REVERT: A 471 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: A 556 GLU cc_start: 0.6935 (tp30) cc_final: 0.6530 (tp30) REVERT: B 86 MET cc_start: 0.7024 (mmm) cc_final: 0.6227 (mmm) REVERT: C 38 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6834 (ptt180) REVERT: C 80 LEU cc_start: 0.8665 (tp) cc_final: 0.8218 (tp) outliers start: 57 outliers final: 43 residues processed: 225 average time/residue: 0.1728 time to fit residues: 54.3667 Evaluate side-chains 233 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 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 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 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU 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 615 SER 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 A residue 708 ILE 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 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 Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.0040 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7731 Z= 0.263 Angle : 0.676 7.843 10554 Z= 0.347 Chirality : 0.045 0.259 1271 Planarity : 0.005 0.042 1346 Dihedral : 7.728 124.380 1093 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.31 % Favored : 89.30 % Rotamer: Outliers : 7.44 % Allowed : 27.15 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.26), residues: 1009 helix: -1.23 (0.33), residues: 244 sheet: -0.82 (0.34), residues: 236 loop : -2.49 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 53 HIS 0.003 0.001 HIS A 456 PHE 0.017 0.002 PHE A 115 TYR 0.012 0.001 TYR B 60 ARG 0.006 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 190 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7966 (mm-40) REVERT: A 235 LEU cc_start: 0.7308 (mt) cc_final: 0.7026 (mt) REVERT: A 254 ILE cc_start: 0.7287 (tp) cc_final: 0.6984 (tp) REVERT: A 338 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7440 (mm110) REVERT: A 378 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7470 (p) REVERT: A 402 PHE cc_start: 0.6205 (t80) cc_final: 0.5910 (t80) REVERT: A 471 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8008 (pp30) REVERT: A 556 GLU cc_start: 0.6967 (tp30) cc_final: 0.6562 (tp30) REVERT: A 706 TYR cc_start: 0.4194 (t80) cc_final: 0.2781 (t80) REVERT: B 86 MET cc_start: 0.6965 (mmm) cc_final: 0.6172 (mmm) REVERT: C 38 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6862 (ptt180) REVERT: C 80 LEU cc_start: 0.8535 (tp) cc_final: 0.8082 (tp) outliers start: 57 outliers final: 47 residues processed: 226 average time/residue: 0.1714 time to fit residues: 53.5393 Evaluate side-chains 236 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 185 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 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 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 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU 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 615 SER 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 A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 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 57 ILE Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7731 Z= 0.321 Angle : 0.716 10.030 10554 Z= 0.365 Chirality : 0.046 0.219 1271 Planarity : 0.005 0.045 1346 Dihedral : 7.991 128.007 1093 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.51 % Favored : 89.10 % Rotamer: Outliers : 7.44 % Allowed : 26.63 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.25), residues: 1009 helix: -1.33 (0.33), residues: 238 sheet: -0.91 (0.34), residues: 236 loop : -2.46 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 53 HIS 0.003 0.001 HIS A 526 PHE 0.017 0.002 PHE A 115 TYR 0.014 0.002 TYR A 536 ARG 0.007 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 193 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6465 (mmt90) cc_final: 0.6252 (mmt90) REVERT: A 74 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7945 (mm-40) REVERT: A 86 SER cc_start: 0.7830 (p) cc_final: 0.7303 (p) REVERT: A 235 LEU cc_start: 0.7362 (mt) cc_final: 0.7075 (mt) REVERT: A 254 ILE cc_start: 0.7152 (tp) cc_final: 0.6919 (tp) REVERT: A 338 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7526 (mm110) REVERT: A 378 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7496 (p) REVERT: A 556 GLU cc_start: 0.6518 (tp30) cc_final: 0.6172 (tp30) REVERT: B 86 MET cc_start: 0.6928 (mmm) cc_final: 0.6103 (mmm) REVERT: C 11 LEU cc_start: 0.8178 (tt) cc_final: 0.7957 (tt) REVERT: C 80 LEU cc_start: 0.8646 (tp) cc_final: 0.8180 (tp) outliers start: 57 outliers final: 52 residues processed: 224 average time/residue: 0.1687 time to fit residues: 52.7784 Evaluate side-chains 243 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 189 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 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 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 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 615 SER 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 A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 58 THR 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 57 ILE Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.0040 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 58 optimal weight: 0.0870 overall best weight: 0.4570 ------------------------------------------------------------------------------- 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** B 61 GLN C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7731 Z= 0.240 Angle : 0.691 9.052 10554 Z= 0.352 Chirality : 0.044 0.183 1271 Planarity : 0.005 0.047 1346 Dihedral : 7.759 128.718 1093 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.71 % Favored : 89.89 % Rotamer: Outliers : 7.05 % Allowed : 27.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.25), residues: 1009 helix: -1.27 (0.34), residues: 238 sheet: -0.92 (0.34), residues: 237 loop : -2.41 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.007 0.001 HIS A 523 PHE 0.016 0.002 PHE A 115 TYR 0.013 0.001 TYR B 60 ARG 0.007 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 194 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7961 (mm-40) REVERT: A 86 SER cc_start: 0.7712 (p) cc_final: 0.7165 (p) REVERT: A 254 ILE cc_start: 0.7314 (tp) cc_final: 0.7035 (tp) REVERT: A 338 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7519 (mm110) REVERT: A 378 VAL cc_start: 0.8206 (OUTLIER) cc_final: 0.7992 (m) REVERT: A 556 GLU cc_start: 0.6608 (tp30) cc_final: 0.6326 (tp30) REVERT: B 86 MET cc_start: 0.6920 (mmm) cc_final: 0.6164 (mmm) REVERT: C 38 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6708 (ptt180) REVERT: C 80 LEU cc_start: 0.8606 (tp) cc_final: 0.8119 (tp) outliers start: 54 outliers final: 48 residues processed: 225 average time/residue: 0.1767 time to fit residues: 54.8478 Evaluate side-chains 240 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 189 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 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 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 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER 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 A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 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 57 ILE Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 92 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN C 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7731 Z= 0.265 Angle : 0.733 16.656 10554 Z= 0.366 Chirality : 0.045 0.204 1271 Planarity : 0.005 0.047 1346 Dihedral : 7.840 129.995 1093 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.81 % Favored : 89.79 % Rotamer: Outliers : 6.27 % Allowed : 29.77 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.25), residues: 1009 helix: -1.34 (0.33), residues: 245 sheet: -0.91 (0.34), residues: 236 loop : -2.51 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 53 HIS 0.007 0.001 HIS A 523 PHE 0.016 0.002 PHE A 115 TYR 0.017 0.002 TYR A 684 ARG 0.007 0.001 ARG C 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 193 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7973 (mm-40) REVERT: A 86 SER cc_start: 0.7729 (p) cc_final: 0.7193 (p) REVERT: A 254 ILE cc_start: 0.7339 (tp) cc_final: 0.7073 (tp) REVERT: A 338 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7546 (mm110) REVERT: A 378 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7994 (m) REVERT: A 556 GLU cc_start: 0.6634 (tp30) cc_final: 0.6368 (tp30) REVERT: A 706 TYR cc_start: 0.4213 (t80) cc_final: 0.2764 (t80) REVERT: B 86 MET cc_start: 0.6912 (mmm) cc_final: 0.6141 (mmm) REVERT: C 38 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6729 (ptt180) REVERT: C 80 LEU cc_start: 0.8604 (tp) cc_final: 0.8111 (tp) outliers start: 48 outliers final: 45 residues processed: 221 average time/residue: 0.1676 time to fit residues: 51.2519 Evaluate side-chains 241 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 193 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 204 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 248 SER 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 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 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 615 SER 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 A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 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 57 ILE Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 471 GLN A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.096322 restraints weight = 16204.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098371 restraints weight = 10425.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099787 restraints weight = 7506.617| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7731 Z= 0.256 Angle : 0.709 9.949 10554 Z= 0.359 Chirality : 0.045 0.184 1271 Planarity : 0.005 0.048 1346 Dihedral : 7.816 132.134 1093 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.81 % Favored : 89.79 % Rotamer: Outliers : 6.92 % Allowed : 29.11 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.25), residues: 1009 helix: -1.31 (0.33), residues: 244 sheet: -0.92 (0.34), residues: 236 loop : -2.51 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 53 HIS 0.007 0.001 HIS A 523 PHE 0.016 0.002 PHE A 115 TYR 0.016 0.002 TYR A 684 ARG 0.008 0.001 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.01 seconds wall clock time: 34 minutes 57.90 seconds (2097.90 seconds total)