Starting phenix.real_space_refine on Tue Mar 11 23:50:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iws_35778/03_2025/8iws_35778.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iws_35778/03_2025/8iws_35778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iws_35778/03_2025/8iws_35778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iws_35778/03_2025/8iws_35778.map" model { file = "/net/cci-nas-00/data/ceres_data/8iws_35778/03_2025/8iws_35778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iws_35778/03_2025/8iws_35778.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 Mg 1 5.21 5 S 52 5.16 5 Be 1 3.05 5 C 4336 2.51 5 N 1137 2.21 5 O 1278 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6809 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6803 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 854} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' CA': 1, ' MG': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.95, per 1000 atoms: 0.73 Number of scatterers: 6809 At special positions: 0 Unit cell: (93.24, 90.72, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 1 19.99 S 52 16.00 Mg 1 11.99 F 3 9.00 O 1278 8.00 N 1137 7.00 C 4336 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.0 seconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 53.5% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.681A pdb=" N LYS A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 100 through 128 Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.565A pdb=" N ASP A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 249 removed outlier: 3.614A pdb=" N VAL A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 288 Processing helix chain 'A' and resid 290 through 306 removed outlier: 3.650A pdb=" N ILE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.517A pdb=" N VAL A 338 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.653A pdb=" N MET A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 595 through 602 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.999A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 654 removed outlier: 4.372A pdb=" N VAL A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 673 removed outlier: 3.534A pdb=" N LYS A 670 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 723 removed outlier: 3.777A pdb=" N SER A 687 " --> pdb=" O GLN A 683 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 Processing helix chain 'A' and resid 743 through 750 removed outlier: 3.986A pdb=" N GLY A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 798 Processing helix chain 'A' and resid 804 through 826 removed outlier: 3.694A pdb=" N THR A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 860 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 886 through 905 removed outlier: 3.611A pdb=" N ILE A 890 " --> pdb=" O SER A 886 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 148 removed outlier: 4.516A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL A 223 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASP A 184 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS A 227 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP A 180 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LYS A 229 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA A 178 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N VAL A 231 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 176 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 233 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ARG A 174 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 183 " --> pdb=" O CYS A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 148 removed outlier: 4.516A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL A 223 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASP A 184 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS A 227 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP A 180 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LYS A 229 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA A 178 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N VAL A 231 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 176 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 233 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ARG A 174 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 removed outlier: 4.982A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 462 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLU A 451 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS A 464 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 removed outlier: 4.982A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 13.857A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AA8, first strand: chain 'A' and resid 568 through 569 removed outlier: 7.355A pdb=" N MET A 568 " --> pdb=" O PHE A 617 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 405 hydrogen bonds defined for protein. 1167 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: 2.51 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1141 1.28 - 1.41: 1484 1.41 - 1.55: 4195 1.55 - 1.68: 10 1.68 - 1.81: 84 Bond restraints: 6914 Sorted by residual: bond pdb=" C ASP A 350 " pdb=" O ASP A 350 " ideal model delta sigma weight residual 1.236 1.148 0.088 1.24e-02 6.50e+03 5.06e+01 bond pdb=" CA ASP A 350 " pdb=" CB ASP A 350 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.35e-02 5.49e+03 3.62e+01 bond pdb=" CA PRO A 762 " pdb=" CB PRO A 762 " ideal model delta sigma weight residual 1.536 1.473 0.063 1.37e-02 5.33e+03 2.09e+01 bond pdb=" C PRO A 762 " pdb=" O PRO A 762 " ideal model delta sigma weight residual 1.240 1.192 0.048 1.12e-02 7.97e+03 1.86e+01 bond pdb=" F2 BEF A1003 " pdb="BE BEF A1003 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 6909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 9277 2.75 - 5.51: 63 5.51 - 8.26: 15 8.26 - 11.01: 5 11.01 - 13.76: 2 Bond angle restraints: 9362 Sorted by residual: angle pdb=" C ASP A 350 " pdb=" N LYS A 351 " pdb=" CA LYS A 351 " ideal model delta sigma weight residual 120.28 133.16 -12.88 1.34e+00 5.57e-01 9.25e+01 angle pdb=" CA ASP A 350 " pdb=" C ASP A 350 " pdb=" N LYS A 351 " ideal model delta sigma weight residual 116.39 126.88 -10.49 1.26e+00 6.30e-01 6.93e+01 angle pdb=" O SER A 349 " pdb=" C SER A 349 " pdb=" N ASP A 350 " ideal model delta sigma weight residual 123.48 114.91 8.57 1.14e+00 7.69e-01 5.65e+01 angle pdb=" C PRO A 762 " pdb=" N PRO A 763 " pdb=" CA PRO A 763 " ideal model delta sigma weight residual 119.90 126.33 -6.43 1.02e+00 9.61e-01 3.98e+01 angle pdb=" C PRO A 30 " pdb=" CA PRO A 30 " pdb=" CB PRO A 30 " ideal model delta sigma weight residual 111.56 101.37 10.19 1.65e+00 3.67e-01 3.81e+01 ... (remaining 9357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3603 17.84 - 35.68: 484 35.68 - 53.52: 115 53.52 - 71.36: 16 71.36 - 89.19: 8 Dihedral angle restraints: 4226 sinusoidal: 1664 harmonic: 2562 Sorted by residual: dihedral pdb=" C PRO A 30 " pdb=" N PRO A 30 " pdb=" CA PRO A 30 " pdb=" CB PRO A 30 " ideal model delta harmonic sigma weight residual -120.70 -108.53 -12.17 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" N ASP A 350 " pdb=" C ASP A 350 " pdb=" CA ASP A 350 " pdb=" CB ASP A 350 " ideal model delta harmonic sigma weight residual 122.80 110.99 11.81 0 2.50e+00 1.60e-01 2.23e+01 dihedral pdb=" C ASP A 350 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " pdb=" CB ASP A 350 " ideal model delta harmonic sigma weight residual -122.60 -112.43 -10.17 0 2.50e+00 1.60e-01 1.66e+01 ... (remaining 4223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 805 0.036 - 0.073: 240 0.073 - 0.109: 67 0.109 - 0.146: 15 0.146 - 0.182: 1 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA ILE A 545 " pdb=" N ILE A 545 " pdb=" C ILE A 545 " pdb=" CB ILE A 545 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ASP A 350 " pdb=" N ASP A 350 " pdb=" C ASP A 350 " pdb=" CB ASP A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1125 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 349 " 0.019 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C SER A 349 " -0.062 2.00e-02 2.50e+03 pdb=" O SER A 349 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP A 350 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 29 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C LEU A 29 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A 29 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO A 30 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 452 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO A 453 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.029 5.00e-02 4.00e+02 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 10 2.39 - 3.01: 3753 3.01 - 3.64: 10245 3.64 - 4.27: 14241 4.27 - 4.90: 24755 Nonbonded interactions: 53004 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" F1 BEF A1003 " model vdw 1.757 2.120 nonbonded pdb=" OD1 ASP A 644 " pdb="MG MG A1001 " model vdw 1.804 2.170 nonbonded pdb=" O THR A 352 " pdb="MG MG A1001 " model vdw 2.093 2.170 nonbonded pdb=" OD1 ASP A 350 " pdb="BE BEF A1003 " model vdw 2.098 1.936 nonbonded pdb=" O ARG A 417 " pdb=" OG1 THR A 420 " model vdw 2.252 3.040 ... (remaining 52999 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 individual isotropic 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.000 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 0.088 6914 Z= 0.199 Angle : 0.655 13.764 9362 Z= 0.380 Chirality : 0.039 0.182 1128 Planarity : 0.004 0.053 1183 Dihedral : 16.815 89.194 2568 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.92 % Allowed : 25.26 % Favored : 73.82 % Cbeta Deviations : 0.24 % 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: 2.06 (0.30), residues: 888 helix: 2.83 (0.25), residues: 431 sheet: 0.63 (0.55), residues: 99 loop : -0.25 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 766 HIS 0.001 0.000 HIS A 58 PHE 0.008 0.001 PHE A 454 TYR 0.004 0.000 TYR A 587 ARG 0.007 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 629 ILE cc_start: 0.7533 (mm) cc_final: 0.7227 (mm) outliers start: 7 outliers final: 4 residues processed: 108 average time/residue: 0.1935 time to fit residues: 28.0425 Evaluate side-chains 104 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 843 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.203374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.176602 restraints weight = 8049.410| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.80 r_work: 0.3436 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6914 Z= 0.262 Angle : 0.627 10.275 9362 Z= 0.327 Chirality : 0.043 0.153 1128 Planarity : 0.005 0.043 1183 Dihedral : 4.547 34.773 946 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.71 % Allowed : 24.87 % Favored : 70.42 % 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: 1.30 (0.29), residues: 888 helix: 2.06 (0.24), residues: 443 sheet: -0.06 (0.52), residues: 103 loop : -0.41 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 460 HIS 0.003 0.001 HIS A 149 PHE 0.023 0.002 PHE A 118 TYR 0.020 0.002 TYR A 618 ARG 0.008 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.801 Fit side-chains REVERT: A 97 MET cc_start: 0.7769 (mmm) cc_final: 0.7224 (mtt) REVERT: A 276 ILE cc_start: 0.8699 (tp) cc_final: 0.8241 (mt) REVERT: A 292 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6938 (mm) REVERT: A 376 THR cc_start: 0.8684 (m) cc_final: 0.8282 (p) REVERT: A 652 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8191 (mp) outliers start: 36 outliers final: 15 residues processed: 161 average time/residue: 0.1820 time to fit residues: 39.6609 Evaluate side-chains 139 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 901 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 0.0030 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 727 ASN A 738 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.205865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.180675 restraints weight = 8111.019| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.70 r_work: 0.3449 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6914 Z= 0.199 Angle : 0.554 8.833 9362 Z= 0.286 Chirality : 0.041 0.145 1128 Planarity : 0.004 0.046 1183 Dihedral : 4.036 19.409 938 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.32 % Allowed : 26.83 % Favored : 68.85 % 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: 1.37 (0.30), residues: 888 helix: 2.15 (0.24), residues: 442 sheet: -0.11 (0.52), residues: 97 loop : -0.39 (0.37), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 766 HIS 0.001 0.000 HIS A 364 PHE 0.012 0.001 PHE A 176 TYR 0.016 0.001 TYR A 618 ARG 0.006 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7708 (mmm) cc_final: 0.7252 (mtt) REVERT: A 292 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6921 (mm) REVERT: A 535 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7256 (tm-30) REVERT: A 634 LYS cc_start: 0.8265 (pttp) cc_final: 0.7823 (ptmt) outliers start: 33 outliers final: 17 residues processed: 150 average time/residue: 0.1880 time to fit residues: 39.0247 Evaluate side-chains 138 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN A 865 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.194060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.167371 restraints weight = 8238.576| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.77 r_work: 0.3684 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6914 Z= 0.270 Angle : 0.598 7.399 9362 Z= 0.311 Chirality : 0.042 0.155 1128 Planarity : 0.005 0.051 1183 Dihedral : 4.289 19.769 937 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.94 % Favored : 95.95 % Rotamer: Outliers : 6.28 % Allowed : 25.52 % Favored : 68.19 % 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: 1.03 (0.30), residues: 888 helix: 1.88 (0.24), residues: 442 sheet: -0.04 (0.50), residues: 107 loop : -0.65 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 766 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.002 PHE A 725 TYR 0.019 0.001 TYR A 618 ARG 0.007 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8209 (mp) REVERT: A 97 MET cc_start: 0.8007 (mmm) cc_final: 0.7621 (mtt) REVERT: A 292 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7139 (mm) REVERT: A 535 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 602 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.3946 (ptt) REVERT: A 634 LYS cc_start: 0.8350 (pttp) cc_final: 0.7956 (ptmt) REVERT: A 641 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8225 (ttt) outliers start: 48 outliers final: 35 residues processed: 163 average time/residue: 0.1652 time to fit residues: 37.4881 Evaluate side-chains 164 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 82 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.161679 restraints weight = 8275.327| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.81 r_work: 0.3717 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6914 Z= 0.216 Angle : 0.565 8.114 9362 Z= 0.294 Chirality : 0.041 0.179 1128 Planarity : 0.004 0.051 1183 Dihedral : 4.199 19.448 937 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.15 % Allowed : 26.57 % Favored : 67.28 % 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: 1.04 (0.30), residues: 888 helix: 1.91 (0.25), residues: 444 sheet: -0.19 (0.51), residues: 107 loop : -0.64 (0.38), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 766 HIS 0.002 0.000 HIS A 364 PHE 0.014 0.001 PHE A 725 TYR 0.016 0.001 TYR A 618 ARG 0.005 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.932 Fit side-chains REVERT: A 87 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 97 MET cc_start: 0.7975 (mmm) cc_final: 0.7644 (mtt) REVERT: A 459 LYS cc_start: 0.8533 (tppt) cc_final: 0.8156 (mmmt) REVERT: A 535 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 602 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.4050 (ptt) REVERT: A 634 LYS cc_start: 0.8327 (pttp) cc_final: 0.8030 (ptmt) outliers start: 47 outliers final: 28 residues processed: 167 average time/residue: 0.1744 time to fit residues: 40.5978 Evaluate side-chains 156 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 882 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 86 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 0.0670 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.188868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161638 restraints weight = 8359.322| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.81 r_work: 0.3648 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6914 Z= 0.217 Angle : 0.565 8.452 9362 Z= 0.292 Chirality : 0.041 0.182 1128 Planarity : 0.004 0.052 1183 Dihedral : 4.159 18.854 937 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.68 % Allowed : 26.31 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.30), residues: 888 helix: 1.90 (0.24), residues: 445 sheet: -0.29 (0.51), residues: 107 loop : -0.66 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 766 HIS 0.002 0.000 HIS A 364 PHE 0.014 0.001 PHE A 725 TYR 0.016 0.001 TYR A 618 ARG 0.006 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8051 (mp) REVERT: A 97 MET cc_start: 0.7971 (mmm) cc_final: 0.7673 (mtt) REVERT: A 323 MET cc_start: 0.7343 (mmt) cc_final: 0.7016 (mtt) REVERT: A 459 LYS cc_start: 0.8562 (tppt) cc_final: 0.8170 (mmmt) REVERT: A 535 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7510 (tm-30) REVERT: A 634 LYS cc_start: 0.8337 (pttp) cc_final: 0.8050 (ttmm) outliers start: 51 outliers final: 34 residues processed: 163 average time/residue: 0.1695 time to fit residues: 37.9205 Evaluate side-chains 164 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 3 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.0970 chunk 59 optimal weight: 0.0040 chunk 68 optimal weight: 1.9990 chunk 6 optimal weight: 0.0010 chunk 56 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN A 747 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.204994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.180241 restraints weight = 8039.495| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.71 r_work: 0.3464 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6914 Z= 0.164 Angle : 0.552 8.488 9362 Z= 0.283 Chirality : 0.040 0.178 1128 Planarity : 0.004 0.050 1183 Dihedral : 3.935 17.677 937 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.71 % Allowed : 28.66 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.30), residues: 888 helix: 2.15 (0.25), residues: 442 sheet: -0.71 (0.53), residues: 95 loop : -0.49 (0.37), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 766 HIS 0.001 0.000 HIS A 467 PHE 0.013 0.001 PHE A 725 TYR 0.012 0.001 TYR A 618 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7646 (mmm) cc_final: 0.7363 (mtt) REVERT: A 459 LYS cc_start: 0.8545 (tppt) cc_final: 0.8074 (mmmt) REVERT: A 535 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 602 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.4189 (ptt) REVERT: A 634 LYS cc_start: 0.8319 (pttp) cc_final: 0.8042 (tttp) REVERT: A 723 MET cc_start: 0.8120 (mmm) cc_final: 0.7745 (mmt) outliers start: 36 outliers final: 24 residues processed: 161 average time/residue: 0.1880 time to fit residues: 40.6758 Evaluate side-chains 153 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.190786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163371 restraints weight = 8372.887| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.83 r_work: 0.3684 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6914 Z= 0.220 Angle : 0.585 11.560 9362 Z= 0.298 Chirality : 0.041 0.170 1128 Planarity : 0.004 0.052 1183 Dihedral : 4.058 17.798 937 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.71 % Allowed : 28.14 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.30), residues: 888 helix: 2.08 (0.25), residues: 443 sheet: -0.38 (0.51), residues: 107 loop : -0.56 (0.39), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 766 HIS 0.002 0.001 HIS A 364 PHE 0.013 0.001 PHE A 725 TYR 0.015 0.001 TYR A 618 ARG 0.005 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7941 (mmm) cc_final: 0.7619 (mtt) REVERT: A 459 LYS cc_start: 0.8594 (tppt) cc_final: 0.8208 (mmmt) REVERT: A 535 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7545 (tm-30) REVERT: A 602 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.4273 (ptt) REVERT: A 634 LYS cc_start: 0.8429 (pttp) cc_final: 0.8105 (ptmt) REVERT: A 671 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7492 (mt-10) outliers start: 36 outliers final: 26 residues processed: 155 average time/residue: 0.1797 time to fit residues: 38.1414 Evaluate side-chains 153 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.192740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.165700 restraints weight = 8298.413| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.80 r_work: 0.3754 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6914 Z= 0.187 Angle : 0.584 11.698 9362 Z= 0.297 Chirality : 0.041 0.205 1128 Planarity : 0.004 0.052 1183 Dihedral : 4.005 16.995 937 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.19 % Allowed : 28.93 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.30), residues: 888 helix: 2.00 (0.25), residues: 449 sheet: -0.80 (0.53), residues: 95 loop : -0.51 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 766 HIS 0.001 0.000 HIS A 467 PHE 0.013 0.001 PHE A 725 TYR 0.013 0.001 TYR A 618 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7888 (mmm) cc_final: 0.7585 (mtt) REVERT: A 202 GLN cc_start: 0.6454 (mp10) cc_final: 0.5992 (mp10) REVERT: A 243 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7585 (mm-30) REVERT: A 459 LYS cc_start: 0.8576 (tppt) cc_final: 0.8176 (mmmt) REVERT: A 535 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 602 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.4062 (ptt) REVERT: A 634 LYS cc_start: 0.8399 (pttp) cc_final: 0.8092 (ptmt) REVERT: A 671 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7446 (mt-10) outliers start: 32 outliers final: 23 residues processed: 151 average time/residue: 0.1763 time to fit residues: 36.2361 Evaluate side-chains 149 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 0.0050 chunk 6 optimal weight: 0.4980 overall best weight: 0.2932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.193890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.166707 restraints weight = 8518.094| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.85 r_work: 0.3763 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6914 Z= 0.178 Angle : 0.594 12.146 9362 Z= 0.299 Chirality : 0.041 0.184 1128 Planarity : 0.004 0.051 1183 Dihedral : 3.931 16.511 937 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.40 % Allowed : 29.71 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.30), residues: 888 helix: 2.06 (0.25), residues: 449 sheet: -0.73 (0.54), residues: 95 loop : -0.48 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 766 HIS 0.002 0.000 HIS A 58 PHE 0.013 0.001 PHE A 725 TYR 0.012 0.001 TYR A 618 ARG 0.011 0.000 ARG A 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7879 (mmm) cc_final: 0.7537 (mtt) REVERT: A 243 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7621 (mm-30) REVERT: A 435 MET cc_start: 0.8682 (ttm) cc_final: 0.8467 (ttm) REVERT: A 535 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7571 (tm-30) REVERT: A 602 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.3922 (ptt) REVERT: A 634 LYS cc_start: 0.8407 (pttp) cc_final: 0.8105 (ptmt) REVERT: A 671 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7450 (mt-10) outliers start: 26 outliers final: 21 residues processed: 141 average time/residue: 0.1710 time to fit residues: 33.1608 Evaluate side-chains 146 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 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 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.188393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161130 restraints weight = 8327.115| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.80 r_work: 0.3718 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6914 Z= 0.227 Angle : 0.632 12.008 9362 Z= 0.317 Chirality : 0.042 0.214 1128 Planarity : 0.005 0.053 1183 Dihedral : 4.138 19.570 937 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.66 % Allowed : 29.58 % Favored : 66.75 % 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: 1.02 (0.30), residues: 888 helix: 1.85 (0.25), residues: 456 sheet: -0.41 (0.52), residues: 107 loop : -0.60 (0.39), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 766 HIS 0.002 0.001 HIS A 467 PHE 0.014 0.001 PHE A 725 TYR 0.016 0.001 TYR A 618 ARG 0.005 0.000 ARG A 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3974.09 seconds wall clock time: 68 minutes 57.91 seconds (4137.91 seconds total)