Starting phenix.real_space_refine on Fri Aug 22 18:34:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iws_35778/08_2025/8iws_35778.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iws_35778/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8iws_35778/08_2025/8iws_35778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iws_35778/08_2025/8iws_35778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iws_35778/08_2025/8iws_35778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iws_35778/08_2025/8iws_35778.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.55, per 1000 atoms: 0.23 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: 0.98 Conformation dependent library (CDL) restraints added in 351.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.21 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: 1.30 Time building geometry restraints manager: 1.23 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.710 Find NCS groups from input model: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- 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 : 0.005 0.346 6915 Z= 0.466 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (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 ARG 0.007 0.000 ARG A 583 TYR 0.004 0.000 TYR A 587 PHE 0.008 0.001 PHE A 454 TRP 0.022 0.001 TRP A 766 HIS 0.001 0.000 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6914) covalent geometry : angle 0.65453 ( 9362) hydrogen bonds : bond 0.14117 ( 382) hydrogen bonds : angle 5.86770 ( 1167) Misc. bond : bond 0.34647 ( 1) *********************** 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 : 0.241 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: 0.0703 time to fit residues: 10.2674 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 : 0.245 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.193170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.166155 restraints weight = 8126.042| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.76 r_work: 0.3335 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6915 Z= 0.242 Angle : 0.713 10.009 9362 Z= 0.375 Chirality : 0.046 0.159 1128 Planarity : 0.005 0.050 1183 Dihedral : 5.043 34.407 946 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % Rotamer: Outliers : 4.97 % Allowed : 25.92 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.29), residues: 888 helix: 1.62 (0.24), residues: 442 sheet: 0.10 (0.49), residues: 109 loop : -0.66 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 55 TYR 0.028 0.002 TYR A 618 PHE 0.021 0.002 PHE A 118 TRP 0.008 0.002 TRP A 460 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 6914) covalent geometry : angle 0.71250 ( 9362) hydrogen bonds : bond 0.05806 ( 382) hydrogen bonds : angle 4.62906 ( 1167) Misc. bond : bond 0.00181 ( 1) *********************** 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 183 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.275 Fit side-chains REVERT: A 97 MET cc_start: 0.7914 (mmm) cc_final: 0.7550 (mtt) REVERT: A 276 ILE cc_start: 0.8762 (tp) cc_final: 0.8333 (mt) REVERT: A 292 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6938 (mm) REVERT: A 376 THR cc_start: 0.8821 (m) cc_final: 0.8500 (p) REVERT: A 652 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8355 (mp) outliers start: 38 outliers final: 19 residues processed: 170 average time/residue: 0.0633 time to fit residues: 14.7943 Evaluate side-chains 142 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 LEU 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 536 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 611 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 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 = 0.4218 r_free = 0.4218 target = 0.195458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168860 restraints weight = 8156.739| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.76 r_work: 0.3708 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6915 Z= 0.151 Angle : 0.582 10.492 9362 Z= 0.301 Chirality : 0.042 0.149 1128 Planarity : 0.005 0.048 1183 Dihedral : 4.372 20.789 938 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.50 % Allowed : 26.18 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.29), residues: 888 helix: 1.80 (0.24), residues: 445 sheet: -0.08 (0.49), residues: 109 loop : -0.58 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 55 TYR 0.018 0.001 TYR A 618 PHE 0.014 0.001 PHE A 176 TRP 0.014 0.001 TRP A 766 HIS 0.002 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6914) covalent geometry : angle 0.58215 ( 9362) hydrogen bonds : bond 0.04351 ( 382) hydrogen bonds : angle 4.20203 ( 1167) Misc. bond : bond 0.00088 ( 1) *********************** 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 175 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.8030 (mmm) cc_final: 0.7755 (mtt) REVERT: A 535 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7350 (tm-30) REVERT: A 602 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.3999 (ptt) REVERT: A 652 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 657 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8339 (tp) REVERT: A 671 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7574 (mt-10) outliers start: 42 outliers final: 25 residues processed: 158 average time/residue: 0.0632 time to fit residues: 13.6103 Evaluate side-chains 148 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 111 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 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 313 VAL Chi-restraints excluded: chain A residue 354 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 602 MET Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 663 GLN 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 723 MET Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 828 SER 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 39 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 0.0170 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.171054 restraints weight = 8193.326| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.76 r_work: 0.3788 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6915 Z= 0.121 Angle : 0.555 7.973 9362 Z= 0.288 Chirality : 0.041 0.154 1128 Planarity : 0.004 0.050 1183 Dihedral : 4.197 19.419 938 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.28 % Allowed : 26.05 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.30), residues: 888 helix: 2.00 (0.25), residues: 441 sheet: -0.36 (0.52), residues: 97 loop : -0.41 (0.38), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.016 0.001 TYR A 618 PHE 0.013 0.001 PHE A 725 TRP 0.017 0.001 TRP A 766 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6914) covalent geometry : angle 0.55493 ( 9362) hydrogen bonds : bond 0.03918 ( 382) hydrogen bonds : angle 4.07363 ( 1167) Misc. bond : bond 0.00043 ( 1) *********************** 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 173 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7983 (mmm) cc_final: 0.7748 (mtt) REVERT: A 535 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 602 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.3902 (ptt) REVERT: A 634 LYS cc_start: 0.8266 (pttp) cc_final: 0.7986 (tttp) outliers start: 48 outliers final: 27 residues processed: 154 average time/residue: 0.0553 time to fit residues: 12.0307 Evaluate side-chains 146 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 165 VAL 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 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 388 VAL Chi-restraints excluded: chain A residue 415 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 641 MET Chi-restraints excluded: chain A residue 663 GLN 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 810 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 31 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 738 ASN A 747 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.192321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164826 restraints weight = 8341.894| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.82 r_work: 0.3737 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.003 0.034 6915 Z= 0.114 Angle : 0.544 8.219 9362 Z= 0.282 Chirality : 0.041 0.171 1128 Planarity : 0.004 0.051 1183 Dihedral : 4.103 18.241 938 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.10 % Allowed : 27.23 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.30), residues: 888 helix: 2.10 (0.25), residues: 441 sheet: -0.51 (0.53), residues: 97 loop : -0.43 (0.37), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.014 0.001 TYR A 618 PHE 0.014 0.001 PHE A 725 TRP 0.020 0.001 TRP A 766 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6914) covalent geometry : angle 0.54383 ( 9362) hydrogen bonds : bond 0.03668 ( 382) hydrogen bonds : angle 3.92740 ( 1167) Misc. bond : bond 0.00040 ( 1) *********************** 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 168 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.251 Fit side-chains REVERT: A 97 MET cc_start: 0.7896 (mmm) cc_final: 0.7694 (mtt) REVERT: A 248 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7657 (ttt) REVERT: A 459 LYS cc_start: 0.8513 (tppt) cc_final: 0.8217 (mmmt) REVERT: A 535 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 602 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.3963 (ptt) REVERT: A 634 LYS cc_start: 0.8277 (pttp) cc_final: 0.8027 (tttp) REVERT: A 652 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8286 (mp) outliers start: 39 outliers final: 24 residues processed: 154 average time/residue: 0.0609 time to fit residues: 13.2023 Evaluate side-chains 147 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 196 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 463 VAL 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 611 VAL Chi-restraints excluded: chain A residue 652 LEU 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 810 MET Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 865 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.187674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.159726 restraints weight = 8420.032| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.84 r_work: 0.3653 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6915 Z= 0.153 Angle : 0.576 8.610 9362 Z= 0.298 Chirality : 0.042 0.194 1128 Planarity : 0.004 0.053 1183 Dihedral : 4.278 18.236 937 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 6.68 % Allowed : 25.79 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.30), residues: 888 helix: 2.00 (0.25), residues: 440 sheet: -0.37 (0.51), residues: 107 loop : -0.70 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 55 TYR 0.017 0.001 TYR A 618 PHE 0.014 0.001 PHE A 176 TRP 0.025 0.002 TRP A 766 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6914) covalent geometry : angle 0.57588 ( 9362) hydrogen bonds : bond 0.04270 ( 382) hydrogen bonds : angle 4.02202 ( 1167) Misc. bond : bond 0.00078 ( 1) *********************** 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 181 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 0.151 Fit side-chains REVERT: A 459 LYS cc_start: 0.8582 (tppt) cc_final: 0.8221 (mmmt) REVERT: A 535 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 634 LYS cc_start: 0.8380 (pttp) cc_final: 0.8066 (tttp) REVERT: A 652 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8387 (mp) outliers start: 51 outliers final: 37 residues processed: 162 average time/residue: 0.0679 time to fit residues: 15.0478 Evaluate side-chains 163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 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 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 463 VAL 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 611 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 710 SER 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 Chi-restraints excluded: chain A residue 877 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.185622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158178 restraints weight = 8290.064| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.77 r_work: 0.3681 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6915 Z= 0.152 Angle : 0.585 8.237 9362 Z= 0.304 Chirality : 0.042 0.213 1128 Planarity : 0.004 0.053 1183 Dihedral : 4.302 17.820 937 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 6.28 % Allowed : 26.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.30), residues: 888 helix: 1.79 (0.25), residues: 446 sheet: -0.51 (0.49), residues: 114 loop : -0.83 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 55 TYR 0.016 0.001 TYR A 618 PHE 0.015 0.001 PHE A 725 TRP 0.025 0.002 TRP A 766 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6914) covalent geometry : angle 0.58456 ( 9362) hydrogen bonds : bond 0.04298 ( 382) hydrogen bonds : angle 4.03127 ( 1167) Misc. bond : bond 0.00072 ( 1) *********************** 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 179 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 0.254 Fit side-chains REVERT: A 323 MET cc_start: 0.7478 (mmt) cc_final: 0.7175 (mtt) REVERT: A 535 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7571 (tm-30) REVERT: A 634 LYS cc_start: 0.8378 (pttp) cc_final: 0.8043 (tttp) REVERT: A 652 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8434 (mp) REVERT: A 810 MET cc_start: 0.7893 (mmm) cc_final: 0.7627 (mmm) outliers start: 48 outliers final: 37 residues processed: 161 average time/residue: 0.0639 time to fit residues: 14.2782 Evaluate side-chains 168 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 94 SER 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 116 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 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 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 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 652 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 0.0370 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- 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 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156156 restraints weight = 8389.519| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.80 r_work: 0.3660 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6915 Z= 0.159 Angle : 0.611 8.543 9362 Z= 0.316 Chirality : 0.042 0.176 1128 Planarity : 0.005 0.054 1183 Dihedral : 4.396 19.715 937 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 6.15 % Allowed : 28.27 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.30), residues: 888 helix: 1.77 (0.25), residues: 445 sheet: -0.58 (0.49), residues: 114 loop : -0.88 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 55 TYR 0.016 0.001 TYR A 618 PHE 0.015 0.001 PHE A 725 TRP 0.023 0.002 TRP A 766 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6914) covalent geometry : angle 0.61090 ( 9362) hydrogen bonds : bond 0.04426 ( 382) hydrogen bonds : angle 4.08911 ( 1167) Misc. bond : bond 0.00079 ( 1) *********************** 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 181 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.291 Fit side-chains REVERT: A 535 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 634 LYS cc_start: 0.8380 (pttp) cc_final: 0.8021 (ttmm) REVERT: A 652 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8488 (mp) outliers start: 47 outliers final: 36 residues processed: 165 average time/residue: 0.0699 time to fit residues: 15.7871 Evaluate side-chains 164 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 94 SER 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 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 313 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 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 463 VAL 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 611 VAL Chi-restraints excluded: chain A residue 652 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 691 GLU 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 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 49 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.187288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.159969 restraints weight = 8343.665| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.79 r_work: 0.3640 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6915 Z= 0.127 Angle : 0.584 9.256 9362 Z= 0.299 Chirality : 0.042 0.223 1128 Planarity : 0.004 0.053 1183 Dihedral : 4.288 19.143 937 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.37 % Allowed : 28.40 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.30), residues: 888 helix: 1.87 (0.25), residues: 451 sheet: -0.93 (0.51), residues: 102 loop : -0.73 (0.38), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.013 0.001 TYR A 618 PHE 0.015 0.001 PHE A 725 TRP 0.040 0.002 TRP A 766 HIS 0.002 0.000 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6914) covalent geometry : angle 0.58434 ( 9362) hydrogen bonds : bond 0.03895 ( 382) hydrogen bonds : angle 3.96873 ( 1167) Misc. bond : bond 0.00049 ( 1) *********************** 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 172 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.249 Fit side-chains REVERT: A 202 GLN cc_start: 0.6578 (mp10) cc_final: 0.6060 (mp10) REVERT: A 535 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7567 (tm-30) REVERT: A 634 LYS cc_start: 0.8408 (pttp) cc_final: 0.8073 (tttp) REVERT: A 652 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8400 (mp) REVERT: A 843 MET cc_start: 0.7673 (ttt) cc_final: 0.7457 (ttt) outliers start: 41 outliers final: 34 residues processed: 156 average time/residue: 0.0657 time to fit residues: 13.9596 Evaluate side-chains 163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 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 231 VAL Chi-restraints excluded: chain A residue 235 THR 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 354 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 463 VAL 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 611 VAL Chi-restraints excluded: chain A residue 652 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 691 GLU 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 828 SER Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 41 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 53 optimal weight: 0.2980 chunk 57 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.189265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162216 restraints weight = 8255.979| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.78 r_work: 0.3666 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6915 Z= 0.119 Angle : 0.579 9.717 9362 Z= 0.295 Chirality : 0.042 0.190 1128 Planarity : 0.004 0.053 1183 Dihedral : 4.143 19.605 937 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.58 % Allowed : 29.45 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.30), residues: 888 helix: 1.98 (0.25), residues: 452 sheet: -1.13 (0.52), residues: 96 loop : -0.58 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 55 TYR 0.013 0.001 TYR A 618 PHE 0.015 0.001 PHE A 725 TRP 0.041 0.002 TRP A 766 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6914) covalent geometry : angle 0.57903 ( 9362) hydrogen bonds : bond 0.03618 ( 382) hydrogen bonds : angle 3.86280 ( 1167) Misc. bond : bond 0.00038 ( 1) ********************** 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 167 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.194 Fit side-chains REVERT: A 243 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7737 (mm-30) REVERT: A 435 MET cc_start: 0.8667 (ttm) cc_final: 0.8452 (ttm) REVERT: A 535 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7567 (tm-30) REVERT: A 602 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.4376 (ptt) REVERT: A 634 LYS cc_start: 0.8359 (pttp) cc_final: 0.8018 (tttp) REVERT: A 652 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8304 (mp) outliers start: 35 outliers final: 30 residues processed: 153 average time/residue: 0.0645 time to fit residues: 13.8184 Evaluate side-chains 158 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 231 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 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 388 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 652 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 691 GLU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.189522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161598 restraints weight = 8330.339| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.85 r_work: 0.3708 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6915 Z= 0.126 Angle : 0.607 10.020 9362 Z= 0.307 Chirality : 0.042 0.208 1128 Planarity : 0.004 0.054 1183 Dihedral : 4.177 23.227 937 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.71 % Allowed : 29.32 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.30), residues: 888 helix: 1.98 (0.24), residues: 452 sheet: -0.76 (0.51), residues: 108 loop : -0.71 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 55 TYR 0.013 0.001 TYR A 618 PHE 0.015 0.001 PHE A 725 TRP 0.049 0.002 TRP A 766 HIS 0.002 0.000 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6914) covalent geometry : angle 0.60739 ( 9362) hydrogen bonds : bond 0.03719 ( 382) hydrogen bonds : angle 3.89030 ( 1167) Misc. bond : bond 0.00054 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1680.06 seconds wall clock time: 29 minutes 30.93 seconds (1770.93 seconds total)