Starting phenix.real_space_refine on Wed Feb 12 00:16:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iws_35778/02_2025/8iws_35778.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iws_35778/02_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_35778/02_2025/8iws_35778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iws_35778/02_2025/8iws_35778.map" model { file = "/net/cci-nas-00/data/ceres_data/8iws_35778/02_2025/8iws_35778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iws_35778/02_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-5592/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: 4.91, per 1000 atoms: 0.72 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: 1.71 Conformation dependent library (CDL) restraints added in 835.6 milliseconds 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: 0.88 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: 2.42 Time building geometry restraints manager: 1.96 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.100 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- 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 : 1.129 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: 0.2180 time to fit residues: 30.8531 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 : 0.781 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.203322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.176546 restraints weight = 8049.388| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.81 r_work: 0.3437 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: 0.7879 moved from start: 0.3170 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 : 0.626 10.275 9362 Z= 0.327 Chirality : 0.043 0.153 1128 Planarity : 0.005 0.044 1183 Dihedral : 4.547 34.740 946 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.71 % Allowed : 25.00 % Favored : 70.29 % 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 0.024 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 : 0.772 Fit side-chains REVERT: A 97 MET cc_start: 0.7768 (mmm) cc_final: 0.7226 (mtt) REVERT: A 276 ILE cc_start: 0.8700 (tp) cc_final: 0.8242 (mt) REVERT: A 292 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6937 (mm) REVERT: A 376 THR cc_start: 0.8684 (m) cc_final: 0.8282 (p) REVERT: A 652 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8190 (mp) outliers start: 36 outliers final: 15 residues processed: 161 average time/residue: 0.1862 time to fit residues: 40.4919 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 : 0.864 ------------------------------------------------------------------------------- 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: 0.4980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.204289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.178446 restraints weight = 8103.427| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.75 r_work: 0.3420 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6914 Z= 0.212 Angle : 0.563 8.436 9362 Z= 0.292 Chirality : 0.041 0.143 1128 Planarity : 0.004 0.046 1183 Dihedral : 4.089 19.592 938 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.45 % Allowed : 26.70 % 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: 1.33 (0.30), residues: 888 helix: 2.12 (0.24), residues: 440 sheet: 0.16 (0.49), residues: 109 loop : -0.50 (0.38), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 766 HIS 0.001 0.000 HIS A 364 PHE 0.013 0.001 PHE A 176 TYR 0.017 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 163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7735 (mmm) cc_final: 0.7348 (mtt) REVERT: A 418 ASN cc_start: 0.7767 (t0) cc_final: 0.7563 (t0) REVERT: A 535 GLN cc_start: 0.7665 (tm-30) cc_final: 0.7259 (tm-30) REVERT: A 588 SER cc_start: 0.8162 (m) cc_final: 0.7956 (p) REVERT: A 634 LYS cc_start: 0.8312 (pttp) cc_final: 0.7863 (ptmt) outliers start: 34 outliers final: 18 residues processed: 149 average time/residue: 0.1686 time to fit residues: 34.6720 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 : 0.764 ------------------------------------------------------------------------------- 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 313 VAL Chi-restraints excluded: chain A residue 326 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 602 MET Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 666 THR 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: 0.3980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4243 r_free = 0.4243 target = 0.198129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.171890 restraints weight = 8249.093| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.77 r_work: 0.3796 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6914 Z= 0.213 Angle : 0.565 8.317 9362 Z= 0.292 Chirality : 0.041 0.171 1128 Planarity : 0.004 0.049 1183 Dihedral : 4.059 19.299 937 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.50 % Allowed : 25.79 % Favored : 68.72 % 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: 1.23 (0.30), residues: 888 helix: 2.01 (0.24), residues: 443 sheet: 0.05 (0.50), residues: 109 loop : -0.52 (0.38), residues: 336 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 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 170 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7988 (mmm) cc_final: 0.7529 (mtt) REVERT: A 292 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7043 (mm) REVERT: A 535 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7406 (tm-30) REVERT: A 634 LYS cc_start: 0.8281 (pttp) cc_final: 0.7989 (ptmt) outliers start: 42 outliers final: 27 residues processed: 155 average time/residue: 0.1676 time to fit residues: 35.8236 Evaluate side-chains 149 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 326 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 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 602 MET Chi-restraints excluded: chain A residue 607 LEU 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 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: 3.9990 chunk 54 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158926 restraints weight = 8301.257| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.82 r_work: 0.3693 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6914 Z= 0.262 Angle : 0.596 8.391 9362 Z= 0.311 Chirality : 0.042 0.189 1128 Planarity : 0.005 0.051 1183 Dihedral : 4.334 20.518 937 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 7.07 % Allowed : 25.52 % Favored : 67.41 % 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: 0.93 (0.30), residues: 888 helix: 1.80 (0.24), residues: 445 sheet: -0.24 (0.51), residues: 107 loop : -0.66 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 766 HIS 0.002 0.001 HIS A 149 PHE 0.016 0.001 PHE A 176 TYR 0.019 0.001 TYR A 618 ARG 0.007 0.001 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 192 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 138 time to evaluate : 0.807 Fit side-chains REVERT: A 97 MET cc_start: 0.8005 (mmm) cc_final: 0.7720 (mtt) REVERT: A 292 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7088 (mm) REVERT: A 459 LYS cc_start: 0.8569 (tppt) cc_final: 0.8164 (mmmt) REVERT: A 535 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 588 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8251 (m) REVERT: A 634 LYS cc_start: 0.8415 (pttp) cc_final: 0.8112 (ptmt) outliers start: 54 outliers final: 34 residues processed: 172 average time/residue: 0.1762 time to fit residues: 41.0667 Evaluate side-chains 163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 292 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 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 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 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 754 VAL Chi-restraints excluded: chain A residue 828 SER 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 86 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 82 optimal weight: 0.0470 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.190060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.162323 restraints weight = 8357.977| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.87 r_work: 0.3716 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4782 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= 0.198 Angle : 0.567 9.070 9362 Z= 0.294 Chirality : 0.041 0.181 1128 Planarity : 0.004 0.052 1183 Dihedral : 4.135 18.501 937 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.50 % Allowed : 26.96 % 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 (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: 1.86 (0.25), residues: 446 sheet: -0.32 (0.51), residues: 107 loop : -0.57 (0.38), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 766 HIS 0.001 0.000 HIS A 364 PHE 0.013 0.001 PHE A 725 TYR 0.015 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 174 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.953 Fit side-chains REVERT: A 97 MET cc_start: 0.7976 (mmm) cc_final: 0.7680 (mtt) REVERT: A 292 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7018 (mm) REVERT: A 459 LYS cc_start: 0.8556 (tppt) cc_final: 0.8174 (mmmt) REVERT: A 535 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7530 (tm-30) REVERT: A 634 LYS cc_start: 0.8367 (pttp) cc_final: 0.8050 (ttmm) REVERT: A 723 MET cc_start: 0.8169 (mmm) cc_final: 0.7808 (mmt) REVERT: A 810 MET cc_start: 0.7613 (mmm) cc_final: 0.7267 (mtp) outliers start: 42 outliers final: 27 residues processed: 163 average time/residue: 0.1781 time to fit residues: 39.5355 Evaluate side-chains 156 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 244 VAL Chi-restraints excluded: chain A residue 292 LEU 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 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 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 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: 4.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 6 optimal weight: 0.0000 chunk 56 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5522 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.189873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.162164 restraints weight = 8253.826| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.86 r_work: 0.3713 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6914 Z= 0.205 Angle : 0.569 8.475 9362 Z= 0.292 Chirality : 0.041 0.192 1128 Planarity : 0.004 0.052 1183 Dihedral : 4.119 18.083 937 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.10 % Allowed : 27.09 % Favored : 67.80 % 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: 1.06 (0.30), residues: 888 helix: 1.97 (0.25), residues: 442 sheet: -0.41 (0.51), residues: 107 loop : -0.60 (0.38), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 766 HIS 0.002 0.000 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 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 172 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.748 Fit side-chains REVERT: A 97 MET cc_start: 0.7945 (mmm) cc_final: 0.7670 (mtt) REVERT: A 292 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7013 (mm) REVERT: A 323 MET cc_start: 0.7454 (mmt) cc_final: 0.7215 (mtt) REVERT: A 459 LYS cc_start: 0.8580 (tppt) cc_final: 0.8197 (mmmt) REVERT: A 535 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 634 LYS cc_start: 0.8349 (pttp) cc_final: 0.8076 (ttmm) REVERT: A 671 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7479 (mt-10) REVERT: A 723 MET cc_start: 0.8242 (mmm) cc_final: 0.7876 (mmt) REVERT: A 810 MET cc_start: 0.7813 (mmm) cc_final: 0.7593 (mmm) outliers start: 39 outliers final: 31 residues processed: 158 average time/residue: 0.1833 time to fit residues: 39.9967 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 : 0.804 ------------------------------------------------------------------------------- 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 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 292 LEU 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 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 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 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: 1.9990 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 5 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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** A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.190364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.162709 restraints weight = 8341.762| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.87 r_work: 0.3721 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6914 Z= 0.192 Angle : 0.571 11.204 9362 Z= 0.291 Chirality : 0.041 0.170 1128 Planarity : 0.004 0.053 1183 Dihedral : 4.062 17.885 937 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.24 % Allowed : 27.36 % Favored : 67.41 % 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: 1.95 (0.25), residues: 448 sheet: -0.47 (0.51), residues: 107 loop : -0.63 (0.38), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 766 HIS 0.002 0.000 HIS A 364 PHE 0.013 0.001 PHE A 725 TYR 0.014 0.001 TYR A 618 ARG 0.003 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 175 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7945 (mmm) cc_final: 0.7646 (mtt) REVERT: A 292 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6964 (mm) REVERT: A 459 LYS cc_start: 0.8573 (tppt) cc_final: 0.8168 (mmmt) REVERT: A 535 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 634 LYS cc_start: 0.8424 (pttp) cc_final: 0.8085 (ptmt) REVERT: A 671 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7483 (mt-10) outliers start: 40 outliers final: 29 residues processed: 159 average time/residue: 0.1691 time to fit residues: 36.9730 Evaluate side-chains 162 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 244 VAL Chi-restraints excluded: chain A residue 292 LEU 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 361 THR Chi-restraints excluded: chain A residue 388 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 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 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: 0.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 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 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 = 0.4135 r_free = 0.4135 target = 0.187290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159547 restraints weight = 8310.349| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.86 r_work: 0.3645 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6914 Z= 0.244 Angle : 0.607 10.931 9362 Z= 0.310 Chirality : 0.042 0.228 1128 Planarity : 0.004 0.054 1183 Dihedral : 4.195 18.607 937 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.71 % Allowed : 28.27 % 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: 0.89 (0.30), residues: 888 helix: 1.87 (0.25), residues: 447 sheet: -0.56 (0.51), residues: 107 loop : -0.76 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 766 HIS 0.003 0.001 HIS A 364 PHE 0.014 0.001 PHE A 176 TYR 0.016 0.001 TYR A 618 ARG 0.003 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 171 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7954 (mmm) cc_final: 0.7697 (mtt) REVERT: A 292 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6973 (mm) REVERT: A 535 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7504 (tm-30) REVERT: A 634 LYS cc_start: 0.8456 (pttp) cc_final: 0.8130 (ptmt) REVERT: A 671 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7573 (mt-10) outliers start: 36 outliers final: 32 residues processed: 156 average time/residue: 0.1658 time to fit residues: 35.8596 Evaluate side-chains 163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 292 LEU 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 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 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 739 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.182032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.154926 restraints weight = 8424.822| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.80 r_work: 0.3667 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6914 Z= 0.270 Angle : 0.635 11.720 9362 Z= 0.325 Chirality : 0.043 0.232 1128 Planarity : 0.005 0.054 1183 Dihedral : 4.347 18.588 937 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.97 % Allowed : 28.27 % 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: 0.75 (0.30), residues: 888 helix: 1.75 (0.25), residues: 448 sheet: -0.67 (0.51), residues: 107 loop : -0.82 (0.37), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 766 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 176 TYR 0.016 0.001 TYR A 618 ARG 0.003 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 171 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.8000 (mmm) cc_final: 0.7785 (mtt) REVERT: A 243 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7762 (mm-30) REVERT: A 292 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7096 (mm) REVERT: A 341 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7834 (tt) REVERT: A 535 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 634 LYS cc_start: 0.8467 (pttp) cc_final: 0.8140 (ptmt) REVERT: A 652 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8388 (mp) REVERT: A 671 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7552 (mt-10) outliers start: 38 outliers final: 30 residues processed: 158 average time/residue: 0.1853 time to fit residues: 40.1015 Evaluate side-chains 164 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 292 LEU 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 422 MET Chi-restraints excluded: chain A residue 533 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 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 739 ILE 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 836 ILE 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: 0.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 chunk 64 optimal weight: 0.0270 chunk 19 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 15 optimal weight: 0.0050 chunk 73 optimal weight: 0.0970 chunk 51 optimal weight: 0.0670 overall best weight: 0.0586 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.199572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174654 restraints weight = 8151.714| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.71 r_work: 0.3481 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6914 Z= 0.168 Angle : 0.614 12.276 9362 Z= 0.309 Chirality : 0.041 0.169 1128 Planarity : 0.005 0.050 1183 Dihedral : 4.023 20.773 937 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.62 % Allowed : 30.50 % 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: 1.15 (0.30), residues: 888 helix: 2.08 (0.25), residues: 449 sheet: -0.66 (0.58), residues: 85 loop : -0.58 (0.37), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 766 HIS 0.001 0.000 HIS A 58 PHE 0.014 0.001 PHE A 725 TYR 0.009 0.001 TYR A 618 ARG 0.003 0.000 ARG A 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3794.75 seconds wall clock time: 68 minutes 30.97 seconds (4110.97 seconds total)