Starting phenix.real_space_refine on Thu Nov 14 17:21:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/11_2024/8iws_35778.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/11_2024/8iws_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/11_2024/8iws_35778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/11_2024/8iws_35778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/11_2024/8iws_35778.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/11_2024/8iws_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-5513/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: 4.23, per 1000 atoms: 0.62 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: 1.69 Conformation dependent library (CDL) restraints added in 957.0 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: 0.93 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: 1.91 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: 3.220 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.520 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 6914 Z= 0.199 Angle : 0.655 13.764 9362 Z= 0.380 Chirality : 0.039 0.182 1128 Planarity : 0.004 0.053 1183 Dihedral : 16.815 89.194 2568 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.92 % Allowed : 25.26 % Favored : 73.82 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.30), residues: 888 helix: 2.83 (0.25), residues: 431 sheet: 0.63 (0.55), residues: 99 loop : -0.25 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 766 HIS 0.001 0.000 HIS A 58 PHE 0.008 0.001 PHE A 454 TYR 0.004 0.000 TYR A 587 ARG 0.007 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.775 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: 0.2141 time to fit residues: 30.8256 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 : 0.766 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.969 Fit side-chains REVERT: A 97 MET cc_start: 0.7676 (mmm) cc_final: 0.7109 (mtt) REVERT: A 276 ILE cc_start: 0.8617 (tp) cc_final: 0.8208 (mt) REVERT: A 376 THR cc_start: 0.8759 (m) cc_final: 0.8464 (p) REVERT: A 588 SER cc_start: 0.8163 (p) cc_final: 0.7831 (m) REVERT: A 652 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8310 (mp) outliers start: 36 outliers final: 15 residues processed: 161 average time/residue: 0.1770 time to fit residues: 38.3530 Evaluate side-chains 138 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 727 ASN A 738 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6914 Z= 0.198 Angle : 0.553 8.919 9362 Z= 0.286 Chirality : 0.041 0.148 1128 Planarity : 0.004 0.046 1183 Dihedral : 4.037 19.359 938 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.58 % Allowed : 26.57 % 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: 1.36 (0.30), residues: 888 helix: 2.17 (0.24), residues: 441 sheet: -0.12 (0.52), residues: 97 loop : -0.41 (0.37), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 766 HIS 0.001 0.000 HIS A 58 PHE 0.012 0.001 PHE A 176 TYR 0.016 0.001 TYR A 618 ARG 0.006 0.001 ARG A 900 *********************** 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 168 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7741 (mmm) cc_final: 0.7305 (mtt) REVERT: A 588 SER cc_start: 0.8167 (p) cc_final: 0.7932 (p) REVERT: A 634 LYS cc_start: 0.8101 (pttp) cc_final: 0.7767 (ptmt) outliers start: 35 outliers final: 19 residues processed: 152 average time/residue: 0.1692 time to fit residues: 35.5886 Evaluate side-chains 139 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 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 388 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 669 CYS 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 60 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6914 Z= 0.254 Angle : 0.588 8.260 9362 Z= 0.306 Chirality : 0.042 0.162 1128 Planarity : 0.005 0.050 1183 Dihedral : 4.211 19.183 937 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.89 % Allowed : 25.79 % 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 (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: 1.10 (0.30), residues: 888 helix: 1.95 (0.24), residues: 442 sheet: -0.00 (0.50), residues: 107 loop : -0.65 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 766 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 725 TYR 0.018 0.001 TYR A 618 ARG 0.007 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 174 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7782 (mmm) cc_final: 0.7424 (mtt) REVERT: A 588 SER cc_start: 0.8181 (p) cc_final: 0.7967 (p) REVERT: A 634 LYS cc_start: 0.8171 (pttp) cc_final: 0.7961 (ptmt) REVERT: A 641 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8435 (ttt) outliers start: 45 outliers final: 33 residues processed: 158 average time/residue: 0.1677 time to fit residues: 36.8736 Evaluate side-chains 159 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 110 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 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 1 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 0.0270 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 17 optimal weight: 0.0270 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 6914 Z= 0.158 Angle : 0.536 8.272 9362 Z= 0.278 Chirality : 0.040 0.182 1128 Planarity : 0.004 0.049 1183 Dihedral : 3.923 18.366 937 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.84 % Allowed : 27.49 % 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 (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: 1.31 (0.30), residues: 888 helix: 2.16 (0.24), residues: 444 sheet: -0.34 (0.55), residues: 93 loop : -0.45 (0.37), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 766 HIS 0.001 0.000 HIS A 140 PHE 0.012 0.001 PHE A 725 TYR 0.013 0.001 TYR A 618 ARG 0.004 0.000 ARG A 900 *********************** 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 175 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7695 (mmm) cc_final: 0.7273 (mtt) REVERT: A 588 SER cc_start: 0.8294 (p) cc_final: 0.7995 (p) REVERT: A 810 MET cc_start: 0.7294 (mmm) cc_final: 0.6939 (mtp) outliers start: 37 outliers final: 22 residues processed: 163 average time/residue: 0.1786 time to fit residues: 39.5572 Evaluate side-chains 145 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 165 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 740 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4734 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= 0.257 Angle : 0.599 8.044 9362 Z= 0.309 Chirality : 0.043 0.197 1128 Planarity : 0.005 0.051 1183 Dihedral : 4.202 18.153 937 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.24 % Allowed : 27.75 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.30), residues: 888 helix: 2.04 (0.25), residues: 441 sheet: -0.24 (0.52), residues: 107 loop : -0.64 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 766 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 725 TYR 0.017 0.001 TYR A 618 ARG 0.008 0.001 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 173 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.773 Fit side-chains REVERT: A 97 MET cc_start: 0.7778 (mmm) cc_final: 0.7487 (mtt) REVERT: A 276 ILE cc_start: 0.8668 (tp) cc_final: 0.8260 (mt) REVERT: A 588 SER cc_start: 0.8343 (p) cc_final: 0.8089 (p) REVERT: A 602 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.3979 (ptt) outliers start: 40 outliers final: 20 residues processed: 160 average time/residue: 0.1790 time to fit residues: 38.8181 Evaluate side-chains 147 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 110 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 536 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6914 Z= 0.238 Angle : 0.601 9.851 9362 Z= 0.309 Chirality : 0.042 0.207 1128 Planarity : 0.005 0.052 1183 Dihedral : 4.276 17.823 937 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.45 % Allowed : 28.53 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.30), residues: 888 helix: 1.98 (0.24), residues: 441 sheet: -0.40 (0.51), residues: 107 loop : -0.62 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 766 HIS 0.002 0.001 HIS A 364 PHE 0.014 0.001 PHE A 176 TYR 0.016 0.001 TYR A 618 ARG 0.006 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 165 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7758 (mmm) cc_final: 0.7548 (mtt) REVERT: A 723 MET cc_start: 0.7753 (mmm) cc_final: 0.7417 (mmt) outliers start: 34 outliers final: 26 residues processed: 152 average time/residue: 0.1848 time to fit residues: 37.8365 Evaluate side-chains 153 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 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 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 536 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 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 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 0.0770 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5056 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= 0.221 Angle : 0.587 8.675 9362 Z= 0.302 Chirality : 0.041 0.169 1128 Planarity : 0.005 0.052 1183 Dihedral : 4.237 18.844 937 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.19 % Allowed : 28.80 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.30), residues: 888 helix: 2.02 (0.24), residues: 439 sheet: -0.51 (0.52), residues: 107 loop : -0.61 (0.38), residues: 342 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 0.016 0.001 TYR A 618 ARG 0.006 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 163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 723 MET cc_start: 0.7760 (mmm) cc_final: 0.7417 (mmt) outliers start: 32 outliers final: 26 residues processed: 152 average time/residue: 0.1938 time to fit residues: 39.6414 Evaluate side-chains 154 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 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 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 536 LEU 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 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 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6914 Z= 0.245 Angle : 0.617 11.456 9362 Z= 0.315 Chirality : 0.043 0.245 1128 Planarity : 0.005 0.053 1183 Dihedral : 4.319 18.437 937 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.80 % Allowed : 29.84 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.30), residues: 888 helix: 1.91 (0.25), residues: 444 sheet: -0.41 (0.52), residues: 106 loop : -0.73 (0.38), residues: 338 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 0.014 0.001 PHE A 176 TYR 0.016 0.001 TYR A 618 ARG 0.006 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 156 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.723 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 25 residues processed: 146 average time/residue: 0.1837 time to fit residues: 36.7827 Evaluate side-chains 151 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 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 536 LEU 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 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 853 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 0.0020 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN A 747 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5151 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= 0.192 Angle : 0.594 11.816 9362 Z= 0.304 Chirality : 0.041 0.221 1128 Planarity : 0.005 0.054 1183 Dihedral : 4.178 18.349 937 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.66 % Allowed : 29.97 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.30), residues: 888 helix: 2.00 (0.25), residues: 445 sheet: -0.71 (0.54), residues: 94 loop : -0.58 (0.38), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 766 HIS 0.003 0.001 HIS A 53 PHE 0.012 0.001 PHE A 725 TYR 0.013 0.001 TYR A 618 ARG 0.003 0.000 ARG A 468 ********************** 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 156 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.828 Fit side-chains REVERT: A 341 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7912 (tt) outliers start: 28 outliers final: 22 residues processed: 145 average time/residue: 0.1851 time to fit residues: 36.9890 Evaluate side-chains 149 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 7.9990 chunk 70 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.190196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163175 restraints weight = 8273.789| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.79 r_work: 0.3722 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6914 Z= 0.207 Angle : 0.627 11.955 9362 Z= 0.316 Chirality : 0.042 0.224 1128 Planarity : 0.005 0.058 1183 Dihedral : 4.195 21.851 937 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.14 % Allowed : 29.71 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.30), residues: 888 helix: 2.04 (0.25), residues: 445 sheet: -0.66 (0.55), residues: 94 loop : -0.64 (0.37), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 766 HIS 0.002 0.000 HIS A 467 PHE 0.013 0.001 PHE A 725 TYR 0.015 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: 1959.46 seconds wall clock time: 43 minutes 57.74 seconds (2637.74 seconds total)