Starting phenix.real_space_refine on Mon Mar 11 05:22:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/03_2024/7w88_32353.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/03_2024/7w88_32353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/03_2024/7w88_32353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/03_2024/7w88_32353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/03_2024/7w88_32353.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/03_2024/7w88_32353.pdb" } resolution = 3.5 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= 0.002 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 4541 2.51 5 N 1241 2.21 5 O 1311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 125": "OE1" <-> "OE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A ASP 682": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 730": "OD1" <-> "OD2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A PHE 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A ASP 844": "OD1" <-> "OD2" Residue "A ASP 877": "OD1" <-> "OD2" Residue "A ASP 914": "OD1" <-> "OD2" Residue "A PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 935": "OD1" <-> "OD2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A ASP 1035": "OD1" <-> "OD2" Residue "A TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1044": "OD1" <-> "OD2" Residue "A ASP 1051": "OD1" <-> "OD2" Residue "A TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A GLU 1088": "OE1" <-> "OE2" Residue "A PHE 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7138 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7138 Classifications: {'peptide': 896} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 854} Chain breaks: 7 Time building chain proxies: 4.38, per 1000 atoms: 0.61 Number of scatterers: 7138 At special positions: 0 Unit cell: (79.18, 94.72, 105.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1311 8.00 N 1241 7.00 C 4541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 805 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.3 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 31.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.525A pdb=" N LEU A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.790A pdb=" N LEU A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 395 through 401 Processing helix chain 'A' and resid 402 through 408 removed outlier: 4.260A pdb=" N SER A 406 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 removed outlier: 3.781A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 427' Processing helix chain 'A' and resid 441 through 453 removed outlier: 4.075A pdb=" N HIS A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.948A pdb=" N GLY A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.647A pdb=" N CYS A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 554 through 566 removed outlier: 3.771A pdb=" N LYS A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 641 through 651 removed outlier: 4.990A pdb=" N MET A 647 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLN A 648 " --> pdb=" O PHE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 694 through 715 Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 794 through 800 Processing helix chain 'A' and resid 815 through 821 removed outlier: 4.410A pdb=" N SER A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 removed outlier: 3.673A pdb=" N MET A 874 " --> pdb=" O PHE A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 removed outlier: 3.503A pdb=" N ILE A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 909 removed outlier: 3.807A pdb=" N VAL A 903 " --> pdb=" O SER A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 956 Processing helix chain 'A' and resid 997 through 1009 Processing helix chain 'A' and resid 1017 through 1022 Processing helix chain 'A' and resid 1039 through 1060 Processing helix chain 'A' and resid 1073 through 1078 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 131 removed outlier: 3.562A pdb=" N ALA A 129 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 117 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A 131 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 115 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 238 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 removed outlier: 7.266A pdb=" N GLN A 183 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.567A pdb=" N GLU A 390 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 384 through 386 removed outlier: 7.036A pdb=" N TRP A 478 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 455 " --> pdb=" O TYR A 462 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA8, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 575 through 576 removed outlier: 3.504A pdb=" N PHE A 576 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 726 through 727 removed outlier: 7.404A pdb=" N ILE A 726 " --> pdb=" O VAL A 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 740 removed outlier: 3.599A pdb=" N VAL A 740 " --> pdb=" O GLU A 790 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 789 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 776 " --> pdb=" O PHE A 831 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 744 through 745 removed outlier: 3.618A pdb=" N ILE A 744 " --> pdb=" O ALA A 767 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 540 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: 2.15 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2334 1.34 - 1.46: 1638 1.46 - 1.58: 3252 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 7293 Sorted by residual: bond pdb=" N GLU A 391 " pdb=" CA GLU A 391 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.43e+00 bond pdb=" N GLU A 390 " pdb=" CA GLU A 390 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.58e+00 bond pdb=" N ASP A 590 " pdb=" CA ASP A 590 " ideal model delta sigma weight residual 1.457 1.486 -0.030 1.41e-02 5.03e+03 4.40e+00 bond pdb=" N GLU A 938 " pdb=" CA GLU A 938 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.60e+00 bond pdb=" CA VAL A 529 " pdb=" CB VAL A 529 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.34e-02 5.57e+03 1.49e+00 ... (remaining 7288 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.06: 235 107.06 - 113.82: 4022 113.82 - 120.58: 2895 120.58 - 127.34: 2617 127.34 - 134.11: 81 Bond angle restraints: 9850 Sorted by residual: angle pdb=" C ARG A 898 " pdb=" N SER A 899 " pdb=" CA SER A 899 " ideal model delta sigma weight residual 120.49 114.60 5.89 1.42e+00 4.96e-01 1.72e+01 angle pdb=" N VAL A 247 " pdb=" CA VAL A 247 " pdb=" C VAL A 247 " ideal model delta sigma weight residual 113.71 110.18 3.53 9.50e-01 1.11e+00 1.38e+01 angle pdb=" N GLY A 638 " pdb=" CA GLY A 638 " pdb=" C GLY A 638 " ideal model delta sigma weight residual 113.18 120.68 -7.50 2.37e+00 1.78e-01 1.00e+01 angle pdb=" N SER A 339 " pdb=" CA SER A 339 " pdb=" C SER A 339 " ideal model delta sigma weight residual 108.32 113.51 -5.19 1.64e+00 3.72e-01 1.00e+01 angle pdb=" N LYS A 640 " pdb=" CA LYS A 640 " pdb=" C LYS A 640 " ideal model delta sigma weight residual 110.80 117.23 -6.43 2.13e+00 2.20e-01 9.10e+00 ... (remaining 9845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3779 17.99 - 35.98: 492 35.98 - 53.97: 122 53.97 - 71.96: 20 71.96 - 89.95: 5 Dihedral angle restraints: 4418 sinusoidal: 1806 harmonic: 2612 Sorted by residual: dihedral pdb=" CA SER A 547 " pdb=" C SER A 547 " pdb=" N ASP A 548 " pdb=" CA ASP A 548 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA MET A1009 " pdb=" C MET A1009 " pdb=" N THR A1010 " pdb=" CA THR A1010 " ideal model delta harmonic sigma weight residual 180.00 157.54 22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ALA A1108 " pdb=" C ALA A1108 " pdb=" N ARG A1109 " pdb=" CA ARG A1109 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 4415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 738 0.039 - 0.078: 246 0.078 - 0.118: 82 0.118 - 0.157: 17 0.157 - 0.196: 1 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CB VAL A 740 " pdb=" CA VAL A 740 " pdb=" CG1 VAL A 740 " pdb=" CG2 VAL A 740 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CB ILE A 265 " pdb=" CA ILE A 265 " pdb=" CG1 ILE A 265 " pdb=" CG2 ILE A 265 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 377 " pdb=" N ILE A 377 " pdb=" C ILE A 377 " pdb=" CB ILE A 377 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1081 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 589 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C ILE A 589 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 589 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A 590 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 380 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 381 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 933 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO A 934 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 934 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 934 " 0.026 5.00e-02 4.00e+02 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1190 2.76 - 3.29: 6891 3.29 - 3.83: 11142 3.83 - 4.36: 12501 4.36 - 4.90: 21855 Nonbonded interactions: 53579 Sorted by model distance: nonbonded pdb=" O MET A 603 " pdb=" NZ LYS A 605 " model vdw 2.225 2.520 nonbonded pdb=" N ASP A 165 " pdb=" OD1 ASP A 165 " model vdw 2.237 2.520 nonbonded pdb=" OE2 GLU A 642 " pdb=" NZ LYS A 837 " model vdw 2.249 2.520 nonbonded pdb=" O CYS A 624 " pdb=" ND1 HIS A 718 " model vdw 2.258 2.520 nonbonded pdb=" NH2 ARG A 519 " pdb=" O ILE A 565 " model vdw 2.263 2.520 ... (remaining 53574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 5.130 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.550 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 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 0.038 7293 Z= 0.199 Angle : 0.705 8.829 9850 Z= 0.406 Chirality : 0.045 0.196 1084 Planarity : 0.004 0.053 1260 Dihedral : 16.867 89.950 2727 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.23 % Favored : 84.77 % Rotamer: Outliers : 8.23 % Allowed : 23.26 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -5.15 (0.23), residues: 880 helix: -1.89 (0.28), residues: 236 sheet: -4.61 (0.35), residues: 129 loop : -4.04 (0.23), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1096 HIS 0.005 0.001 HIS A 718 PHE 0.012 0.001 PHE A 464 TYR 0.012 0.001 TYR A 695 ARG 0.003 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 114 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7529 (ptpt) cc_final: 0.7271 (ptmt) REVERT: A 329 ARG cc_start: 0.7495 (mpp80) cc_final: 0.6665 (mpp80) REVERT: A 446 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.5784 (ttt-90) REVERT: A 519 ARG cc_start: 0.7342 (mtp180) cc_final: 0.7083 (ptp-110) REVERT: A 606 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7621 (p90) REVERT: A 630 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6570 (mp) REVERT: A 708 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7391 (mt) REVERT: A 942 ARG cc_start: 0.1645 (OUTLIER) cc_final: -0.0978 (ptt-90) outliers start: 64 outliers final: 35 residues processed: 166 average time/residue: 0.2166 time to fit residues: 46.6198 Evaluate side-chains 130 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 90 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 715 CYS Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 998 TYR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1081 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1101 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 276 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 661 ASN A 686 GLN A 706 ASN A 739 GLN A 748 HIS A 756 GLN A 778 ASN ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 7293 Z= 0.559 Angle : 0.868 9.536 9850 Z= 0.455 Chirality : 0.052 0.223 1084 Planarity : 0.007 0.066 1260 Dihedral : 10.411 59.374 1063 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.50 % Favored : 77.50 % Rotamer: Outliers : 10.80 % Allowed : 25.19 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -5.01 (0.25), residues: 880 helix: -1.85 (0.28), residues: 245 sheet: -4.59 (0.30), residues: 145 loop : -3.85 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 940 HIS 0.007 0.002 HIS A 401 PHE 0.027 0.003 PHE A 480 TYR 0.025 0.003 TYR A 695 ARG 0.005 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 87 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 HIS cc_start: 0.6261 (OUTLIER) cc_final: 0.5606 (m-70) REVERT: A 329 ARG cc_start: 0.7421 (mpp80) cc_final: 0.7160 (mpp80) REVERT: A 519 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7355 (ptp-170) REVERT: A 606 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7876 (p90) REVERT: A 630 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6851 (mp) REVERT: A 708 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7308 (mt) REVERT: A 721 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7509 (mttp) REVERT: A 731 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: A 942 ARG cc_start: 0.2155 (OUTLIER) cc_final: -0.1012 (ptt-90) outliers start: 84 outliers final: 59 residues processed: 158 average time/residue: 0.1911 time to fit residues: 40.4043 Evaluate side-chains 147 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 82 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 715 CYS Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 998 TYR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1081 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1091 PHE Chi-restraints excluded: chain A residue 1099 CYS Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain A residue 1101 THR 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: 0.7980 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7293 Z= 0.236 Angle : 0.679 8.048 9850 Z= 0.350 Chirality : 0.045 0.179 1084 Planarity : 0.005 0.064 1260 Dihedral : 9.143 58.344 1042 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.73 % Favored : 82.27 % Rotamer: Outliers : 9.25 % Allowed : 27.63 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -4.38 (0.26), residues: 880 helix: -1.09 (0.30), residues: 248 sheet: -4.13 (0.33), residues: 147 loop : -3.63 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 618 HIS 0.006 0.001 HIS A 718 PHE 0.014 0.002 PHE A 464 TYR 0.016 0.002 TYR A 695 ARG 0.004 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 92 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7569 (ptmt) cc_final: 0.6982 (mptt) REVERT: A 173 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5390 (m-70) REVERT: A 329 ARG cc_start: 0.7381 (mpp80) cc_final: 0.6813 (mpp80) REVERT: A 630 ILE cc_start: 0.7045 (mp) cc_final: 0.6637 (mp) REVERT: A 708 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7152 (mt) REVERT: A 731 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6656 (pt0) REVERT: A 739 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7956 (mm110) REVERT: A 924 MET cc_start: 0.7815 (mpp) cc_final: 0.7137 (mpp) REVERT: A 942 ARG cc_start: 0.1883 (OUTLIER) cc_final: 0.0064 (ptt-90) outliers start: 72 outliers final: 47 residues processed: 154 average time/residue: 0.2237 time to fit residues: 45.3502 Evaluate side-chains 138 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 86 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 998 TYR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1081 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1091 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7293 Z= 0.204 Angle : 0.650 8.167 9850 Z= 0.332 Chirality : 0.044 0.168 1084 Planarity : 0.005 0.063 1260 Dihedral : 8.532 57.926 1031 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Rotamer: Outliers : 9.00 % Allowed : 27.89 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.94 (0.27), residues: 880 helix: -0.63 (0.32), residues: 246 sheet: -3.88 (0.35), residues: 138 loop : -3.43 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1096 HIS 0.004 0.001 HIS A 703 PHE 0.015 0.001 PHE A 464 TYR 0.016 0.001 TYR A 695 ARG 0.005 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 91 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7553 (ptmt) cc_final: 0.7052 (mptt) REVERT: A 329 ARG cc_start: 0.7477 (mpp80) cc_final: 0.7028 (mpp80) REVERT: A 446 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.5853 (ttt-90) REVERT: A 630 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6658 (mp) REVERT: A 708 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7163 (mt) REVERT: A 731 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6507 (pt0) REVERT: A 924 MET cc_start: 0.7780 (mpp) cc_final: 0.7362 (mpp) REVERT: A 942 ARG cc_start: 0.1685 (OUTLIER) cc_final: -0.0133 (ptt-90) REVERT: A 1081 TYR cc_start: 0.4340 (OUTLIER) cc_final: 0.3565 (m-80) outliers start: 70 outliers final: 44 residues processed: 148 average time/residue: 0.2079 time to fit residues: 40.4753 Evaluate side-chains 136 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 86 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 998 TYR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1081 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1091 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 73 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7293 Z= 0.183 Angle : 0.643 9.793 9850 Z= 0.327 Chirality : 0.044 0.169 1084 Planarity : 0.005 0.060 1260 Dihedral : 8.216 58.950 1025 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.25 % Favored : 83.75 % Rotamer: Outliers : 9.00 % Allowed : 28.41 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.71 (0.27), residues: 880 helix: -0.41 (0.33), residues: 248 sheet: -3.76 (0.35), residues: 140 loop : -3.30 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 618 HIS 0.004 0.001 HIS A 718 PHE 0.019 0.001 PHE A1040 TYR 0.015 0.001 TYR A 695 ARG 0.003 0.000 ARG A 855 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 97 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7469 (ptmt) cc_final: 0.7024 (mptt) REVERT: A 446 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.5867 (ttt-90) REVERT: A 617 ASN cc_start: 0.7300 (t0) cc_final: 0.7037 (m-40) REVERT: A 630 ILE cc_start: 0.7062 (mp) cc_final: 0.6651 (mp) REVERT: A 647 MET cc_start: 0.6657 (mpt) cc_final: 0.6453 (mpt) REVERT: A 662 LYS cc_start: 0.6879 (mttt) cc_final: 0.6613 (mttt) REVERT: A 708 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7145 (mt) REVERT: A 924 MET cc_start: 0.7730 (mpp) cc_final: 0.7529 (mpt) REVERT: A 935 ASP cc_start: 0.0353 (OUTLIER) cc_final: 0.0081 (m-30) REVERT: A 942 ARG cc_start: 0.1503 (OUTLIER) cc_final: -0.0267 (ptt-90) REVERT: A 1081 TYR cc_start: 0.4098 (OUTLIER) cc_final: 0.3474 (m-80) outliers start: 70 outliers final: 47 residues processed: 157 average time/residue: 0.2117 time to fit residues: 43.8290 Evaluate side-chains 142 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 90 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 998 TYR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1081 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1091 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7293 Z= 0.237 Angle : 0.657 8.375 9850 Z= 0.338 Chirality : 0.045 0.244 1084 Planarity : 0.005 0.059 1260 Dihedral : 8.228 59.694 1021 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.84 % Favored : 82.16 % Rotamer: Outliers : 9.38 % Allowed : 26.86 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.70 (0.27), residues: 880 helix: -0.50 (0.32), residues: 248 sheet: -3.62 (0.36), residues: 136 loop : -3.29 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 618 HIS 0.004 0.001 HIS A 718 PHE 0.017 0.002 PHE A 464 TYR 0.017 0.001 TYR A 695 ARG 0.006 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 95 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7501 (ptmt) cc_final: 0.7042 (mptt) REVERT: A 173 HIS cc_start: 0.6086 (OUTLIER) cc_final: 0.5500 (m-70) REVERT: A 240 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8119 (tttm) REVERT: A 241 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 446 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.5913 (ttt-90) REVERT: A 630 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6702 (mp) REVERT: A 708 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7192 (mt) REVERT: A 909 HIS cc_start: 0.7138 (m-70) cc_final: 0.6936 (m-70) REVERT: A 924 MET cc_start: 0.7755 (mpp) cc_final: 0.7539 (mpp) REVERT: A 935 ASP cc_start: 0.0495 (OUTLIER) cc_final: 0.0109 (m-30) REVERT: A 941 GLU cc_start: 0.2844 (OUTLIER) cc_final: 0.2370 (pt0) REVERT: A 942 ARG cc_start: 0.1567 (OUTLIER) cc_final: -0.0067 (ptt-90) REVERT: A 1081 TYR cc_start: 0.4067 (OUTLIER) cc_final: 0.3509 (m-80) outliers start: 73 outliers final: 52 residues processed: 155 average time/residue: 0.2043 time to fit residues: 41.5435 Evaluate side-chains 149 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 88 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 715 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 998 TYR Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1081 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1091 PHE Chi-restraints excluded: chain A residue 1100 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 39 optimal weight: 0.0980 chunk 34 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 560 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A 869 HIS A1036 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 7293 Z= 0.378 Angle : 0.758 8.421 9850 Z= 0.397 Chirality : 0.048 0.175 1084 Planarity : 0.006 0.063 1260 Dihedral : 8.812 58.559 1021 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.57 % Favored : 79.43 % Rotamer: Outliers : 9.77 % Allowed : 27.38 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -4.11 (0.26), residues: 880 helix: -1.07 (0.30), residues: 256 sheet: -3.90 (0.34), residues: 140 loop : -3.41 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 618 HIS 0.004 0.001 HIS A 718 PHE 0.042 0.003 PHE A 522 TYR 0.020 0.002 TYR A 695 ARG 0.007 0.001 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 96 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7513 (ptmt) cc_final: 0.7021 (mptt) REVERT: A 173 HIS cc_start: 0.6138 (OUTLIER) cc_final: 0.5508 (m-70) REVERT: A 241 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8488 (tt) REVERT: A 294 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7980 (mt) REVERT: A 355 MET cc_start: 0.6839 (mtm) cc_final: 0.6622 (mtm) REVERT: A 446 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.5786 (ttt-90) REVERT: A 630 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6772 (mp) REVERT: A 645 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5626 (tt0) REVERT: A 924 MET cc_start: 0.7799 (mpp) cc_final: 0.7122 (mpp) REVERT: A 935 ASP cc_start: 0.0561 (OUTLIER) cc_final: -0.0004 (m-30) REVERT: A 941 GLU cc_start: 0.2749 (OUTLIER) cc_final: 0.2256 (pt0) REVERT: A 942 ARG cc_start: 0.2071 (OUTLIER) cc_final: 0.0363 (ptt-90) REVERT: A 1081 TYR cc_start: 0.4014 (OUTLIER) cc_final: 0.3392 (m-80) outliers start: 76 outliers final: 57 residues processed: 159 average time/residue: 0.2134 time to fit residues: 44.0116 Evaluate side-chains 157 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 90 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 715 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 998 TYR Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1081 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1091 PHE Chi-restraints excluded: chain A residue 1099 CYS Chi-restraints excluded: chain A residue 1100 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 74 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 739 GLN A1036 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7293 Z= 0.261 Angle : 0.704 8.221 9850 Z= 0.365 Chirality : 0.046 0.163 1084 Planarity : 0.005 0.064 1260 Dihedral : 8.680 59.049 1021 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.98 % Favored : 81.02 % Rotamer: Outliers : 9.38 % Allowed : 29.05 % Favored : 61.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.86 (0.26), residues: 880 helix: -0.81 (0.31), residues: 256 sheet: -3.67 (0.36), residues: 138 loop : -3.32 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 618 HIS 0.004 0.001 HIS A 869 PHE 0.041 0.002 PHE A 522 TYR 0.017 0.002 TYR A 695 ARG 0.005 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 93 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7455 (ptmt) cc_final: 0.7023 (mptt) REVERT: A 173 HIS cc_start: 0.6215 (OUTLIER) cc_final: 0.5597 (m-70) REVERT: A 240 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8078 (tttm) REVERT: A 241 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8358 (tt) REVERT: A 355 MET cc_start: 0.6945 (mtm) cc_final: 0.6686 (mtm) REVERT: A 446 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.5803 (ttt-90) REVERT: A 510 ARG cc_start: 0.5616 (mmt-90) cc_final: 0.5358 (ptp-170) REVERT: A 630 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6673 (mp) REVERT: A 645 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5495 (tt0) REVERT: A 708 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7094 (mt) REVERT: A 909 HIS cc_start: 0.7057 (m-70) cc_final: 0.6762 (m-70) REVERT: A 924 MET cc_start: 0.7754 (mpp) cc_final: 0.7507 (mpp) REVERT: A 935 ASP cc_start: 0.0494 (OUTLIER) cc_final: -0.0011 (m-30) REVERT: A 942 ARG cc_start: 0.1829 (OUTLIER) cc_final: -0.0031 (ptt-90) REVERT: A 945 TYR cc_start: -0.0060 (OUTLIER) cc_final: -0.2191 (p90) REVERT: A 1081 TYR cc_start: 0.3942 (OUTLIER) cc_final: 0.3371 (m-80) outliers start: 73 outliers final: 54 residues processed: 152 average time/residue: 0.2317 time to fit residues: 45.3889 Evaluate side-chains 153 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 89 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 715 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 998 TYR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1081 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1091 PHE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1100 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.0170 chunk 58 optimal weight: 0.7980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 560 GLN A1036 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7293 Z= 0.173 Angle : 0.664 8.367 9850 Z= 0.339 Chirality : 0.044 0.171 1084 Planarity : 0.005 0.063 1260 Dihedral : 8.187 58.321 1021 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.25 % Favored : 83.75 % Rotamer: Outliers : 8.35 % Allowed : 29.56 % Favored : 62.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.35 (0.27), residues: 880 helix: -0.43 (0.32), residues: 256 sheet: -3.28 (0.42), residues: 115 loop : -3.07 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 618 HIS 0.005 0.001 HIS A 703 PHE 0.011 0.001 PHE A 464 TYR 0.015 0.001 TYR A 695 ARG 0.008 0.001 ARG A1090 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 102 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7417 (ptmt) cc_final: 0.7040 (mptt) REVERT: A 173 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5562 (m-70) REVERT: A 240 LYS cc_start: 0.8411 (ttmm) cc_final: 0.7950 (tttm) REVERT: A 241 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8273 (tt) REVERT: A 355 MET cc_start: 0.6959 (mtm) cc_final: 0.6725 (mtm) REVERT: A 446 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.5891 (ttt-90) REVERT: A 510 ARG cc_start: 0.5532 (mmt-90) cc_final: 0.5229 (mmt-90) REVERT: A 617 ASN cc_start: 0.7258 (t0) cc_final: 0.6990 (m-40) REVERT: A 630 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6671 (mp) REVERT: A 645 GLU cc_start: 0.5706 (OUTLIER) cc_final: 0.5359 (tt0) REVERT: A 708 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7054 (mt) REVERT: A 909 HIS cc_start: 0.6894 (m-70) cc_final: 0.6645 (m-70) REVERT: A 924 MET cc_start: 0.7705 (mpp) cc_final: 0.7372 (mpp) REVERT: A 935 ASP cc_start: 0.0432 (OUTLIER) cc_final: 0.0061 (m-30) REVERT: A 941 GLU cc_start: 0.2508 (OUTLIER) cc_final: 0.2126 (pt0) REVERT: A 942 ARG cc_start: 0.1507 (OUTLIER) cc_final: -0.0150 (ptt-90) REVERT: A 945 TYR cc_start: -0.0023 (OUTLIER) cc_final: -0.2008 (p90) REVERT: A 1081 TYR cc_start: 0.3882 (OUTLIER) cc_final: 0.3378 (m-80) REVERT: A 1086 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6429 (tmm160) outliers start: 65 outliers final: 47 residues processed: 156 average time/residue: 0.2149 time to fit residues: 43.5756 Evaluate side-chains 149 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 91 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 715 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 998 TYR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1081 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1091 PHE Chi-restraints excluded: chain A residue 1100 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.0170 chunk 81 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 739 GLN A 756 GLN A1036 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7293 Z= 0.250 Angle : 0.702 7.853 9850 Z= 0.360 Chirality : 0.045 0.174 1084 Planarity : 0.006 0.082 1260 Dihedral : 8.245 59.333 1021 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Rotamer: Outliers : 8.10 % Allowed : 29.95 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.50 (0.27), residues: 880 helix: -0.46 (0.32), residues: 250 sheet: -3.39 (0.38), residues: 130 loop : -3.15 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 618 HIS 0.004 0.001 HIS A 718 PHE 0.017 0.002 PHE A 464 TYR 0.018 0.001 TYR A 695 ARG 0.008 0.000 ARG A 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 94 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7439 (ptmt) cc_final: 0.7048 (mptt) REVERT: A 173 HIS cc_start: 0.6186 (OUTLIER) cc_final: 0.5593 (m-70) REVERT: A 240 LYS cc_start: 0.8448 (ttmm) cc_final: 0.7978 (tttm) REVERT: A 241 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 355 MET cc_start: 0.6904 (mtm) cc_final: 0.6694 (mtm) REVERT: A 446 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.5851 (ttt-90) REVERT: A 617 ASN cc_start: 0.7341 (t0) cc_final: 0.6978 (m-40) REVERT: A 630 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6698 (mp) REVERT: A 645 GLU cc_start: 0.5742 (OUTLIER) cc_final: 0.5415 (tt0) REVERT: A 790 GLU cc_start: 0.7625 (mp0) cc_final: 0.7267 (mp0) REVERT: A 909 HIS cc_start: 0.6960 (m-70) cc_final: 0.6703 (m-70) REVERT: A 924 MET cc_start: 0.7741 (mpp) cc_final: 0.7527 (mpp) REVERT: A 935 ASP cc_start: 0.0458 (OUTLIER) cc_final: -0.0011 (m-30) REVERT: A 941 GLU cc_start: 0.2514 (OUTLIER) cc_final: 0.2088 (pt0) REVERT: A 942 ARG cc_start: 0.1634 (OUTLIER) cc_final: 0.0037 (ptt-90) outliers start: 63 outliers final: 50 residues processed: 146 average time/residue: 0.2267 time to fit residues: 42.8509 Evaluate side-chains 149 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 91 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 715 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 998 TYR Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1100 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 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 = 0.4614 r_free = 0.4614 target = 0.213337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.180114 restraints weight = 9240.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.180821 restraints weight = 6235.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.182961 restraints weight = 5242.196| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7293 Z= 0.240 Angle : 0.702 8.349 9850 Z= 0.359 Chirality : 0.045 0.164 1084 Planarity : 0.005 0.076 1260 Dihedral : 7.820 51.948 1017 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 7.97 % Allowed : 29.95 % Favored : 62.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.48 (0.27), residues: 880 helix: -0.44 (0.32), residues: 250 sheet: -3.38 (0.39), residues: 130 loop : -3.14 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 618 HIS 0.004 0.001 HIS A 718 PHE 0.015 0.002 PHE A 464 TYR 0.017 0.001 TYR A 695 ARG 0.010 0.001 ARG A1086 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.46 seconds wall clock time: 32 minutes 57.51 seconds (1977.51 seconds total)