Starting phenix.real_space_refine on Wed Jan 17 23:33:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/01_2024/8iww_35781_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/01_2024/8iww_35781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/01_2024/8iww_35781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/01_2024/8iww_35781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/01_2024/8iww_35781_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/01_2024/8iww_35781_updated.pdb" } resolution = 3.71 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 Al 1 5.89 5 P 2 5.49 5 S 52 5.16 5 C 4355 2.51 5 N 1145 2.21 5 O 1288 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A GLU 690": "OE1" <-> "OE2" Residue "A GLU 903": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6848 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6815 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 35, 'TRANS': 854} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.21, per 1000 atoms: 0.61 Number of scatterers: 6848 At special positions: 0 Unit cell: (115.92, 100.8, 107.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 1 19.99 S 52 16.00 P 2 15.00 Al 1 13.00 F 4 9.00 O 1288 8.00 N 1145 7.00 C 4355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 6838 O3A ADP A1001 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 8 sheets defined 46.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 101 through 129 Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 257 through 285 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 310 through 327 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 399 through 410 removed outlier: 3.514A pdb=" N ILE A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.719A pdb=" N LEU A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.947A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A 444 " --> pdb=" O GLY A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 504 through 520 removed outlier: 3.744A pdb=" N ALA A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 604 through 609 removed outlier: 4.124A pdb=" N GLN A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.745A pdb=" N MET A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 668 through 671 No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 683 through 720 Processing helix chain 'A' and resid 731 through 741 Processing helix chain 'A' and resid 744 through 747 No H-bonds generated for 'chain 'A' and resid 744 through 747' Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'A' and resid 773 through 797 Processing helix chain 'A' and resid 805 through 825 Processing helix chain 'A' and resid 843 through 859 Processing helix chain 'A' and resid 862 through 865 No H-bonds generated for 'chain 'A' and resid 862 through 865' Processing helix chain 'A' and resid 875 through 908 removed outlier: 4.061A pdb=" N SER A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 138 through 143 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 Processing sheet with id= C, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.422A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 415 through 417 Processing sheet with id= E, first strand: chain 'A' and resid 498 through 501 removed outlier: 7.083A pdb=" N LEU A 536 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR A 493 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 538 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER A 495 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.571A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 182 through 184 removed outlier: 5.842A pdb=" N ASP A 184 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A 223 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 592 through 594 removed outlier: 3.574A pdb=" N ALA A 615 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL A 594 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE A 617 " --> pdb=" O VAL A 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 332 hydrogen bonds defined for protein. 948 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: 2.22 Time building geometry restraints manager: 2.97 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: 2204 1.34 - 1.46: 804 1.46 - 1.57: 3858 1.57 - 1.69: 3 1.69 - 1.81: 88 Bond restraints: 6957 Sorted by residual: bond pdb=" F3 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.685 1.792 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.684 1.787 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" F2 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.685 1.777 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" F4 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.686 1.766 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.454 0.036 2.00e-02 2.50e+03 3.26e+00 ... (remaining 6952 not shown) Histogram of bond angle deviations from ideal: 83.92 - 102.22: 38 102.22 - 120.52: 6913 120.52 - 138.82: 2473 138.82 - 157.11: 0 157.11 - 175.41: 2 Bond angle restraints: 9426 Sorted by residual: angle pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " pdb=" F2 ALF A1002 " ideal model delta sigma weight residual 108.68 174.61 -65.93 3.00e+00 1.11e-01 4.83e+02 angle pdb=" F3 ALF A1002 " pdb="AL ALF A1002 " pdb=" F4 ALF A1002 " ideal model delta sigma weight residual 109.63 175.41 -65.78 3.00e+00 1.11e-01 4.81e+02 angle pdb=" F2 ALF A1002 " pdb="AL ALF A1002 " pdb=" F4 ALF A1002 " ideal model delta sigma weight residual 110.21 83.92 26.29 3.00e+00 1.11e-01 7.68e+01 angle pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " pdb=" F4 ALF A1002 " ideal model delta sigma weight residual 109.02 90.70 18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " pdb=" F3 ALF A1002 " ideal model delta sigma weight residual 109.69 91.45 18.24 3.00e+00 1.11e-01 3.70e+01 ... (remaining 9421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 3949 21.92 - 43.84: 254 43.84 - 65.77: 25 65.77 - 87.69: 12 87.69 - 109.61: 1 Dihedral angle restraints: 4241 sinusoidal: 1679 harmonic: 2562 Sorted by residual: dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 -169.61 109.61 1 2.00e+01 2.50e-03 3.21e+01 dihedral pdb=" CA SER A 840 " pdb=" C SER A 840 " pdb=" N ASN A 841 " pdb=" CA ASN A 841 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB GLU A 374 " pdb=" CG GLU A 374 " pdb=" CD GLU A 374 " pdb=" OE1 GLU A 374 " ideal model delta sinusoidal sigma weight residual 0.00 85.10 -85.10 1 3.00e+01 1.11e-03 9.76e+00 ... (remaining 4238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 942 0.052 - 0.104: 166 0.104 - 0.156: 22 0.156 - 0.208: 0 0.208 - 0.260: 1 Chirality restraints: 1131 Sorted by residual: chirality pdb=" C2' ADP A1001 " pdb=" C1' ADP A1001 " pdb=" C3' ADP A1001 " pdb=" O2' ADP A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ASP A 180 " pdb=" N ASP A 180 " pdb=" C ASP A 180 " pdb=" CB ASP A 180 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA LEU A 134 " pdb=" N LEU A 134 " pdb=" C LEU A 134 " pdb=" CB LEU A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1128 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1001 " 0.033 2.00e-02 2.50e+03 1.50e-02 6.17e+00 pdb=" C2 ADP A1001 " -0.005 2.00e-02 2.50e+03 pdb=" C4 ADP A1001 " -0.011 2.00e-02 2.50e+03 pdb=" C5 ADP A1001 " -0.006 2.00e-02 2.50e+03 pdb=" C6 ADP A1001 " 0.019 2.00e-02 2.50e+03 pdb=" C8 ADP A1001 " -0.001 2.00e-02 2.50e+03 pdb=" N1 ADP A1001 " 0.005 2.00e-02 2.50e+03 pdb=" N3 ADP A1001 " -0.016 2.00e-02 2.50e+03 pdb=" N6 ADP A1001 " 0.011 2.00e-02 2.50e+03 pdb=" N7 ADP A1001 " -0.017 2.00e-02 2.50e+03 pdb=" N9 ADP A1001 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 743 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 744 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 744 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 744 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 135 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 136 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.018 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1603 2.79 - 3.31: 6752 3.31 - 3.84: 11358 3.84 - 4.37: 12629 4.37 - 4.90: 21540 Nonbonded interactions: 53882 Sorted by model distance: nonbonded pdb=" O ARG A 417 " pdb=" OG1 THR A 420 " model vdw 2.256 2.440 nonbonded pdb=" OD2 ASP A 172 " pdb=" OG SER A 239 " model vdw 2.259 2.440 nonbonded pdb=" O ILE A 306 " pdb="CA CA A1000 " model vdw 2.303 2.510 nonbonded pdb=" OG SER A 186 " pdb=" O GLU A 191 " model vdw 2.329 2.440 nonbonded pdb=" O ARG A 468 " pdb=" NE2 GLN A 471 " model vdw 2.342 2.520 ... (remaining 53877 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: 2.700 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: 9.970 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.960 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 0.107 6957 Z= 0.215 Angle : 1.221 65.934 9426 Z= 0.496 Chirality : 0.039 0.260 1131 Planarity : 0.004 0.044 1186 Dihedral : 14.519 109.609 2583 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.13 % Allowed : 2.75 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.26), residues: 886 helix: -0.27 (0.23), residues: 438 sheet: -1.86 (0.46), residues: 118 loop : -1.88 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 460 HIS 0.001 0.000 HIS A 624 PHE 0.009 0.001 PHE A 176 TYR 0.005 0.001 TYR A 493 ARG 0.002 0.000 ARG A 842 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3927 (mmm) cc_final: 0.3188 (mmp) REVERT: A 81 ASN cc_start: 0.6219 (t0) cc_final: 0.5666 (m-40) REVERT: A 110 ILE cc_start: 0.8752 (tt) cc_final: 0.8477 (tt) REVERT: A 172 ASP cc_start: 0.7591 (m-30) cc_final: 0.7287 (m-30) REVERT: A 355 LEU cc_start: 0.8674 (tp) cc_final: 0.7621 (tp) REVERT: A 452 TYR cc_start: 0.6880 (m-80) cc_final: 0.6307 (m-80) REVERT: A 510 TYR cc_start: 0.8759 (m-10) cc_final: 0.8448 (m-80) REVERT: A 725 PHE cc_start: 0.3823 (m-80) cc_final: 0.3001 (m-80) REVERT: A 834 PHE cc_start: 0.7042 (m-80) cc_final: 0.6567 (m-10) REVERT: A 881 LEU cc_start: 0.8436 (mt) cc_final: 0.8027 (mp) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.2267 time to fit residues: 71.2373 Evaluate side-chains 150 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 51 optimal weight: 0.0000 chunk 80 optimal weight: 2.9990 overall best weight: 0.4726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 61 ASN A 120 GLN A 149 HIS A 249 GLN A 458 GLN A 592 GLN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN A 855 GLN A 865 GLN A 869 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6957 Z= 0.195 Angle : 0.918 33.198 9426 Z= 0.379 Chirality : 0.041 0.146 1131 Planarity : 0.004 0.043 1186 Dihedral : 5.210 96.544 948 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.88 % Allowed : 15.16 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.28), residues: 886 helix: 0.95 (0.25), residues: 438 sheet: -1.47 (0.49), residues: 109 loop : -1.52 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 795 HIS 0.005 0.001 HIS A 98 PHE 0.018 0.001 PHE A 538 TYR 0.024 0.002 TYR A 618 ARG 0.004 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3897 (mmm) cc_final: 0.3355 (mmp) REVERT: A 81 ASN cc_start: 0.6021 (t0) cc_final: 0.5739 (m-40) REVERT: A 110 ILE cc_start: 0.8650 (tt) cc_final: 0.8433 (tt) REVERT: A 172 ASP cc_start: 0.7864 (m-30) cc_final: 0.7500 (m-30) REVERT: A 219 MET cc_start: 0.8085 (tmm) cc_final: 0.7821 (ppp) REVERT: A 452 TYR cc_start: 0.7018 (m-80) cc_final: 0.6360 (m-80) REVERT: A 510 TYR cc_start: 0.8912 (m-10) cc_final: 0.8613 (m-10) REVERT: A 834 PHE cc_start: 0.7128 (m-80) cc_final: 0.6874 (m-10) REVERT: A 868 PHE cc_start: 0.6378 (OUTLIER) cc_final: 0.4850 (t80) REVERT: A 901 SER cc_start: 0.8807 (m) cc_final: 0.8506 (t) outliers start: 22 outliers final: 13 residues processed: 180 average time/residue: 0.2175 time to fit residues: 51.9841 Evaluate side-chains 157 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 GLN Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 876 LEU 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: 1.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.0570 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 249 GLN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6957 Z= 0.205 Angle : 0.918 29.521 9426 Z= 0.380 Chirality : 0.041 0.142 1131 Planarity : 0.004 0.044 1186 Dihedral : 5.146 93.911 948 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.88 % Allowed : 17.65 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.29), residues: 886 helix: 1.44 (0.25), residues: 440 sheet: -1.34 (0.50), residues: 108 loop : -1.19 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 795 HIS 0.010 0.001 HIS A 98 PHE 0.018 0.001 PHE A 245 TYR 0.025 0.001 TYR A 618 ARG 0.008 0.001 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3875 (mmm) cc_final: 0.3650 (mmm) REVERT: A 81 ASN cc_start: 0.5952 (t0) cc_final: 0.5717 (m-40) REVERT: A 172 ASP cc_start: 0.7945 (m-30) cc_final: 0.7579 (m-30) REVERT: A 452 TYR cc_start: 0.7153 (m-80) cc_final: 0.6434 (m-80) REVERT: A 510 TYR cc_start: 0.8967 (m-10) cc_final: 0.8560 (m-80) REVERT: A 568 MET cc_start: 0.8243 (tpt) cc_final: 0.6906 (tpt) REVERT: A 587 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: A 661 MET cc_start: 0.8403 (mmm) cc_final: 0.7447 (mmm) REVERT: A 784 ILE cc_start: 0.9031 (tp) cc_final: 0.8829 (tp) REVERT: A 868 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.4900 (t80) REVERT: A 881 LEU cc_start: 0.8321 (mp) cc_final: 0.7998 (mp) outliers start: 22 outliers final: 13 residues processed: 174 average time/residue: 0.2054 time to fit residues: 47.3634 Evaluate side-chains 161 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS A 730 ASN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6957 Z= 0.230 Angle : 0.922 29.636 9426 Z= 0.382 Chirality : 0.041 0.148 1131 Planarity : 0.004 0.044 1186 Dihedral : 5.350 94.969 948 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.18 % Allowed : 20.26 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 886 helix: 1.62 (0.25), residues: 440 sheet: -1.36 (0.51), residues: 109 loop : -1.09 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 795 HIS 0.005 0.001 HIS A 98 PHE 0.008 0.001 PHE A 538 TYR 0.026 0.002 TYR A 618 ARG 0.003 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4207 (mmm) cc_final: 0.4006 (mmm) REVERT: A 147 LEU cc_start: 0.6921 (tp) cc_final: 0.6711 (tt) REVERT: A 160 THR cc_start: 0.8714 (m) cc_final: 0.8451 (t) REVERT: A 172 ASP cc_start: 0.8026 (m-30) cc_final: 0.7692 (m-30) REVERT: A 568 MET cc_start: 0.8418 (tpt) cc_final: 0.7227 (tpt) REVERT: A 784 ILE cc_start: 0.9092 (tp) cc_final: 0.8884 (tp) outliers start: 32 outliers final: 20 residues processed: 167 average time/residue: 0.2087 time to fit residues: 47.4250 Evaluate side-chains 152 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 683 GLN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6957 Z= 0.348 Angle : 0.990 29.968 9426 Z= 0.427 Chirality : 0.044 0.169 1131 Planarity : 0.005 0.046 1186 Dihedral : 5.909 101.092 948 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.71 % Allowed : 21.83 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 886 helix: 1.12 (0.25), residues: 466 sheet: -1.82 (0.52), residues: 101 loop : -0.98 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 72 HIS 0.014 0.002 HIS A 98 PHE 0.014 0.002 PHE A 818 TYR 0.019 0.002 TYR A 618 ARG 0.003 0.000 ARG A 799 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7196 (tp) cc_final: 0.6968 (tt) REVERT: A 160 THR cc_start: 0.8828 (m) cc_final: 0.8587 (t) REVERT: A 172 ASP cc_start: 0.8142 (m-30) cc_final: 0.7800 (m-30) REVERT: A 435 MET cc_start: 0.7401 (ttp) cc_final: 0.7180 (ttp) REVERT: A 442 LEU cc_start: 0.8186 (mm) cc_final: 0.7786 (tp) REVERT: A 630 LYS cc_start: 0.8589 (mmmt) cc_final: 0.7845 (mtmt) REVERT: A 757 ASP cc_start: 0.6748 (m-30) cc_final: 0.6212 (m-30) outliers start: 36 outliers final: 24 residues processed: 178 average time/residue: 0.1828 time to fit residues: 43.8771 Evaluate side-chains 164 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 GLN Chi-restraints excluded: chain A residue 856 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 45 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6957 Z= 0.218 Angle : 0.944 29.627 9426 Z= 0.394 Chirality : 0.042 0.176 1131 Planarity : 0.004 0.047 1186 Dihedral : 5.664 100.575 948 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.92 % Allowed : 24.18 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.30), residues: 886 helix: 1.43 (0.25), residues: 460 sheet: -1.49 (0.56), residues: 89 loop : -0.98 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 72 HIS 0.012 0.002 HIS A 98 PHE 0.009 0.001 PHE A 702 TYR 0.020 0.001 TYR A 618 ARG 0.002 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 THR cc_start: 0.8805 (m) cc_final: 0.8572 (t) REVERT: A 172 ASP cc_start: 0.8074 (m-30) cc_final: 0.7741 (m-30) REVERT: A 274 PHE cc_start: 0.8503 (m-10) cc_final: 0.8183 (m-80) REVERT: A 442 LEU cc_start: 0.8021 (mm) cc_final: 0.7710 (tp) REVERT: A 568 MET cc_start: 0.8450 (tpt) cc_final: 0.7595 (tpt) REVERT: A 630 LYS cc_start: 0.8393 (mmmt) cc_final: 0.7727 (mtmt) outliers start: 30 outliers final: 22 residues processed: 168 average time/residue: 0.1673 time to fit residues: 38.7698 Evaluate side-chains 162 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 855 GLN Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.0870 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6957 Z= 0.195 Angle : 0.936 29.646 9426 Z= 0.385 Chirality : 0.042 0.146 1131 Planarity : 0.004 0.047 1186 Dihedral : 5.575 99.563 948 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.66 % Allowed : 24.97 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.30), residues: 886 helix: 1.51 (0.25), residues: 460 sheet: -1.49 (0.56), residues: 91 loop : -0.92 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 795 HIS 0.009 0.001 HIS A 98 PHE 0.010 0.001 PHE A 702 TYR 0.019 0.001 TYR A 618 ARG 0.002 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.6987 (tt) cc_final: 0.6606 (mp) REVERT: A 172 ASP cc_start: 0.8027 (m-30) cc_final: 0.7647 (m-30) REVERT: A 175 LEU cc_start: 0.7653 (mm) cc_final: 0.7385 (mm) REVERT: A 274 PHE cc_start: 0.8533 (m-10) cc_final: 0.8256 (m-80) REVERT: A 442 LEU cc_start: 0.7985 (mm) cc_final: 0.7743 (tp) REVERT: A 568 MET cc_start: 0.8403 (tpt) cc_final: 0.7543 (tpt) REVERT: A 630 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7731 (mtmt) REVERT: A 730 ASN cc_start: 0.7871 (m110) cc_final: 0.7665 (m110) outliers start: 28 outliers final: 25 residues processed: 167 average time/residue: 0.1739 time to fit residues: 39.6104 Evaluate side-chains 169 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 855 GLN Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 882 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.0000 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.0070 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 0.0770 chunk 74 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.2760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6957 Z= 0.175 Angle : 0.936 29.678 9426 Z= 0.386 Chirality : 0.041 0.141 1131 Planarity : 0.004 0.047 1186 Dihedral : 5.487 97.621 948 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.79 % Allowed : 25.36 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 886 helix: 1.58 (0.25), residues: 460 sheet: -1.67 (0.54), residues: 96 loop : -0.91 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 795 HIS 0.008 0.001 HIS A 98 PHE 0.010 0.001 PHE A 176 TYR 0.018 0.001 TYR A 618 ARG 0.002 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7972 (m-30) cc_final: 0.7632 (m-30) REVERT: A 175 LEU cc_start: 0.7622 (mm) cc_final: 0.7345 (mm) REVERT: A 274 PHE cc_start: 0.8462 (m-10) cc_final: 0.8204 (m-80) REVERT: A 568 MET cc_start: 0.8379 (tpt) cc_final: 0.7488 (tpt) REVERT: A 631 SER cc_start: 0.8692 (t) cc_final: 0.8376 (p) REVERT: A 881 LEU cc_start: 0.8461 (mt) cc_final: 0.8233 (mp) outliers start: 29 outliers final: 25 residues processed: 167 average time/residue: 0.1621 time to fit residues: 37.2474 Evaluate side-chains 160 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6957 Z= 0.214 Angle : 0.953 29.658 9426 Z= 0.398 Chirality : 0.042 0.137 1131 Planarity : 0.004 0.048 1186 Dihedral : 5.565 99.637 948 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.44 % Allowed : 24.97 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.30), residues: 886 helix: 1.63 (0.25), residues: 460 sheet: -1.71 (0.53), residues: 97 loop : -0.95 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 795 HIS 0.009 0.001 HIS A 98 PHE 0.010 0.001 PHE A 176 TYR 0.016 0.001 TYR A 618 ARG 0.004 0.000 ARG A 902 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 172 ASP cc_start: 0.8000 (m-30) cc_final: 0.7672 (m-30) REVERT: A 175 LEU cc_start: 0.7824 (mm) cc_final: 0.7513 (mp) REVERT: A 630 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7755 (mtmt) outliers start: 34 outliers final: 27 residues processed: 155 average time/residue: 0.1723 time to fit residues: 36.9397 Evaluate side-chains 160 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 56 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6957 Z= 0.205 Angle : 0.961 29.716 9426 Z= 0.399 Chirality : 0.042 0.143 1131 Planarity : 0.004 0.048 1186 Dihedral : 5.556 98.774 948 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.79 % Allowed : 26.41 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.30), residues: 886 helix: 1.69 (0.26), residues: 449 sheet: -1.80 (0.52), residues: 99 loop : -0.77 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 795 HIS 0.009 0.001 HIS A 98 PHE 0.011 0.001 PHE A 176 TYR 0.017 0.001 TYR A 618 ARG 0.006 0.000 ARG A 902 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7976 (m-30) cc_final: 0.7643 (m-30) REVERT: A 175 LEU cc_start: 0.7807 (mm) cc_final: 0.7533 (mp) REVERT: A 630 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7812 (mtmt) outliers start: 29 outliers final: 26 residues processed: 152 average time/residue: 0.1674 time to fit residues: 35.2015 Evaluate side-chains 154 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 LEU 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: 0.0570 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 51 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.159456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129438 restraints weight = 11433.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131745 restraints weight = 7327.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132610 restraints weight = 5281.006| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6957 Z= 0.176 Angle : 0.955 29.711 9426 Z= 0.395 Chirality : 0.042 0.151 1131 Planarity : 0.004 0.048 1186 Dihedral : 5.489 96.764 948 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.05 % Allowed : 26.27 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.30), residues: 886 helix: 1.67 (0.25), residues: 448 sheet: -1.61 (0.54), residues: 95 loop : -0.79 (0.37), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 795 HIS 0.010 0.001 HIS A 98 PHE 0.011 0.001 PHE A 176 TYR 0.018 0.001 TYR A 618 ARG 0.007 0.000 ARG A 902 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.82 seconds wall clock time: 35 minutes 46.65 seconds (2146.65 seconds total)