Starting phenix.real_space_refine on Fri Mar 15 22:56:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfl_25092/03_2024/7sfl_25092_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfl_25092/03_2024/7sfl_25092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfl_25092/03_2024/7sfl_25092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfl_25092/03_2024/7sfl_25092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfl_25092/03_2024/7sfl_25092_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfl_25092/03_2024/7sfl_25092_updated.pdb" } resolution = 3.87 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= -0.001 sd= 0.044 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: 5 Type Number sf(0) Gaussians S 82 5.16 5 Cl 2 4.86 5 C 8491 2.51 5 N 2137 2.21 5 O 2302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 1138": "OE1" <-> "OE2" Residue "B PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13014 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6479 Classifications: {'peptide': 829} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 29, 'TRANS': 799} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6493 Classifications: {'peptide': 830} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 29, 'TRANS': 800} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.12, per 1000 atoms: 0.55 Number of scatterers: 13014 At special positions: 0 Unit cell: (81.32, 156.22, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 82 16.00 O 2302 8.00 N 2137 7.00 C 8491 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.04 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 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: 5.47 Conformation dependent library (CDL) restraints added in 2.3 seconds 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 4 sheets defined 57.3% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 317 through 342 Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 362 through 398 removed outlier: 4.459A pdb=" N ALA A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 425 removed outlier: 3.626A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 454 removed outlier: 4.810A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 487 through 498 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 517 through 543 Processing helix chain 'A' and resid 592 through 596 Processing helix chain 'A' and resid 600 through 631 removed outlier: 3.726A pdb=" N SER A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 605 " --> pdb=" O PRO A 601 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 636 through 641 removed outlier: 4.966A pdb=" N MET A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 Processing helix chain 'A' and resid 671 through 698 Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 713 through 729 Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'A' and resid 763 through 779 Processing helix chain 'A' and resid 802 through 811 removed outlier: 3.627A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 897 through 912 Processing helix chain 'A' and resid 1035 through 1046 Proline residue: A1040 - end of helix removed outlier: 3.568A pdb=" N THR A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1079 removed outlier: 3.627A pdb=" N LEU A1075 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1111 Proline residue: A1110 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1136 through 1141 Processing helix chain 'A' and resid 1143 through 1162 removed outlier: 3.967A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR A1162 " --> pdb=" O GLU A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1190 Processing helix chain 'B' and resid 288 through 299 removed outlier: 3.885A pdb=" N VAL B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 317 through 343 Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 362 through 397 removed outlier: 3.675A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 424 Processing helix chain 'B' and resid 431 through 454 removed outlier: 4.351A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'B' and resid 487 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 514 through 542 removed outlier: 3.566A pdb=" N ILE B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Proline residue: B 519 - end of helix removed outlier: 3.884A pdb=" N LEU B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 570 No H-bonds generated for 'chain 'B' and resid 567 through 570' Processing helix chain 'B' and resid 590 through 596 removed outlier: 4.530A pdb=" N MET B 593 " --> pdb=" O PHE B 590 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 596 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 632 Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 636 through 641 removed outlier: 5.172A pdb=" N MET B 640 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 667 removed outlier: 3.959A pdb=" N LEU B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 698 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 713 through 729 Processing helix chain 'B' and resid 732 through 757 removed outlier: 4.193A pdb=" N TYR B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS B 753 " --> pdb=" O VAL B 749 " (cutoff:3.500A) Proline residue: B 754 - end of helix Processing helix chain 'B' and resid 764 through 779 removed outlier: 4.258A pdb=" N ASN B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 810 Processing helix chain 'B' and resid 831 through 848 Processing helix chain 'B' and resid 863 through 873 Processing helix chain 'B' and resid 897 through 912 removed outlier: 3.532A pdb=" N PHE B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1044 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1065 through 1079 Processing helix chain 'B' and resid 1098 through 1107 Processing helix chain 'B' and resid 1120 through 1129 Processing helix chain 'B' and resid 1136 through 1141 Processing helix chain 'B' and resid 1143 through 1159 removed outlier: 4.019A pdb=" N ASN B1153 " --> pdb=" O GLN B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1191 Processing sheet with id= A, first strand: chain 'A' and resid 1166 through 1169 removed outlier: 3.790A pdb=" N PHE A 854 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS A 822 " --> pdb=" O ALA A 856 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1023 through 1026 removed outlier: 5.929A pdb=" N LYS A1053 " --> pdb=" O ILE A1024 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL A1026 " --> pdb=" O LYS A1053 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG A1055 " --> pdb=" O VAL A1026 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 791 through 793 removed outlier: 6.681A pdb=" N THR B 883 " --> pdb=" O LEU B 792 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY B 916 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B 886 " --> pdb=" O GLY B 916 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 918 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B1169 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY B1059 " --> pdb=" O TRP B1028 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP B1085 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE B1058 " --> pdb=" O ASP B1085 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET B1087 " --> pdb=" O ILE B1058 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 822 through 824 668 hydrogen bonds defined for protein. 1983 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: 3.71 Time building geometry restraints manager: 5.86 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: 4056 1.34 - 1.47: 3203 1.47 - 1.59: 5906 1.59 - 1.71: 2 1.71 - 1.84: 140 Bond restraints: 13307 Sorted by residual: bond pdb=" C4 FUN A1301 " pdb=" N2 FUN A1301 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C4 FUN B1301 " pdb=" N2 FUN B1301 " ideal model delta sigma weight residual 1.340 1.447 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C7 FUN B1301 " pdb=" C8 FUN B1301 " ideal model delta sigma weight residual 1.429 1.359 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C7 FUN A1301 " pdb=" C8 FUN A1301 " ideal model delta sigma weight residual 1.429 1.360 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N1 FUN A1301 " pdb=" S1 FUN A1301 " ideal model delta sigma weight residual 1.647 1.708 -0.061 2.00e-02 2.50e+03 9.17e+00 ... (remaining 13302 not shown) Histogram of bond angle deviations from ideal: 97.01 - 104.42: 192 104.42 - 111.83: 6526 111.83 - 119.24: 4427 119.24 - 126.65: 6702 126.65 - 134.06: 204 Bond angle restraints: 18051 Sorted by residual: angle pdb=" O1 FUN A1301 " pdb=" S1 FUN A1301 " pdb=" O2 FUN A1301 " ideal model delta sigma weight residual 119.17 101.23 17.94 3.00e+00 1.11e-01 3.58e+01 angle pdb=" O1 FUN B1301 " pdb=" S1 FUN B1301 " pdb=" O2 FUN B1301 " ideal model delta sigma weight residual 119.17 101.25 17.92 3.00e+00 1.11e-01 3.57e+01 angle pdb=" C SER A 760 " pdb=" N SER A 761 " pdb=" CA SER A 761 " ideal model delta sigma weight residual 121.54 128.19 -6.65 1.91e+00 2.74e-01 1.21e+01 angle pdb=" CA MET A 851 " pdb=" CB MET A 851 " pdb=" CG MET A 851 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" N ILE A1081 " pdb=" CA ILE A1081 " pdb=" C ILE A1081 " ideal model delta sigma weight residual 112.29 109.37 2.92 9.40e-01 1.13e+00 9.62e+00 ... (remaining 18046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 7113 17.84 - 35.67: 630 35.67 - 53.51: 92 53.51 - 71.35: 15 71.35 - 89.19: 7 Dihedral angle restraints: 7857 sinusoidal: 3072 harmonic: 4785 Sorted by residual: dihedral pdb=" CB CYS B 563 " pdb=" SG CYS B 563 " pdb=" SG CYS B 568 " pdb=" CB CYS B 568 " ideal model delta sinusoidal sigma weight residual -86.00 -154.94 68.94 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CA ASN B 571 " pdb=" C ASN B 571 " pdb=" N PHE B 572 " pdb=" CA PHE B 572 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA A 505 " pdb=" C ALA A 505 " pdb=" N ASN A 506 " pdb=" CA ASN A 506 " ideal model delta harmonic sigma weight residual 180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 7854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1666 0.054 - 0.108: 366 0.108 - 0.162: 45 0.162 - 0.216: 3 0.216 - 0.270: 1 Chirality restraints: 2081 Sorted by residual: chirality pdb=" CA GLN A 914 " pdb=" N GLN A 914 " pdb=" C GLN A 914 " pdb=" CB GLN A 914 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE A 747 " pdb=" CA ILE A 747 " pdb=" CG1 ILE A 747 " pdb=" CG2 ILE A 747 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA ASP A 755 " pdb=" N ASP A 755 " pdb=" C ASP A 755 " pdb=" CB ASP A 755 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2078 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 461 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 462 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 462 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 462 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 495 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 496 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 496 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 496 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 655 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C TYR B 655 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR B 655 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 656 " -0.012 2.00e-02 2.50e+03 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 291 2.70 - 3.25: 14472 3.25 - 3.80: 21463 3.80 - 4.35: 26523 4.35 - 4.90: 43422 Nonbonded interactions: 106171 Sorted by model distance: nonbonded pdb=" OG SER A 701 " pdb=" OD1 ASN A 769 " model vdw 2.145 2.440 nonbonded pdb=" ND2 ASN A 298 " pdb=" O GLY A 500 " model vdw 2.172 2.520 nonbonded pdb=" NH1 ARG A1151 " pdb=" OE2 GLU A1154 " model vdw 2.180 2.520 nonbonded pdb=" OD2 ASP B1032 " pdb=" OG1 THR B1036 " model vdw 2.191 2.440 nonbonded pdb=" OD2 ASP B1025 " pdb=" OG SER B1160 " model vdw 2.216 2.440 ... (remaining 106166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 287 through 1208 or resid 1301)) selection = (chain 'B' and (resid 287 through 1208 or resid 1301)) } 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: 3.550 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: 13.760 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.440 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.004 0.111 13307 Z= 0.290 Angle : 0.732 17.940 18051 Z= 0.367 Chirality : 0.044 0.270 2081 Planarity : 0.005 0.066 2240 Dihedral : 13.509 89.187 4772 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.07 % Allowed : 0.36 % Favored : 99.57 % 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: -0.26 (0.20), residues: 1651 helix: 1.11 (0.16), residues: 950 sheet: -1.10 (0.48), residues: 122 loop : -2.17 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1028 HIS 0.005 0.001 HIS B 908 PHE 0.023 0.002 PHE A 907 TYR 0.024 0.002 TYR B 751 ARG 0.005 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 322 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: A 321 VAL cc_start: 0.9374 (t) cc_final: 0.9078 (p) REVERT: A 326 MET cc_start: 0.7532 (tpp) cc_final: 0.7026 (tpp) REVERT: A 847 ILE cc_start: 0.8664 (pt) cc_final: 0.8420 (mm) REVERT: B 577 CYS cc_start: 0.5990 (m) cc_final: 0.5394 (m) REVERT: B 694 PHE cc_start: 0.8948 (t80) cc_final: 0.8682 (t80) REVERT: B 713 MET cc_start: 0.8171 (ppp) cc_final: 0.7683 (ppp) REVERT: B 825 MET cc_start: 0.8883 (mpp) cc_final: 0.8229 (mpp) REVERT: B 1101 ILE cc_start: 0.8138 (mt) cc_final: 0.7540 (mm) outliers start: 1 outliers final: 0 residues processed: 323 average time/residue: 0.1965 time to fit residues: 98.7023 Evaluate side-chains 263 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13307 Z= 0.281 Angle : 0.655 8.975 18051 Z= 0.333 Chirality : 0.044 0.172 2081 Planarity : 0.004 0.065 2240 Dihedral : 6.191 86.515 1777 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.51 % Allowed : 11.60 % Favored : 85.89 % 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: -0.25 (0.20), residues: 1651 helix: 1.13 (0.16), residues: 973 sheet: -1.12 (0.48), residues: 123 loop : -2.33 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1028 HIS 0.006 0.001 HIS B 908 PHE 0.030 0.002 PHE B 659 TYR 0.027 0.002 TYR A 711 ARG 0.007 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 286 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.8278 (mtt) cc_final: 0.8049 (mtt) REVERT: A 326 MET cc_start: 0.7534 (tpp) cc_final: 0.7234 (tpp) REVERT: A 847 ILE cc_start: 0.8719 (pt) cc_final: 0.8476 (mm) REVERT: A 878 ARG cc_start: 0.7528 (mmt180) cc_final: 0.7283 (mmt180) REVERT: A 1041 TYR cc_start: 0.8393 (t80) cc_final: 0.8048 (t80) REVERT: B 577 CYS cc_start: 0.5407 (m) cc_final: 0.4808 (m) REVERT: B 694 PHE cc_start: 0.9083 (t80) cc_final: 0.8522 (t80) REVERT: B 713 MET cc_start: 0.7898 (ppp) cc_final: 0.7326 (ppp) REVERT: B 1065 ILE cc_start: 0.8286 (mm) cc_final: 0.8058 (mm) REVERT: B 1101 ILE cc_start: 0.8200 (mt) cc_final: 0.7623 (mm) outliers start: 35 outliers final: 19 residues processed: 296 average time/residue: 0.2014 time to fit residues: 93.7132 Evaluate side-chains 278 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 259 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1158 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 51 optimal weight: 0.0370 chunk 120 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13307 Z= 0.201 Angle : 0.614 13.169 18051 Z= 0.308 Chirality : 0.042 0.172 2081 Planarity : 0.004 0.063 2240 Dihedral : 6.126 87.416 1777 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.79 % Allowed : 15.54 % Favored : 81.66 % 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: -0.09 (0.20), residues: 1651 helix: 1.31 (0.16), residues: 956 sheet: -1.01 (0.47), residues: 122 loop : -2.27 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.004 0.001 HIS A1114 PHE 0.048 0.002 PHE B 659 TYR 0.024 0.001 TYR A 739 ARG 0.005 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 290 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8324 (mtt) cc_final: 0.8093 (mtt) REVERT: A 326 MET cc_start: 0.7515 (tpp) cc_final: 0.7210 (tpp) REVERT: A 847 ILE cc_start: 0.8701 (pt) cc_final: 0.8476 (mm) REVERT: A 878 ARG cc_start: 0.7617 (mmt180) cc_final: 0.7300 (mmt180) REVERT: B 547 ASP cc_start: 0.8547 (m-30) cc_final: 0.8193 (t0) REVERT: B 577 CYS cc_start: 0.5420 (m) cc_final: 0.4038 (m) REVERT: B 694 PHE cc_start: 0.8995 (t80) cc_final: 0.8520 (t80) REVERT: B 713 MET cc_start: 0.7775 (ppp) cc_final: 0.7149 (ppp) REVERT: B 818 MET cc_start: 0.7855 (ttm) cc_final: 0.7513 (ttm) REVERT: B 1065 ILE cc_start: 0.8290 (mm) cc_final: 0.8063 (mm) outliers start: 39 outliers final: 23 residues processed: 305 average time/residue: 0.2034 time to fit residues: 96.4080 Evaluate side-chains 286 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 263 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13307 Z= 0.225 Angle : 0.617 9.606 18051 Z= 0.311 Chirality : 0.043 0.192 2081 Planarity : 0.004 0.064 2240 Dihedral : 6.062 88.591 1777 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.72 % Allowed : 17.62 % Favored : 78.65 % 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: -0.11 (0.20), residues: 1651 helix: 1.27 (0.16), residues: 959 sheet: -1.06 (0.47), residues: 123 loop : -2.25 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1028 HIS 0.004 0.001 HIS B 809 PHE 0.046 0.002 PHE B 659 TYR 0.020 0.001 TYR B 751 ARG 0.004 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 277 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8433 (mtt) cc_final: 0.8197 (mtt) REVERT: A 326 MET cc_start: 0.7544 (tpp) cc_final: 0.7010 (tpp) REVERT: A 608 PHE cc_start: 0.7955 (m-80) cc_final: 0.7595 (m-80) REVERT: A 748 TYR cc_start: 0.8182 (t80) cc_final: 0.7846 (t80) REVERT: A 847 ILE cc_start: 0.8701 (pt) cc_final: 0.8483 (mm) REVERT: B 694 PHE cc_start: 0.8990 (t80) cc_final: 0.8570 (t80) REVERT: B 713 MET cc_start: 0.7850 (ppp) cc_final: 0.7286 (ppp) REVERT: B 818 MET cc_start: 0.7884 (ttm) cc_final: 0.7550 (ttm) REVERT: B 1043 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9185 (mm) REVERT: B 1065 ILE cc_start: 0.8321 (mm) cc_final: 0.8095 (mm) REVERT: B 1101 ILE cc_start: 0.8283 (mt) cc_final: 0.8003 (mm) outliers start: 52 outliers final: 27 residues processed: 302 average time/residue: 0.2014 time to fit residues: 94.0207 Evaluate side-chains 279 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 251 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13307 Z= 0.234 Angle : 0.634 9.637 18051 Z= 0.318 Chirality : 0.043 0.179 2081 Planarity : 0.004 0.064 2240 Dihedral : 6.061 89.988 1777 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.72 % Allowed : 19.27 % Favored : 77.01 % 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: -0.09 (0.21), residues: 1651 helix: 1.24 (0.17), residues: 963 sheet: -1.01 (0.48), residues: 121 loop : -2.17 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1028 HIS 0.004 0.001 HIS A1114 PHE 0.078 0.002 PHE B 659 TYR 0.020 0.001 TYR B 751 ARG 0.003 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 271 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8484 (mtt) cc_final: 0.8253 (mtt) REVERT: A 326 MET cc_start: 0.7435 (tpp) cc_final: 0.6977 (tpp) REVERT: A 435 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6038 (tm-30) REVERT: A 748 TYR cc_start: 0.8199 (t80) cc_final: 0.7828 (t80) REVERT: A 847 ILE cc_start: 0.8692 (pt) cc_final: 0.8487 (mm) REVERT: B 577 CYS cc_start: 0.6370 (m) cc_final: 0.5870 (m) REVERT: B 772 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: B 835 MET cc_start: 0.9272 (mmm) cc_final: 0.8684 (mmm) REVERT: B 1065 ILE cc_start: 0.8293 (mm) cc_final: 0.8058 (mm) REVERT: B 1101 ILE cc_start: 0.8294 (mt) cc_final: 0.7958 (mm) outliers start: 52 outliers final: 35 residues processed: 298 average time/residue: 0.2009 time to fit residues: 92.2398 Evaluate side-chains 294 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 257 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 chunk 39 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13307 Z= 0.213 Angle : 0.634 9.882 18051 Z= 0.315 Chirality : 0.042 0.173 2081 Planarity : 0.004 0.064 2240 Dihedral : 6.013 88.845 1777 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 3.80 % Allowed : 20.85 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1651 helix: 1.27 (0.17), residues: 964 sheet: -1.00 (0.48), residues: 121 loop : -2.22 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.076 0.002 PHE B 659 TYR 0.021 0.001 TYR B 751 ARG 0.003 0.000 ARG B 844 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 272 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8482 (mtt) cc_final: 0.8251 (mtt) REVERT: A 326 MET cc_start: 0.7454 (tpp) cc_final: 0.6974 (tpp) REVERT: A 435 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6061 (tm-30) REVERT: A 748 TYR cc_start: 0.8163 (t80) cc_final: 0.7817 (t80) REVERT: A 847 ILE cc_start: 0.8673 (pt) cc_final: 0.8459 (mm) REVERT: B 577 CYS cc_start: 0.6382 (m) cc_final: 0.5893 (m) REVERT: B 772 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: B 776 ARG cc_start: 0.8387 (mtp85) cc_final: 0.8143 (mtp85) REVERT: B 835 MET cc_start: 0.9295 (mmm) cc_final: 0.8804 (mmm) REVERT: B 1043 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9180 (mm) REVERT: B 1065 ILE cc_start: 0.8257 (mm) cc_final: 0.8026 (mm) REVERT: B 1101 ILE cc_start: 0.8252 (mt) cc_final: 0.7925 (mm) outliers start: 53 outliers final: 35 residues processed: 298 average time/residue: 0.1959 time to fit residues: 90.1621 Evaluate side-chains 298 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 260 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 116 optimal weight: 0.2980 chunk 134 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 99 optimal weight: 0.0570 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13307 Z= 0.186 Angle : 0.634 10.546 18051 Z= 0.312 Chirality : 0.042 0.171 2081 Planarity : 0.004 0.063 2240 Dihedral : 5.943 87.670 1777 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 3.44 % Allowed : 21.70 % Favored : 74.86 % 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: -0.06 (0.21), residues: 1651 helix: 1.31 (0.17), residues: 956 sheet: -0.85 (0.49), residues: 121 loop : -2.25 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 892 HIS 0.003 0.001 HIS B 908 PHE 0.073 0.002 PHE B 659 TYR 0.022 0.001 TYR B 751 ARG 0.003 0.000 ARG B 844 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 289 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8460 (mtt) cc_final: 0.8232 (mtt) REVERT: A 326 MET cc_start: 0.7443 (tpp) cc_final: 0.6955 (tpp) REVERT: A 748 TYR cc_start: 0.8122 (t80) cc_final: 0.7787 (t80) REVERT: B 523 LEU cc_start: 0.8760 (mt) cc_final: 0.8424 (mt) REVERT: B 577 CYS cc_start: 0.6223 (m) cc_final: 0.5731 (m) REVERT: B 713 MET cc_start: 0.7806 (ppp) cc_final: 0.7032 (ppp) REVERT: B 772 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: B 835 MET cc_start: 0.9299 (mmm) cc_final: 0.8807 (mmm) REVERT: B 1043 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9172 (mm) REVERT: B 1065 ILE cc_start: 0.8242 (mm) cc_final: 0.8027 (mm) REVERT: B 1101 ILE cc_start: 0.8211 (mt) cc_final: 0.7877 (mm) REVERT: B 1184 MET cc_start: 0.6933 (tmm) cc_final: 0.6546 (tmm) outliers start: 48 outliers final: 29 residues processed: 313 average time/residue: 0.1969 time to fit residues: 94.9461 Evaluate side-chains 299 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 ASN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13307 Z= 0.278 Angle : 0.694 11.429 18051 Z= 0.343 Chirality : 0.044 0.184 2081 Planarity : 0.004 0.062 2240 Dihedral : 5.980 86.426 1777 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.44 % Allowed : 23.28 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.21), residues: 1651 helix: 1.22 (0.17), residues: 958 sheet: -1.02 (0.48), residues: 120 loop : -2.23 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A 892 HIS 0.004 0.001 HIS B 908 PHE 0.074 0.002 PHE B 659 TYR 0.028 0.002 TYR A 739 ARG 0.006 0.000 ARG A 878 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 262 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.7476 (tpp) cc_final: 0.7014 (tpp) REVERT: A 748 TYR cc_start: 0.8240 (t80) cc_final: 0.7881 (t80) REVERT: A 902 MET cc_start: 0.8746 (tpp) cc_final: 0.7996 (tpp) REVERT: B 523 LEU cc_start: 0.8781 (mt) cc_final: 0.8451 (mt) REVERT: B 577 CYS cc_start: 0.6432 (m) cc_final: 0.5968 (m) REVERT: B 772 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8474 (tm-30) REVERT: B 776 ARG cc_start: 0.8410 (mtp85) cc_final: 0.7957 (mtp85) REVERT: B 835 MET cc_start: 0.9306 (mmm) cc_final: 0.8807 (mmm) REVERT: B 1043 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9197 (mm) REVERT: B 1065 ILE cc_start: 0.8297 (mm) cc_final: 0.8069 (mm) REVERT: B 1101 ILE cc_start: 0.8328 (mt) cc_final: 0.7947 (mm) outliers start: 48 outliers final: 32 residues processed: 291 average time/residue: 0.1977 time to fit residues: 89.7639 Evaluate side-chains 290 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 256 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 0.0980 chunk 116 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 ASN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13307 Z= 0.210 Angle : 0.694 11.046 18051 Z= 0.339 Chirality : 0.044 0.219 2081 Planarity : 0.004 0.058 2240 Dihedral : 5.924 85.003 1777 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.08 % Allowed : 24.07 % Favored : 72.85 % 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: -0.13 (0.21), residues: 1651 helix: 1.26 (0.17), residues: 958 sheet: -0.94 (0.48), residues: 120 loop : -2.28 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP A 892 HIS 0.003 0.001 HIS B 908 PHE 0.068 0.002 PHE B 659 TYR 0.042 0.002 TYR A 354 ARG 0.005 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 274 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.7426 (tpp) cc_final: 0.7053 (tpp) REVERT: A 748 TYR cc_start: 0.8224 (t80) cc_final: 0.7886 (t80) REVERT: A 902 MET cc_start: 0.8718 (tpp) cc_final: 0.8134 (tpp) REVERT: B 523 LEU cc_start: 0.8729 (mt) cc_final: 0.8398 (mt) REVERT: B 577 CYS cc_start: 0.6272 (m) cc_final: 0.5803 (m) REVERT: B 772 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8433 (tm-30) REVERT: B 776 ARG cc_start: 0.8343 (mtp85) cc_final: 0.7876 (mtp85) REVERT: B 835 MET cc_start: 0.9233 (mmm) cc_final: 0.8786 (mmm) REVERT: B 1043 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9179 (mm) REVERT: B 1065 ILE cc_start: 0.8272 (mm) cc_final: 0.8040 (mm) REVERT: B 1101 ILE cc_start: 0.8249 (mt) cc_final: 0.7907 (mm) REVERT: B 1184 MET cc_start: 0.6864 (tmm) cc_final: 0.6572 (tmm) outliers start: 43 outliers final: 35 residues processed: 297 average time/residue: 0.1990 time to fit residues: 90.9951 Evaluate side-chains 301 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 264 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 633 ASN Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 151 optimal weight: 0.0030 chunk 130 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 103 optimal weight: 0.7980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13307 Z= 0.203 Angle : 0.709 11.016 18051 Z= 0.344 Chirality : 0.044 0.204 2081 Planarity : 0.005 0.064 2240 Dihedral : 5.875 83.830 1777 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.79 % Allowed : 24.36 % Favored : 72.85 % 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: -0.12 (0.21), residues: 1651 helix: 1.26 (0.17), residues: 961 sheet: -0.90 (0.48), residues: 121 loop : -2.30 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 892 HIS 0.003 0.001 HIS B 908 PHE 0.068 0.002 PHE B 659 TYR 0.046 0.002 TYR A 354 ARG 0.003 0.000 ARG B 844 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 269 time to evaluate : 1.898 Fit side-chains revert: symmetry clash REVERT: A 713 MET cc_start: 0.7722 (pmm) cc_final: 0.7427 (pmm) REVERT: A 748 TYR cc_start: 0.8220 (t80) cc_final: 0.7896 (t80) REVERT: A 757 ASN cc_start: 0.5470 (OUTLIER) cc_final: 0.4730 (p0) REVERT: A 902 MET cc_start: 0.8694 (tpp) cc_final: 0.8100 (tpp) REVERT: B 523 LEU cc_start: 0.8664 (mt) cc_final: 0.8359 (mt) REVERT: B 577 CYS cc_start: 0.6227 (m) cc_final: 0.5749 (m) REVERT: B 772 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: B 776 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7865 (mtp85) REVERT: B 835 MET cc_start: 0.9228 (mmm) cc_final: 0.8801 (mmm) REVERT: B 1043 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9173 (mm) REVERT: B 1065 ILE cc_start: 0.8265 (mm) cc_final: 0.8025 (mm) REVERT: B 1101 ILE cc_start: 0.8231 (mt) cc_final: 0.7885 (mm) outliers start: 39 outliers final: 29 residues processed: 290 average time/residue: 0.2014 time to fit residues: 91.4072 Evaluate side-chains 298 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 633 ASN Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 0.0170 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 131 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.136789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112330 restraints weight = 28363.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.115876 restraints weight = 19623.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.117018 restraints weight = 13274.758| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 13307 Z= 0.257 Angle : 0.933 59.197 18051 Z= 0.516 Chirality : 0.043 0.238 2081 Planarity : 0.005 0.061 2240 Dihedral : 5.889 83.821 1777 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.65 % Allowed : 24.64 % Favored : 72.71 % Cbeta Deviations : 0.07 % 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: -0.12 (0.21), residues: 1651 helix: 1.26 (0.17), residues: 961 sheet: -0.90 (0.48), residues: 121 loop : -2.31 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 892 HIS 0.003 0.001 HIS B 908 PHE 0.068 0.002 PHE B 659 TYR 0.041 0.001 TYR A 354 ARG 0.003 0.000 ARG A 878 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.54 seconds wall clock time: 51 minutes 0.61 seconds (3060.61 seconds total)