Starting phenix.real_space_refine on Sat Mar 16 01:15:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/03_2024/8om9_16971_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/03_2024/8om9_16971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/03_2024/8om9_16971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/03_2024/8om9_16971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/03_2024/8om9_16971_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/03_2024/8om9_16971_updated.pdb" } resolution = 3.32 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= 0.021 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 8317 2.51 5 N 2286 2.21 5 O 2599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "B GLU 976": "OE1" <-> "OE2" 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: 13314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5783 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 22, 'TRANS': 709} Chain breaks: 7 Chain: "B" Number of atoms: 6566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6566 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 25, 'TRANS': 790} Chain breaks: 6 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 499 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.68, per 1000 atoms: 0.50 Number of scatterers: 13314 At special positions: 0 Unit cell: (95.0768, 170.041, 134.387, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 48 15.00 Mg 2 11.99 O 2599 8.00 N 2286 7.00 C 8317 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.59 Conformation dependent library (CDL) restraints added in 2.1 seconds 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 12 sheets defined 49.4% alpha, 8.4% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 6.09 Creating SS restraints... Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.641A pdb=" N GLN A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.593A pdb=" N SER A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 326 through 330 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 401 through 412 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 437 through 455 removed outlier: 4.704A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 4.120A pdb=" N ASN A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 502 Processing helix chain 'A' and resid 527 through 535 removed outlier: 4.683A pdb=" N ARG A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASN A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 614 removed outlier: 3.780A pdb=" N ASN A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'A' and resid 640 through 643 No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 724 through 738 Processing helix chain 'A' and resid 756 through 772 Processing helix chain 'A' and resid 786 through 793 Processing helix chain 'A' and resid 829 through 832 Processing helix chain 'A' and resid 838 through 851 Processing helix chain 'A' and resid 877 through 893 Processing helix chain 'A' and resid 901 through 918 removed outlier: 3.881A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.907A pdb=" N GLN B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 removed outlier: 4.148A pdb=" N LEU B 270 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 412 through 421 Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 497 through 513 removed outlier: 3.606A pdb=" N PHE B 513 " --> pdb=" O TYR B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'B' and resid 587 through 602 Processing helix chain 'B' and resid 609 through 615 Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 635 through 662 Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 668 through 687 Proline residue: B 676 - end of helix Proline residue: B 681 - end of helix removed outlier: 4.823A pdb=" N HIS B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 695 Processing helix chain 'B' and resid 710 through 736 Processing helix chain 'B' and resid 758 through 761 No H-bonds generated for 'chain 'B' and resid 758 through 761' Processing helix chain 'B' and resid 783 through 842 removed outlier: 3.574A pdb=" N GLU B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 Processing helix chain 'B' and resid 902 through 917 Processing helix chain 'B' and resid 952 through 963 Processing helix chain 'B' and resid 983 through 999 Processing helix chain 'B' and resid 1012 through 1021 removed outlier: 3.775A pdb=" N LEU B1017 " --> pdb=" O PRO B1013 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU B1018 " --> pdb=" O VAL B1014 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYS B1019 " --> pdb=" O CYS B1015 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1075 Processing helix chain 'B' and resid 1080 through 1111 Processing helix chain 'B' and resid 1116 through 1122 Processing sheet with id= A, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.977A pdb=" N GLU A 198 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 223 " --> pdb=" O CYS A 199 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU A 201 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 225 " --> pdb=" O LEU A 201 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 173 through 175 Processing sheet with id= C, first strand: chain 'A' and resid 512 through 516 Processing sheet with id= D, first strand: chain 'A' and resid 623 through 625 Processing sheet with id= E, first strand: chain 'A' and resid 778 through 781 removed outlier: 4.593A pdb=" N GLN A 816 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.163A pdb=" N LEU A 744 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ARG A 711 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 746 " --> pdb=" O ARG A 711 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 246 through 250 removed outlier: 6.580A pdb=" N LYS B 303 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS B 249 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY B 305 " --> pdb=" O CYS B 249 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 255 through 259 Processing sheet with id= I, first strand: chain 'B' and resid 368 through 371 removed outlier: 6.875A pdb=" N GLU B 425 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE B 371 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 427 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG B 454 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU B 428 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B 456 " --> pdb=" O LEU B 428 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 386 through 392 Processing sheet with id= K, first strand: chain 'B' and resid 882 through 884 removed outlier: 3.643A pdb=" N VAL B 858 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1059 through 1061 removed outlier: 6.519A pdb=" N VAL B 891 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR B1028 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 893 " --> pdb=" O TYR B1028 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N MET B1030 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 895 " --> pdb=" O MET B1030 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR B1005 " --> pdb=" O MET B 892 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE B 894 " --> pdb=" O THR B1005 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE B1007 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY B 934 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE B 973 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 5.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2681 1.33 - 1.46: 4196 1.46 - 1.58: 6562 1.58 - 1.71: 91 1.71 - 1.83: 99 Bond restraints: 13629 Sorted by residual: bond pdb=" C LEU A 414 " pdb=" N PRO A 415 " ideal model delta sigma weight residual 1.331 1.385 -0.054 7.90e-03 1.60e+04 4.64e+01 bond pdb=" C4 ADP A2000 " pdb=" C5 ADP A2000 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP B2000 " pdb=" C5 ADP B2000 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" N PRO A 415 " pdb=" CA PRO A 415 " ideal model delta sigma weight residual 1.470 1.417 0.053 1.01e-02 9.80e+03 2.77e+01 bond pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.03e+01 ... (remaining 13624 not shown) Histogram of bond angle deviations from ideal: 67.52 - 82.19: 3 82.19 - 96.86: 1 96.86 - 111.53: 5423 111.53 - 126.20: 12902 126.20 - 140.87: 249 Bond angle restraints: 18578 Sorted by residual: angle pdb=" C PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 110.00 140.87 -30.87 1.12e+00 7.97e-01 7.60e+02 angle pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 102.17 75.57 26.60 1.05e+00 9.07e-01 6.42e+02 angle pdb=" N PRO A 415 " pdb=" CD PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 103.20 74.69 28.51 1.50e+00 4.44e-01 3.61e+02 angle pdb=" CB PRO A 415 " pdb=" CG PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 106.10 67.52 38.58 3.20e+00 9.77e-02 1.45e+02 angle pdb=" C LEU A 414 " pdb=" N PRO A 415 " pdb=" CA PRO A 415 " ideal model delta sigma weight residual 121.00 109.91 11.09 1.16e+00 7.43e-01 9.14e+01 ... (remaining 18573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 7694 33.71 - 67.43: 476 67.43 - 101.14: 15 101.14 - 134.85: 2 134.85 - 168.56: 1 Dihedral angle restraints: 8188 sinusoidal: 3661 harmonic: 4527 Sorted by residual: dihedral pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta harmonic sigma weight residual 115.10 86.80 28.30 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" C PRO A 415 " pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta harmonic sigma weight residual -120.70 -139.41 18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" O1B ADP B2000 " pdb=" O3A ADP B2000 " pdb=" PB ADP B2000 " pdb=" PA ADP B2000 " ideal model delta sinusoidal sigma weight residual 300.00 131.43 168.56 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1966 0.146 - 0.293: 162 0.293 - 0.439: 4 0.439 - 0.585: 0 0.585 - 0.731: 1 Chirality restraints: 2133 Sorted by residual: chirality pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CB PRO A 415 " both_signs ideal model delta sigma weight residual False 2.72 1.99 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA LEU A 414 " pdb=" N LEU A 414 " pdb=" C LEU A 414 " pdb=" CB LEU A 414 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C3' DG C 36 " pdb=" C4' DG C 36 " pdb=" O3' DG C 36 " pdb=" C2' DG C 36 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 2130 not shown) Planarity restraints: 2201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 415 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PRO A 415 " 0.071 2.00e-02 2.50e+03 pdb=" O PRO A 415 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 416 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 414 " -0.039 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO A 415 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B2000 " -0.029 2.00e-02 2.50e+03 1.30e-02 4.62e+00 pdb=" C2 ADP B2000 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ADP B2000 " 0.006 2.00e-02 2.50e+03 pdb=" C5 ADP B2000 " -0.004 2.00e-02 2.50e+03 pdb=" C6 ADP B2000 " -0.006 2.00e-02 2.50e+03 pdb=" C8 ADP B2000 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ADP B2000 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ADP B2000 " -0.001 2.00e-02 2.50e+03 pdb=" N6 ADP B2000 " -0.008 2.00e-02 2.50e+03 pdb=" N7 ADP B2000 " -0.003 2.00e-02 2.50e+03 pdb=" N9 ADP B2000 " 0.022 2.00e-02 2.50e+03 ... (remaining 2198 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 191 2.60 - 3.18: 11994 3.18 - 3.75: 23270 3.75 - 4.33: 31826 4.33 - 4.90: 48478 Nonbonded interactions: 115759 Sorted by model distance: nonbonded pdb=" O3B ADP A2000 " pdb="MG MG A2001 " model vdw 2.025 2.170 nonbonded pdb=" OH TYR A 757 " pdb=" CD1 ILE B1097 " model vdw 2.056 3.460 nonbonded pdb=" O2B ADP B2000 " pdb="MG MG B2001 " model vdw 2.073 2.170 nonbonded pdb=" OG SER B 903 " pdb=" OD2 ASP B 975 " model vdw 2.079 2.440 nonbonded pdb=" O HIS A 785 " pdb=" OG1 THR A 788 " model vdw 2.118 2.440 ... (remaining 115754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 7.350 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 40.780 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.008 0.188 13629 Z= 0.493 Angle : 1.286 38.579 18578 Z= 0.843 Chirality : 0.088 0.731 2133 Planarity : 0.005 0.057 2201 Dihedral : 18.878 168.563 5240 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 25.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.76 % Allowed : 22.53 % Favored : 74.71 % Cbeta Deviations : 0.20 % 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: -1.44 (0.21), residues: 1518 helix: 0.15 (0.18), residues: 766 sheet: -2.38 (0.36), residues: 172 loop : -1.92 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP A 764 HIS 0.011 0.003 HIS A 829 PHE 0.027 0.004 PHE B 784 TYR 0.027 0.004 TYR B1021 ARG 0.013 0.002 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 271 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLN cc_start: 0.6585 (mp10) cc_final: 0.6260 (mp10) REVERT: A 347 LYS cc_start: 0.8169 (pttp) cc_final: 0.7923 (pttp) REVERT: A 364 GLU cc_start: 0.7710 (tp30) cc_final: 0.7506 (tp30) REVERT: A 429 GLN cc_start: 0.7845 (mt0) cc_final: 0.7541 (mt0) REVERT: A 480 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 482 ARG cc_start: 0.8699 (tpm170) cc_final: 0.8484 (tpm170) REVERT: A 626 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8085 (mp0) REVERT: A 647 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7987 (tm-30) REVERT: A 817 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8266 (p) REVERT: A 818 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7361 (mttp) REVERT: A 846 GLN cc_start: 0.7773 (mt0) cc_final: 0.7514 (mm110) REVERT: A 850 GLU cc_start: 0.7825 (mp0) cc_final: 0.7509 (mp0) REVERT: B 434 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8543 (pm20) REVERT: B 526 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7777 (mmmm) REVERT: B 626 CYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8539 (t) REVERT: B 860 LYS cc_start: 0.8413 (mttt) cc_final: 0.8185 (mmmt) REVERT: B 883 ASP cc_start: 0.7686 (t0) cc_final: 0.7395 (t0) REVERT: B 1015 CYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7145 (t) REVERT: B 1085 LYS cc_start: 0.8252 (tttt) cc_final: 0.8014 (tttt) REVERT: B 1091 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7994 (mmmm) outliers start: 38 outliers final: 16 residues processed: 298 average time/residue: 0.2857 time to fit residues: 118.9319 Evaluate side-chains 279 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 260 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13629 Z= 0.241 Angle : 0.617 7.003 18578 Z= 0.322 Chirality : 0.041 0.164 2133 Planarity : 0.004 0.048 2201 Dihedral : 17.983 174.312 2176 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.36 % Allowed : 22.17 % Favored : 73.47 % 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: -1.08 (0.22), residues: 1518 helix: 0.48 (0.19), residues: 775 sheet: -2.25 (0.36), residues: 181 loop : -1.80 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.008 0.001 HIS B 984 PHE 0.020 0.002 PHE A 468 TYR 0.017 0.002 TYR B 846 ARG 0.005 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 270 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ILE cc_start: 0.6353 (OUTLIER) cc_final: 0.5944 (mp) REVERT: A 347 LYS cc_start: 0.8061 (pttp) cc_final: 0.7785 (pttp) REVERT: A 364 GLU cc_start: 0.7690 (tp30) cc_final: 0.7411 (tp30) REVERT: A 429 GLN cc_start: 0.7812 (mt0) cc_final: 0.7607 (mt0) REVERT: A 480 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7992 (mm-30) REVERT: A 482 ARG cc_start: 0.8689 (tpm170) cc_final: 0.8417 (tpm170) REVERT: A 626 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7946 (mp0) REVERT: A 647 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7899 (tm-30) REVERT: A 728 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6365 (pm20) REVERT: A 846 GLN cc_start: 0.7705 (mt0) cc_final: 0.7369 (mm-40) REVERT: A 850 GLU cc_start: 0.8141 (mp0) cc_final: 0.7932 (mp0) REVERT: B 407 ASP cc_start: 0.7756 (m-30) cc_final: 0.7546 (m-30) REVERT: B 434 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8458 (pm20) REVERT: B 526 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7777 (mmmm) REVERT: B 626 CYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8332 (t) REVERT: B 630 HIS cc_start: 0.7356 (m90) cc_final: 0.7056 (m90) REVERT: B 636 GLN cc_start: 0.8595 (tp40) cc_final: 0.8329 (tp40) REVERT: B 692 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8332 (tp40) REVERT: B 732 GLU cc_start: 0.8194 (mp0) cc_final: 0.7881 (tm-30) REVERT: B 860 LYS cc_start: 0.8435 (mttt) cc_final: 0.8146 (mmmt) REVERT: B 902 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7159 (mtpm) REVERT: B 938 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6531 (tpm-80) REVERT: B 1030 MET cc_start: 0.4409 (mmm) cc_final: 0.3997 (mmm) REVERT: B 1085 LYS cc_start: 0.8233 (tttt) cc_final: 0.7967 (tttt) REVERT: B 1091 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7833 (mmmm) REVERT: B 1093 LEU cc_start: 0.7689 (tp) cc_final: 0.7334 (tp) REVERT: B 1094 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7773 (mt-10) outliers start: 60 outliers final: 30 residues processed: 306 average time/residue: 0.2822 time to fit residues: 120.2751 Evaluate side-chains 298 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 263 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1071 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 119 optimal weight: 0.0010 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN B 544 ASN B 729 HIS ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13629 Z= 0.252 Angle : 0.602 6.768 18578 Z= 0.315 Chirality : 0.041 0.196 2133 Planarity : 0.004 0.055 2201 Dihedral : 17.909 169.322 2157 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.94 % Allowed : 22.38 % Favored : 72.67 % 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: -0.91 (0.22), residues: 1518 helix: 0.57 (0.19), residues: 763 sheet: -2.02 (0.38), residues: 179 loop : -1.67 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.006 0.001 HIS B 817 PHE 0.018 0.002 PHE A 468 TYR 0.021 0.002 TYR B1011 ARG 0.006 0.001 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 270 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ILE cc_start: 0.6354 (OUTLIER) cc_final: 0.6131 (mp) REVERT: A 452 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8028 (pt0) REVERT: A 480 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8051 (mm-30) REVERT: A 647 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7909 (tm-30) REVERT: A 685 ILE cc_start: 0.8675 (mm) cc_final: 0.8101 (tt) REVERT: A 698 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8005 (tm-30) REVERT: A 784 PHE cc_start: 0.7482 (m-80) cc_final: 0.7169 (m-80) REVERT: A 817 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8169 (p) REVERT: A 838 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8369 (mmmm) REVERT: A 849 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7476 (mp) REVERT: A 850 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7930 (mp0) REVERT: B 367 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7568 (t80) REVERT: B 383 LYS cc_start: 0.8234 (tppt) cc_final: 0.7865 (mptt) REVERT: B 434 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8470 (pm20) REVERT: B 457 ARG cc_start: 0.8418 (mmt90) cc_final: 0.8184 (mmm160) REVERT: B 526 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7782 (mmmm) REVERT: B 580 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7006 (t) REVERT: B 626 CYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8297 (t) REVERT: B 630 HIS cc_start: 0.7444 (m90) cc_final: 0.7134 (m90) REVERT: B 636 GLN cc_start: 0.8605 (tp40) cc_final: 0.8251 (tp-100) REVERT: B 713 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7784 (mmtt) REVERT: B 729 HIS cc_start: 0.8155 (t-90) cc_final: 0.7846 (t-90) REVERT: B 732 GLU cc_start: 0.8319 (mp0) cc_final: 0.7878 (tm-30) REVERT: B 812 GLU cc_start: 0.7829 (tp30) cc_final: 0.7351 (tp30) REVERT: B 860 LYS cc_start: 0.8465 (mttt) cc_final: 0.8191 (mmtm) REVERT: B 902 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7143 (mtpm) REVERT: B 1030 MET cc_start: 0.4590 (mmm) cc_final: 0.4128 (mmm) REVERT: B 1085 LYS cc_start: 0.8258 (tttt) cc_final: 0.8025 (tttt) outliers start: 68 outliers final: 40 residues processed: 312 average time/residue: 0.2792 time to fit residues: 121.8646 Evaluate side-chains 315 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 268 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1071 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13629 Z= 0.252 Angle : 0.612 11.298 18578 Z= 0.317 Chirality : 0.042 0.284 2133 Planarity : 0.004 0.059 2201 Dihedral : 17.864 165.151 2155 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 6.18 % Allowed : 21.44 % Favored : 72.38 % 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: -0.92 (0.22), residues: 1518 helix: 0.53 (0.19), residues: 767 sheet: -1.97 (0.39), residues: 177 loop : -1.66 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 764 HIS 0.007 0.001 HIS B 729 PHE 0.016 0.002 PHE A 836 TYR 0.022 0.002 TYR B1011 ARG 0.011 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 268 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8014 (pt0) REVERT: A 480 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8117 (mm-30) REVERT: A 482 ARG cc_start: 0.8759 (tpm170) cc_final: 0.8417 (tpm170) REVERT: A 647 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7910 (tm-30) REVERT: A 685 ILE cc_start: 0.8676 (mm) cc_final: 0.8113 (tt) REVERT: A 698 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 784 PHE cc_start: 0.7468 (m-80) cc_final: 0.7005 (m-80) REVERT: A 817 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8158 (p) REVERT: A 838 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8270 (mmtp) REVERT: A 850 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7826 (mp0) REVERT: B 290 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6183 (pp) REVERT: B 367 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7620 (t80) REVERT: B 434 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8451 (pm20) REVERT: B 457 ARG cc_start: 0.8404 (mmt90) cc_final: 0.7431 (mmt90) REVERT: B 526 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7796 (mmmm) REVERT: B 580 VAL cc_start: 0.7353 (OUTLIER) cc_final: 0.7021 (t) REVERT: B 626 CYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8274 (t) REVERT: B 630 HIS cc_start: 0.7439 (m90) cc_final: 0.7087 (m90) REVERT: B 713 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7840 (mmtt) REVERT: B 714 LYS cc_start: 0.8982 (ttpt) cc_final: 0.8763 (tmmt) REVERT: B 729 HIS cc_start: 0.8150 (t-90) cc_final: 0.7874 (t-90) REVERT: B 732 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: B 812 GLU cc_start: 0.7855 (tp30) cc_final: 0.7386 (tp30) REVERT: B 860 LYS cc_start: 0.8475 (mttt) cc_final: 0.8187 (mmmt) REVERT: B 902 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7099 (mtpm) REVERT: B 1085 LYS cc_start: 0.8248 (tttt) cc_final: 0.8024 (tttt) REVERT: B 1093 LEU cc_start: 0.7688 (tp) cc_final: 0.7311 (tp) outliers start: 85 outliers final: 49 residues processed: 320 average time/residue: 0.2722 time to fit residues: 123.1774 Evaluate side-chains 326 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 270 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 105 optimal weight: 0.0050 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13629 Z= 0.229 Angle : 0.613 9.639 18578 Z= 0.316 Chirality : 0.041 0.181 2133 Planarity : 0.004 0.061 2201 Dihedral : 17.741 156.972 2155 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 6.25 % Allowed : 22.75 % Favored : 71.00 % 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: -0.86 (0.22), residues: 1518 helix: 0.62 (0.19), residues: 758 sheet: -2.03 (0.38), residues: 183 loop : -1.61 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 764 HIS 0.007 0.001 HIS A 829 PHE 0.023 0.002 PHE A 468 TYR 0.020 0.001 TYR B1011 ARG 0.010 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 264 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8325 (ptpt) cc_final: 0.7856 (pttp) REVERT: A 402 GLN cc_start: 0.8624 (mm110) cc_final: 0.8415 (mm-40) REVERT: A 452 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8000 (pt0) REVERT: A 647 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7891 (tm-30) REVERT: A 685 ILE cc_start: 0.8676 (mm) cc_final: 0.8201 (tt) REVERT: A 698 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 784 PHE cc_start: 0.7437 (m-80) cc_final: 0.7052 (m-80) REVERT: A 817 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8074 (p) REVERT: A 838 LYS cc_start: 0.8570 (mmmm) cc_final: 0.8220 (mmmm) REVERT: A 850 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7823 (mp0) REVERT: B 290 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6262 (pp) REVERT: B 367 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7586 (t80) REVERT: B 434 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8444 (pm20) REVERT: B 457 ARG cc_start: 0.8380 (mmt90) cc_final: 0.7392 (mmt90) REVERT: B 526 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7764 (mmmm) REVERT: B 580 VAL cc_start: 0.7368 (OUTLIER) cc_final: 0.7040 (t) REVERT: B 626 CYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8254 (t) REVERT: B 630 HIS cc_start: 0.7398 (m90) cc_final: 0.7008 (m90) REVERT: B 636 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8152 (tp40) REVERT: B 687 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7658 (mmtt) REVERT: B 713 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7756 (mmtt) REVERT: B 714 LYS cc_start: 0.8984 (ttpt) cc_final: 0.8763 (tmmt) REVERT: B 729 HIS cc_start: 0.8130 (t-90) cc_final: 0.7790 (t-90) REVERT: B 732 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: B 812 GLU cc_start: 0.7865 (tp30) cc_final: 0.7363 (tp30) REVERT: B 860 LYS cc_start: 0.8467 (mttt) cc_final: 0.8214 (mmtm) REVERT: B 902 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7051 (mtpm) REVERT: B 938 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6491 (tpm-80) REVERT: B 1030 MET cc_start: 0.4657 (mmm) cc_final: 0.4270 (mmm) REVERT: B 1094 GLU cc_start: 0.8145 (tt0) cc_final: 0.7869 (tt0) outliers start: 86 outliers final: 58 residues processed: 317 average time/residue: 0.2839 time to fit residues: 125.0919 Evaluate side-chains 327 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 260 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 750 GLN Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 30 optimal weight: 0.0270 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 126 optimal weight: 0.0670 chunk 70 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13629 Z= 0.203 Angle : 0.596 9.574 18578 Z= 0.308 Chirality : 0.040 0.180 2133 Planarity : 0.004 0.064 2201 Dihedral : 17.658 154.511 2155 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 6.10 % Allowed : 23.11 % Favored : 70.78 % 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: -0.80 (0.22), residues: 1518 helix: 0.63 (0.19), residues: 768 sheet: -1.93 (0.37), residues: 188 loop : -1.57 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 768 HIS 0.007 0.001 HIS A 829 PHE 0.020 0.001 PHE A 468 TYR 0.019 0.001 TYR A 678 ARG 0.008 0.000 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 257 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLN cc_start: 0.8600 (mm110) cc_final: 0.8388 (mm-40) REVERT: A 429 GLN cc_start: 0.7859 (mt0) cc_final: 0.7594 (mt0) REVERT: A 452 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7926 (pt0) REVERT: A 482 ARG cc_start: 0.8785 (tpm170) cc_final: 0.8400 (tpm170) REVERT: A 647 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7883 (tm-30) REVERT: A 685 ILE cc_start: 0.8673 (mm) cc_final: 0.8165 (tt) REVERT: A 698 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 784 PHE cc_start: 0.7398 (m-80) cc_final: 0.7030 (m-80) REVERT: A 817 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.7953 (p) REVERT: A 838 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8342 (mmtp) REVERT: A 850 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7838 (mp0) REVERT: B 290 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6292 (pp) REVERT: B 367 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7614 (t80) REVERT: B 383 LYS cc_start: 0.8164 (tppt) cc_final: 0.7774 (mptt) REVERT: B 434 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8354 (pm20) REVERT: B 457 ARG cc_start: 0.8415 (mmt90) cc_final: 0.7403 (mmt90) REVERT: B 526 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7761 (mmmm) REVERT: B 626 CYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8227 (t) REVERT: B 630 HIS cc_start: 0.7340 (m90) cc_final: 0.6972 (m90) REVERT: B 636 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8203 (tp40) REVERT: B 687 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7589 (mmtt) REVERT: B 713 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7701 (mmtt) REVERT: B 714 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8762 (tmmt) REVERT: B 729 HIS cc_start: 0.8126 (t-90) cc_final: 0.7785 (t-90) REVERT: B 732 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: B 812 GLU cc_start: 0.7835 (tp30) cc_final: 0.7327 (tp30) REVERT: B 848 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.6664 (ttt90) REVERT: B 859 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7317 (mt) REVERT: B 860 LYS cc_start: 0.8449 (mttt) cc_final: 0.8207 (mmtm) REVERT: B 902 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7180 (mtpm) REVERT: B 1030 MET cc_start: 0.4571 (mmm) cc_final: 0.4218 (mmm) REVERT: B 1094 GLU cc_start: 0.8138 (tt0) cc_final: 0.7859 (tt0) outliers start: 84 outliers final: 53 residues processed: 311 average time/residue: 0.2786 time to fit residues: 122.1611 Evaluate side-chains 322 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 260 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13629 Z= 0.233 Angle : 0.616 9.876 18578 Z= 0.317 Chirality : 0.041 0.163 2133 Planarity : 0.004 0.065 2201 Dihedral : 17.680 152.378 2155 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.45 % Allowed : 24.56 % Favored : 69.99 % 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: -0.86 (0.22), residues: 1518 helix: 0.59 (0.19), residues: 768 sheet: -1.95 (0.37), residues: 188 loop : -1.62 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 768 HIS 0.007 0.001 HIS B 781 PHE 0.018 0.002 PHE A 468 TYR 0.019 0.001 TYR B1011 ARG 0.010 0.000 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 263 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8345 (ptpt) cc_final: 0.7928 (pttp) REVERT: A 372 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8570 (pt) REVERT: A 402 GLN cc_start: 0.8575 (mm110) cc_final: 0.8352 (mm-40) REVERT: A 430 LYS cc_start: 0.8642 (ptpp) cc_final: 0.8369 (ptpp) REVERT: A 452 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7940 (pt0) REVERT: A 482 ARG cc_start: 0.8767 (tpm170) cc_final: 0.8409 (tpm170) REVERT: A 647 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7902 (tm-30) REVERT: A 685 ILE cc_start: 0.8668 (mm) cc_final: 0.8194 (tt) REVERT: A 698 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7841 (tm-30) REVERT: A 784 PHE cc_start: 0.7425 (m-80) cc_final: 0.7048 (m-80) REVERT: A 850 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7845 (mp0) REVERT: B 290 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6288 (pp) REVERT: B 367 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7621 (t80) REVERT: B 383 LYS cc_start: 0.8201 (tppt) cc_final: 0.7832 (mptt) REVERT: B 434 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8421 (pm20) REVERT: B 457 ARG cc_start: 0.8358 (mmt90) cc_final: 0.7394 (mmt90) REVERT: B 626 CYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8484 (t) REVERT: B 713 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7831 (mmtt) REVERT: B 729 HIS cc_start: 0.8125 (t-90) cc_final: 0.7781 (t-90) REVERT: B 732 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: B 812 GLU cc_start: 0.7835 (tp30) cc_final: 0.7342 (tp30) REVERT: B 848 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6646 (ttt90) REVERT: B 859 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7314 (mt) REVERT: B 860 LYS cc_start: 0.8462 (mttt) cc_final: 0.8176 (mmtm) REVERT: B 938 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6561 (tpm-80) REVERT: B 1094 GLU cc_start: 0.8156 (tt0) cc_final: 0.7907 (tt0) outliers start: 75 outliers final: 54 residues processed: 307 average time/residue: 0.3199 time to fit residues: 136.3270 Evaluate side-chains 316 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 254 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13629 Z= 0.232 Angle : 0.617 9.585 18578 Z= 0.319 Chirality : 0.041 0.164 2133 Planarity : 0.004 0.066 2201 Dihedral : 17.656 148.559 2155 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.60 % Allowed : 25.00 % Favored : 69.40 % 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: -0.79 (0.22), residues: 1518 helix: 0.65 (0.19), residues: 759 sheet: -1.81 (0.37), residues: 191 loop : -1.60 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 768 HIS 0.006 0.001 HIS B 729 PHE 0.016 0.002 PHE B 402 TYR 0.031 0.002 TYR A 678 ARG 0.010 0.000 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 254 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8564 (pt) REVERT: A 402 GLN cc_start: 0.8571 (mm110) cc_final: 0.8343 (mm-40) REVERT: A 452 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7928 (pt0) REVERT: A 482 ARG cc_start: 0.8754 (tpm170) cc_final: 0.8307 (tpm170) REVERT: A 647 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7905 (tm-30) REVERT: A 681 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: A 685 ILE cc_start: 0.8670 (mm) cc_final: 0.8206 (tt) REVERT: A 698 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 724 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.7001 (t) REVERT: A 784 PHE cc_start: 0.7434 (m-80) cc_final: 0.7056 (m-80) REVERT: A 838 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8336 (mmtp) REVERT: A 850 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7867 (mp0) REVERT: B 290 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6306 (pp) REVERT: B 367 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7639 (t80) REVERT: B 383 LYS cc_start: 0.8189 (tppt) cc_final: 0.7816 (mptt) REVERT: B 434 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8420 (pm20) REVERT: B 457 ARG cc_start: 0.8366 (mmt90) cc_final: 0.7412 (mmt90) REVERT: B 626 CYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8484 (t) REVERT: B 713 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7819 (mmtt) REVERT: B 729 HIS cc_start: 0.8124 (t-90) cc_final: 0.7761 (t-90) REVERT: B 732 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: B 812 GLU cc_start: 0.7873 (tp30) cc_final: 0.7373 (tp30) REVERT: B 848 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6649 (ttt90) REVERT: B 859 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7326 (mt) REVERT: B 938 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6570 (tpm-80) REVERT: B 1094 GLU cc_start: 0.8159 (tt0) cc_final: 0.7911 (tt0) outliers start: 77 outliers final: 56 residues processed: 300 average time/residue: 0.2994 time to fit residues: 124.6392 Evaluate side-chains 320 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 254 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.0070 chunk 133 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 150 optimal weight: 2.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13629 Z= 0.208 Angle : 0.612 9.752 18578 Z= 0.317 Chirality : 0.041 0.160 2133 Planarity : 0.005 0.066 2201 Dihedral : 17.606 142.126 2155 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.09 % Allowed : 25.58 % Favored : 69.33 % 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: -0.73 (0.22), residues: 1518 helix: 0.67 (0.19), residues: 764 sheet: -1.74 (0.37), residues: 191 loop : -1.56 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 768 HIS 0.007 0.001 HIS B 729 PHE 0.025 0.002 PHE A 286 TYR 0.015 0.001 TYR B1011 ARG 0.014 0.000 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 247 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5744 (mp) REVERT: A 347 LYS cc_start: 0.8329 (ptpt) cc_final: 0.7807 (pttp) REVERT: A 372 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8552 (pt) REVERT: A 402 GLN cc_start: 0.8567 (mm110) cc_final: 0.8325 (mm-40) REVERT: A 430 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8334 (ptpp) REVERT: A 452 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7919 (pt0) REVERT: A 482 ARG cc_start: 0.8733 (tpm170) cc_final: 0.8289 (tpm170) REVERT: A 647 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7917 (tm-30) REVERT: A 681 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6908 (tt0) REVERT: A 685 ILE cc_start: 0.8661 (mm) cc_final: 0.8205 (tt) REVERT: A 698 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 784 PHE cc_start: 0.7399 (m-80) cc_final: 0.7043 (m-80) REVERT: A 850 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7858 (mp0) REVERT: B 290 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6415 (pp) REVERT: B 367 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7645 (t80) REVERT: B 434 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8382 (pm20) REVERT: B 526 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7729 (mmmm) REVERT: B 626 CYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8472 (t) REVERT: B 729 HIS cc_start: 0.8149 (t-90) cc_final: 0.7870 (t-90) REVERT: B 732 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: B 812 GLU cc_start: 0.7816 (tp30) cc_final: 0.7330 (tp30) REVERT: B 848 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6662 (ttt90) REVERT: B 859 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7322 (mt) REVERT: B 902 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7251 (mtpm) REVERT: B 938 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6641 (tpm-80) REVERT: B 1094 GLU cc_start: 0.8131 (tt0) cc_final: 0.7881 (tt0) outliers start: 70 outliers final: 49 residues processed: 293 average time/residue: 0.2893 time to fit residues: 117.9683 Evaluate side-chains 298 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 238 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13629 Z= 0.284 Angle : 0.656 9.755 18578 Z= 0.340 Chirality : 0.042 0.170 2133 Planarity : 0.005 0.066 2201 Dihedral : 17.630 139.416 2153 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 5.23 % Allowed : 25.44 % Favored : 69.33 % 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: -0.90 (0.22), residues: 1518 helix: 0.53 (0.19), residues: 759 sheet: -1.86 (0.37), residues: 186 loop : -1.61 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 768 HIS 0.007 0.001 HIS B 864 PHE 0.018 0.002 PHE A 286 TYR 0.023 0.002 TYR B1011 ARG 0.015 0.001 ARG B 796 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 253 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8021 (tppt) REVERT: A 347 LYS cc_start: 0.8451 (ptpt) cc_final: 0.7966 (pttp) REVERT: A 372 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8527 (pt) REVERT: A 402 GLN cc_start: 0.8569 (mm110) cc_final: 0.8357 (mm-40) REVERT: A 430 LYS cc_start: 0.8697 (ptpp) cc_final: 0.8426 (ptpp) REVERT: A 452 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7968 (pt0) REVERT: A 647 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7913 (tm-30) REVERT: A 681 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: A 685 ILE cc_start: 0.8703 (mm) cc_final: 0.8254 (tt) REVERT: A 698 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7852 (tm-30) REVERT: A 784 PHE cc_start: 0.7469 (m-80) cc_final: 0.7088 (m-80) REVERT: A 850 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7876 (mp0) REVERT: B 290 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6329 (pp) REVERT: B 367 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7623 (t80) REVERT: B 434 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8449 (pm20) REVERT: B 457 ARG cc_start: 0.8409 (mmt90) cc_final: 0.7429 (mmt90) REVERT: B 526 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7759 (mmmm) REVERT: B 626 CYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8545 (t) REVERT: B 636 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8336 (tp40) REVERT: B 729 HIS cc_start: 0.8157 (t-90) cc_final: 0.7836 (t-90) REVERT: B 732 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: B 812 GLU cc_start: 0.7959 (tp30) cc_final: 0.7414 (tp30) REVERT: B 848 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6675 (ttt90) REVERT: B 860 LYS cc_start: 0.8495 (mttt) cc_final: 0.8237 (mmtm) REVERT: B 938 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6598 (tpm-80) outliers start: 72 outliers final: 54 residues processed: 298 average time/residue: 0.2879 time to fit residues: 119.6589 Evaluate side-chains 314 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 250 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 732 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 847 CYS Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 898 ASN Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1078 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 110 optimal weight: 0.0170 chunk 7 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 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 = 0.4639 r_free = 0.4639 target = 0.203462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.164925 restraints weight = 20691.688| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 3.12 r_work: 0.4045 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13629 Z= 0.204 Angle : 0.634 9.280 18578 Z= 0.325 Chirality : 0.042 0.506 2133 Planarity : 0.004 0.066 2201 Dihedral : 17.546 139.281 2153 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.43 % Allowed : 26.38 % Favored : 69.19 % 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: -0.78 (0.22), residues: 1518 helix: 0.61 (0.19), residues: 765 sheet: -1.77 (0.37), residues: 188 loop : -1.57 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 768 HIS 0.006 0.001 HIS B 729 PHE 0.026 0.002 PHE A 760 TYR 0.016 0.001 TYR B1011 ARG 0.009 0.000 ARG B 796 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.99 seconds wall clock time: 64 minutes 21.72 seconds (3861.72 seconds total)