Starting phenix.real_space_refine on Fri Mar 15 23:53:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/03_2024/8om5_16969_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/03_2024/8om5_16969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/03_2024/8om5_16969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/03_2024/8om5_16969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/03_2024/8om5_16969_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om5_16969/03_2024/8om5_16969_updated.pdb" } resolution = 3.52 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= 0.025 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 4 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 8366 2.51 5 N 2239 2.21 5 O 2465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 786": "OE1" <-> "OE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 589": "OE1" <-> "OE2" Residue "B GLU 683": "OE1" <-> "OE2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B GLU 886": "OE1" <-> "OE2" Residue "B GLU 995": "OE1" <-> "OE2" Residue "B GLU 1081": "OE1" <-> "OE2" Residue "B GLU 1094": "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: 13138 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6551 Classifications: {'peptide': 828} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 802} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 6531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6531 Classifications: {'peptide': 812} Link IDs: {'PTRANS': 26, 'TRANS': 785} Chain breaks: 9 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: 6.60, per 1000 atoms: 0.50 Number of scatterers: 13138 At special positions: 0 Unit cell: (94.1626, 162.728, 119.76, 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 4 15.00 Mg 2 11.99 O 2465 8.00 N 2239 7.00 C 8366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS B 274 " distance=2.50 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: 5.09 Conformation dependent library (CDL) restraints added in 2.4 seconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 11 sheets defined 47.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 208 through 220 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 243 removed outlier: 4.326A pdb=" N ARG A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.867A 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 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 371 through 378 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 401 through 420 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 430 through 456 removed outlier: 5.015A pdb=" N VAL A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Proline residue: A 439 - end of helix removed outlier: 4.628A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 503 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.660A pdb=" N GLU A 530 " --> pdb=" O CYS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 587 removed outlier: 5.410A pdb=" N ALA A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 613 Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 724 through 737 Processing helix chain 'A' and resid 756 through 772 Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 828 through 831 No H-bonds generated for 'chain 'A' and resid 828 through 831' Processing helix chain 'A' and resid 840 through 851 Processing helix chain 'A' and resid 876 through 890 Processing helix chain 'A' and resid 909 through 918 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 434 through 445 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 468 through 475 Processing helix chain 'B' and resid 492 through 494 No H-bonds generated for 'chain 'B' and resid 492 through 494' Processing helix chain 'B' and resid 497 through 513 removed outlier: 4.396A pdb=" N GLU B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE B 513 " --> pdb=" O TYR B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 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 601 Processing helix chain 'B' and resid 607 through 615 Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 635 through 661 Proline residue: B 657 - end of helix removed outlier: 5.001A pdb=" N SER B 661 " --> pdb=" O PRO B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 678 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 681 through 688 removed outlier: 3.598A pdb=" N ILE B 688 " --> pdb=" O HIS B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 696 No H-bonds generated for 'chain 'B' and resid 694 through 696' Processing helix chain 'B' and resid 710 through 736 Processing helix chain 'B' and resid 783 through 816 Processing helix chain 'B' and resid 818 through 842 Processing helix chain 'B' and resid 865 through 870 removed outlier: 3.879A pdb=" N VAL B 869 " --> pdb=" O PRO B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 918 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 1020 removed outlier: 3.896A pdb=" N LEU B1017 " --> pdb=" O PRO B1013 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU B1018 " --> pdb=" O VAL B1014 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS B1019 " --> pdb=" O CYS B1015 " (cutoff:3.500A) removed outlier: 4.566A 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 1124 Processing sheet with id= A, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.865A pdb=" N HIS A 46 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG A 35 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG A 99 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU A 36 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU A 101 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASP A 38 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TYR A 103 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.845A pdb=" N GLU A 198 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 223 " --> pdb=" O CYS A 199 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU A 201 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 225 " --> pdb=" O LEU A 201 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 172 through 174 removed outlier: 6.061A pdb=" N GLU A 290 " --> pdb=" O LEU A 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 512 through 516 removed outlier: 3.794A pdb=" N LYS A 512 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 623 through 625 Processing sheet with id= F, first strand: chain 'A' and resid 817 through 819 removed outlier: 5.838A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 802 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A 668 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N CYS A 778 " --> pdb=" O HIS A 665 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE A 667 " --> pdb=" O CYS A 778 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE A 780 " --> pdb=" O ILE A 667 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 368 through 370 removed outlier: 5.955A pdb=" N GLU B 425 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG B 454 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 428 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B 456 " --> pdb=" O LEU B 428 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 386 through 390 Processing sheet with id= I, first strand: chain 'B' and resid 754 through 757 removed outlier: 3.569A pdb=" N ILE B 754 " --> pdb=" O PHE B 780 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS B 781 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS B 770 " --> pdb=" O HIS B 781 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 856 through 859 Processing sheet with id= K, first strand: chain 'B' and resid 1056 through 1061 removed outlier: 3.600A pdb=" N LEU B1056 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B1031 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLN B1058 " --> pdb=" O HIS B1029 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N HIS B1029 " --> pdb=" O GLN B1058 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR B1060 " --> pdb=" O ASN B1027 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASN B1027 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 891 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TYR B1028 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE B 893 " --> pdb=" O TYR B1028 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N MET B1030 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR B 895 " --> pdb=" O MET B1030 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR B1005 " --> pdb=" O MET B 892 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE B 894 " --> pdb=" O THR B1005 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE B1007 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY B 934 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE B 973 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3907 1.34 - 1.46: 3260 1.46 - 1.58: 6088 1.58 - 1.70: 5 1.70 - 1.82: 100 Bond restraints: 13360 Sorted by residual: bond pdb=" C4 ADP B1201 " pdb=" C5 ADP B1201 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C4 ADP A2000 " pdb=" C5 ADP A2000 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C5 ADP A2000 " pdb=" C6 ADP A2000 " ideal model delta sigma weight residual 1.490 1.419 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C5 ADP B1201 " pdb=" C6 ADP B1201 " ideal model delta sigma weight residual 1.490 1.422 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" CE1 HIS A 801 " pdb=" NE2 HIS A 801 " ideal model delta sigma weight residual 1.321 1.347 -0.026 1.00e-02 1.00e+04 6.52e+00 ... (remaining 13355 not shown) Histogram of bond angle deviations from ideal: 96.22 - 103.88: 147 103.88 - 111.54: 5019 111.54 - 119.20: 6008 119.20 - 126.85: 6759 126.85 - 134.51: 88 Bond angle restraints: 18021 Sorted by residual: angle pdb=" C HIS B 817 " pdb=" N TYR B 818 " pdb=" CA TYR B 818 " ideal model delta sigma weight residual 120.28 126.60 -6.32 1.44e+00 4.82e-01 1.93e+01 angle pdb=" CA ASP A 446 " pdb=" CB ASP A 446 " pdb=" CG ASP A 446 " ideal model delta sigma weight residual 112.60 116.76 -4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" CB GLU B 496 " pdb=" CG GLU B 496 " pdb=" CD GLU B 496 " ideal model delta sigma weight residual 112.60 119.45 -6.85 1.70e+00 3.46e-01 1.62e+01 angle pdb=" N ILE B 656 " pdb=" CA ILE B 656 " pdb=" CB ILE B 656 " ideal model delta sigma weight residual 110.52 113.18 -2.66 6.70e-01 2.23e+00 1.58e+01 angle pdb=" CB GLU B 415 " pdb=" CG GLU B 415 " pdb=" CD GLU B 415 " ideal model delta sigma weight residual 112.60 119.25 -6.65 1.70e+00 3.46e-01 1.53e+01 ... (remaining 18016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 7802 33.06 - 66.12: 303 66.12 - 99.17: 34 99.17 - 132.23: 2 132.23 - 165.29: 1 Dihedral angle restraints: 8142 sinusoidal: 3355 harmonic: 4787 Sorted by residual: dihedral pdb=" C5' ADP B1201 " pdb=" O5' ADP B1201 " pdb=" PA ADP B1201 " pdb=" O2A ADP B1201 " ideal model delta sinusoidal sigma weight residual -60.00 105.29 -165.29 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O2A ADP B1201 " pdb=" O3A ADP B1201 " pdb=" PA ADP B1201 " pdb=" PB ADP B1201 " ideal model delta sinusoidal sigma weight residual -60.00 71.59 -131.59 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O1B ADP B1201 " pdb=" O3A ADP B1201 " pdb=" PB ADP B1201 " pdb=" PA ADP B1201 " ideal model delta sinusoidal sigma weight residual -60.00 -166.12 106.12 1 2.00e+01 2.50e-03 3.07e+01 ... (remaining 8139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1403 0.077 - 0.154: 577 0.154 - 0.230: 72 0.230 - 0.307: 8 0.307 - 0.384: 3 Chirality restraints: 2063 Sorted by residual: chirality pdb=" CA LEU A 833 " pdb=" N LEU A 833 " pdb=" C LEU A 833 " pdb=" CB LEU A 833 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CG LEU B 828 " pdb=" CB LEU B 828 " pdb=" CD1 LEU B 828 " pdb=" CD2 LEU B 828 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CG LEU B 811 " pdb=" CB LEU B 811 " pdb=" CD1 LEU B 811 " pdb=" CD2 LEU B 811 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 2060 not shown) Planarity restraints: 2286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 815 " 0.021 2.00e-02 2.50e+03 1.54e-02 4.74e+00 pdb=" CG TYR A 815 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 815 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 815 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 815 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 815 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 815 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 815 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1068 " 0.026 2.00e-02 2.50e+03 1.45e-02 4.18e+00 pdb=" CG TYR B1068 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B1068 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B1068 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B1068 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B1068 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B1068 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B1068 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 818 " 0.024 2.00e-02 2.50e+03 1.43e-02 4.10e+00 pdb=" CG TYR B 818 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 818 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 818 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 818 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 818 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 818 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR B 818 " 0.003 2.00e-02 2.50e+03 ... (remaining 2283 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 150 2.56 - 3.14: 11373 3.14 - 3.73: 22195 3.73 - 4.31: 29872 4.31 - 4.90: 46715 Nonbonded interactions: 110305 Sorted by model distance: nonbonded pdb=" O2B ADP B1201 " pdb="MG MG B1202 " model vdw 1.974 2.170 nonbonded pdb=" O3B ADP A2000 " pdb="MG MG A2001 " model vdw 1.996 2.170 nonbonded pdb=" OG SER B 903 " pdb="MG MG B1202 " model vdw 2.011 2.170 nonbonded pdb=" OG SER A 676 " pdb="MG MG A2001 " model vdw 2.022 2.170 nonbonded pdb=" OE2 GLU A 749 " pdb="MG MG A2001 " model vdw 2.113 2.170 ... (remaining 110300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 7.210 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 37.010 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.007 0.105 13360 Z= 0.454 Angle : 1.077 8.802 18021 Z= 0.665 Chirality : 0.078 0.384 2063 Planarity : 0.004 0.047 2286 Dihedral : 17.612 165.291 5025 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer: Outliers : 1.93 % Allowed : 24.72 % Favored : 73.34 % Cbeta Deviations : 0.06 % 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: -1.45 (0.21), residues: 1602 helix: 0.12 (0.18), residues: 783 sheet: -2.07 (0.38), residues: 162 loop : -1.96 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 807 HIS 0.015 0.003 HIS B 614 PHE 0.015 0.003 PHE B 402 TYR 0.037 0.004 TYR A 815 ARG 0.010 0.001 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 404 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8738 (t) cc_final: 0.8520 (p) REVERT: A 198 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 245 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7784 (mp) REVERT: A 261 MET cc_start: 0.7552 (mmp) cc_final: 0.7338 (mmp) REVERT: A 274 ILE cc_start: 0.8501 (mm) cc_final: 0.8272 (mt) REVERT: A 275 LYS cc_start: 0.8902 (tppt) cc_final: 0.8588 (mmmm) REVERT: A 298 GLN cc_start: 0.8948 (tt0) cc_final: 0.8520 (tm-30) REVERT: A 359 ARG cc_start: 0.8150 (mtt90) cc_final: 0.6830 (mtt180) REVERT: A 396 ARG cc_start: 0.8745 (ptp90) cc_final: 0.8395 (ptp90) REVERT: A 460 MET cc_start: 0.8416 (mmt) cc_final: 0.8170 (mmt) REVERT: A 483 GLU cc_start: 0.8442 (tp30) cc_final: 0.8196 (mt-10) REVERT: A 562 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8786 (tp30) REVERT: A 569 GLU cc_start: 0.8755 (tt0) cc_final: 0.8279 (tp30) REVERT: A 579 LYS cc_start: 0.9042 (mttt) cc_final: 0.8687 (mmmm) REVERT: A 621 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8333 (ttt-90) REVERT: A 681 GLN cc_start: 0.8273 (tt0) cc_final: 0.8041 (tt0) REVERT: A 688 MET cc_start: 0.8742 (mtt) cc_final: 0.8493 (mtp) REVERT: A 728 GLU cc_start: 0.8006 (tp30) cc_final: 0.7757 (tp30) REVERT: A 838 LYS cc_start: 0.8693 (mttt) cc_final: 0.8402 (mmmm) REVERT: B 235 GLN cc_start: 0.8617 (tp40) cc_final: 0.8362 (tp40) REVERT: B 296 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8556 (tmm-80) REVERT: B 375 LYS cc_start: 0.9215 (mttt) cc_final: 0.8998 (mtpp) REVERT: B 476 TYR cc_start: 0.8278 (m-10) cc_final: 0.8076 (m-10) REVERT: B 577 LYS cc_start: 0.8816 (tttt) cc_final: 0.8594 (tppp) REVERT: B 674 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 906 ILE cc_start: 0.8996 (pt) cc_final: 0.8679 (tt) REVERT: B 1070 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8576 (mp) REVERT: B 1081 GLU cc_start: 0.8717 (pm20) cc_final: 0.8320 (pm20) REVERT: B 1084 LYS cc_start: 0.8829 (mttt) cc_final: 0.8452 (mmmm) outliers start: 28 outliers final: 19 residues processed: 416 average time/residue: 0.2999 time to fit residues: 170.1330 Evaluate side-chains 400 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 379 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 883 ASP Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1070 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 HIS A 839 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13360 Z= 0.307 Angle : 0.692 11.897 18021 Z= 0.349 Chirality : 0.044 0.216 2063 Planarity : 0.004 0.047 2286 Dihedral : 8.355 172.563 1810 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.38 % Allowed : 25.14 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1602 helix: 0.29 (0.18), residues: 796 sheet: -2.06 (0.38), residues: 173 loop : -1.73 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.020 0.002 PHE B 463 TYR 0.019 0.002 TYR A 815 ARG 0.008 0.001 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 399 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8641 (t) cc_final: 0.8377 (p) REVERT: A 192 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7897 (mp) REVERT: A 198 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 245 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 261 MET cc_start: 0.7450 (mmp) cc_final: 0.7072 (mmp) REVERT: A 369 ASP cc_start: 0.8471 (t0) cc_final: 0.8187 (t0) REVERT: A 386 ASP cc_start: 0.8676 (t0) cc_final: 0.8454 (t0) REVERT: A 389 ARG cc_start: 0.9095 (tpp80) cc_final: 0.8856 (tpp80) REVERT: A 395 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8854 (mm-40) REVERT: A 452 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7998 (mt-10) REVERT: A 460 MET cc_start: 0.8442 (mmt) cc_final: 0.8214 (mmt) REVERT: A 482 ARG cc_start: 0.8765 (mmm160) cc_final: 0.8492 (mmm-85) REVERT: A 561 GLU cc_start: 0.8737 (tp30) cc_final: 0.8359 (mm-30) REVERT: A 562 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8865 (tp30) REVERT: A 569 GLU cc_start: 0.8755 (tt0) cc_final: 0.8276 (tp30) REVERT: A 579 LYS cc_start: 0.9030 (mttt) cc_final: 0.8650 (mmmm) REVERT: A 593 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8808 (mt0) REVERT: A 603 ASP cc_start: 0.8309 (t0) cc_final: 0.8077 (t0) REVERT: A 643 GLU cc_start: 0.8805 (tt0) cc_final: 0.8292 (pt0) REVERT: A 688 MET cc_start: 0.8723 (mtt) cc_final: 0.8521 (mtp) REVERT: A 778 CYS cc_start: 0.8584 (t) cc_final: 0.8237 (t) REVERT: A 790 LEU cc_start: 0.8824 (tp) cc_final: 0.8578 (tp) REVERT: A 838 LYS cc_start: 0.8634 (mttt) cc_final: 0.8305 (mmmm) REVERT: A 850 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: B 307 VAL cc_start: 0.8685 (t) cc_final: 0.8359 (p) REVERT: B 375 LYS cc_start: 0.9218 (mttt) cc_final: 0.9007 (mtpp) REVERT: B 577 LYS cc_start: 0.8870 (tttt) cc_final: 0.8617 (ttmm) REVERT: B 674 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 843 GLN cc_start: 0.8616 (pt0) cc_final: 0.8199 (pt0) REVERT: B 853 GLU cc_start: 0.8870 (tt0) cc_final: 0.8664 (pm20) REVERT: B 1084 LYS cc_start: 0.8795 (mttt) cc_final: 0.8384 (mmmm) REVERT: B 1091 LYS cc_start: 0.8184 (mttt) cc_final: 0.7953 (mtpp) outliers start: 49 outliers final: 27 residues processed: 430 average time/residue: 0.2898 time to fit residues: 173.0373 Evaluate side-chains 403 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 373 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 0.0270 chunk 40 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 GLN B 917 GLN ** B 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13360 Z= 0.198 Angle : 0.646 12.384 18021 Z= 0.321 Chirality : 0.042 0.167 2063 Planarity : 0.004 0.052 2286 Dihedral : 7.230 154.273 1773 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.76 % Rotamer: Outliers : 3.87 % Allowed : 25.55 % Favored : 70.58 % 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: -0.93 (0.22), residues: 1602 helix: 0.54 (0.18), residues: 795 sheet: -2.10 (0.36), residues: 179 loop : -1.61 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 807 HIS 0.007 0.001 HIS B 729 PHE 0.022 0.001 PHE B 638 TYR 0.021 0.002 TYR B 236 ARG 0.008 0.000 ARG B 938 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 386 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8631 (t) cc_final: 0.8338 (p) REVERT: A 198 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 226 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 261 MET cc_start: 0.7481 (mmp) cc_final: 0.7074 (mmp) REVERT: A 275 LYS cc_start: 0.8894 (tppt) cc_final: 0.8581 (mmmm) REVERT: A 299 TYR cc_start: 0.8484 (m-80) cc_final: 0.8175 (m-80) REVERT: A 369 ASP cc_start: 0.8511 (t0) cc_final: 0.8208 (t0) REVERT: A 386 ASP cc_start: 0.8709 (t0) cc_final: 0.8412 (t0) REVERT: A 389 ARG cc_start: 0.9074 (tpp80) cc_final: 0.8774 (tpp80) REVERT: A 452 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7944 (mt-10) REVERT: A 562 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8817 (tp30) REVERT: A 569 GLU cc_start: 0.8721 (tt0) cc_final: 0.8216 (tp30) REVERT: A 579 LYS cc_start: 0.8996 (mttt) cc_final: 0.8617 (mmmm) REVERT: A 593 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8797 (mt0) REVERT: A 701 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7906 (mt-10) REVERT: A 728 GLU cc_start: 0.7891 (tp30) cc_final: 0.7514 (tp30) REVERT: A 729 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8074 (mpp) REVERT: A 742 ASP cc_start: 0.7882 (t0) cc_final: 0.7640 (t0) REVERT: A 809 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8579 (mp0) REVERT: A 838 LYS cc_start: 0.8462 (mttt) cc_final: 0.8177 (mmmm) REVERT: B 296 ARG cc_start: 0.9066 (mmm-85) cc_final: 0.8808 (mmm160) REVERT: B 297 LEU cc_start: 0.8729 (mm) cc_final: 0.8489 (mp) REVERT: B 307 VAL cc_start: 0.8695 (t) cc_final: 0.8343 (p) REVERT: B 425 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7518 (mt-10) REVERT: B 508 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8329 (tttt) REVERT: B 544 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8330 (t0) REVERT: B 577 LYS cc_start: 0.8846 (tttt) cc_final: 0.8550 (ttmm) REVERT: B 653 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8134 (tm-30) REVERT: B 669 ARG cc_start: 0.8710 (tpp80) cc_final: 0.8489 (tpp80) REVERT: B 674 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 853 GLU cc_start: 0.8856 (tt0) cc_final: 0.8650 (pm20) REVERT: B 1018 GLU cc_start: 0.8771 (pp20) cc_final: 0.8564 (pp20) REVERT: B 1084 LYS cc_start: 0.8722 (mttt) cc_final: 0.8321 (mmmm) REVERT: B 1091 LYS cc_start: 0.8191 (mttt) cc_final: 0.7948 (mtpp) outliers start: 56 outliers final: 26 residues processed: 421 average time/residue: 0.2864 time to fit residues: 166.5496 Evaluate side-chains 399 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 370 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 77 optimal weight: 0.0010 chunk 141 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 overall best weight: 0.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13360 Z= 0.198 Angle : 0.648 12.823 18021 Z= 0.318 Chirality : 0.042 0.171 2063 Planarity : 0.004 0.047 2286 Dihedral : 6.657 138.685 1771 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 3.73 % Allowed : 26.73 % Favored : 69.54 % 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: 1602 helix: 0.66 (0.19), residues: 784 sheet: -1.99 (0.37), residues: 178 loop : -1.55 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 807 HIS 0.007 0.001 HIS B 729 PHE 0.017 0.001 PHE A 551 TYR 0.021 0.002 TYR A 619 ARG 0.008 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 382 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8615 (t) cc_final: 0.8316 (p) REVERT: A 192 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 198 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7385 (mm-30) REVERT: A 226 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8055 (mm-30) REVERT: A 245 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7547 (tp) REVERT: A 260 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: A 275 LYS cc_start: 0.8906 (tppt) cc_final: 0.8599 (mmmm) REVERT: A 345 TRP cc_start: 0.8529 (m-10) cc_final: 0.7995 (m-10) REVERT: A 369 ASP cc_start: 0.8500 (t0) cc_final: 0.8205 (t0) REVERT: A 382 ARG cc_start: 0.8919 (ptt90) cc_final: 0.8553 (ttp80) REVERT: A 386 ASP cc_start: 0.8753 (t0) cc_final: 0.8398 (t0) REVERT: A 389 ARG cc_start: 0.9077 (tpp80) cc_final: 0.8707 (tpp80) REVERT: A 482 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8453 (mmm-85) REVERT: A 562 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8836 (tp30) REVERT: A 569 GLU cc_start: 0.8686 (tt0) cc_final: 0.8177 (tp30) REVERT: A 579 LYS cc_start: 0.8997 (mttt) cc_final: 0.8502 (mmmm) REVERT: A 593 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8794 (mt0) REVERT: A 603 ASP cc_start: 0.8248 (t0) cc_final: 0.7979 (t0) REVERT: A 701 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7872 (mt-10) REVERT: A 728 GLU cc_start: 0.7962 (tp30) cc_final: 0.7694 (tp30) REVERT: A 729 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8064 (mpp) REVERT: A 742 ASP cc_start: 0.7993 (t0) cc_final: 0.7663 (t0) REVERT: A 809 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8637 (mp0) REVERT: A 838 LYS cc_start: 0.8476 (mttt) cc_final: 0.8186 (mmmm) REVERT: A 850 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: B 269 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: B 296 ARG cc_start: 0.9064 (mmm-85) cc_final: 0.8716 (mmm160) REVERT: B 297 LEU cc_start: 0.8734 (mm) cc_final: 0.8488 (mp) REVERT: B 307 VAL cc_start: 0.8685 (t) cc_final: 0.8357 (p) REVERT: B 425 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B 476 TYR cc_start: 0.8249 (m-10) cc_final: 0.7988 (m-10) REVERT: B 508 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8353 (tttm) REVERT: B 544 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8339 (t0) REVERT: B 577 LYS cc_start: 0.8853 (tttt) cc_final: 0.8579 (ttmm) REVERT: B 653 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 669 ARG cc_start: 0.8665 (tpp80) cc_final: 0.8430 (tpp80) REVERT: B 674 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 683 GLU cc_start: 0.7298 (tp30) cc_final: 0.6938 (tp30) REVERT: B 698 ASP cc_start: 0.8622 (t0) cc_final: 0.8353 (t0) REVERT: B 823 LYS cc_start: 0.8637 (tptm) cc_final: 0.8282 (tptp) REVERT: B 853 GLU cc_start: 0.8864 (tt0) cc_final: 0.8643 (pm20) REVERT: B 926 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8024 (tm-30) REVERT: B 953 MET cc_start: 0.8577 (mmm) cc_final: 0.8341 (mmm) REVERT: B 1018 GLU cc_start: 0.8772 (pp20) cc_final: 0.8520 (pp20) REVERT: B 1084 LYS cc_start: 0.8720 (mttt) cc_final: 0.8341 (mmmm) REVERT: B 1091 LYS cc_start: 0.8193 (mttt) cc_final: 0.7953 (mtpp) outliers start: 54 outliers final: 31 residues processed: 417 average time/residue: 0.2804 time to fit residues: 162.5158 Evaluate side-chains 410 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 371 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 117 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13360 Z= 0.195 Angle : 0.637 12.719 18021 Z= 0.311 Chirality : 0.042 0.225 2063 Planarity : 0.004 0.062 2286 Dihedral : 6.166 124.808 1771 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.38 % Rotamer: Outliers : 4.14 % Allowed : 26.73 % Favored : 69.13 % 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: -0.71 (0.22), residues: 1602 helix: 0.72 (0.19), residues: 784 sheet: -1.89 (0.37), residues: 178 loop : -1.50 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 807 HIS 0.009 0.001 HIS B 817 PHE 0.017 0.001 PHE A 551 TYR 0.023 0.001 TYR A 678 ARG 0.004 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 392 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8592 (t) cc_final: 0.8283 (p) REVERT: A 192 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7920 (mp) REVERT: A 198 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7301 (mm-30) REVERT: A 245 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7495 (tp) REVERT: A 261 MET cc_start: 0.7532 (mmp) cc_final: 0.7066 (mmp) REVERT: A 345 TRP cc_start: 0.8509 (m-10) cc_final: 0.7798 (m-10) REVERT: A 359 ARG cc_start: 0.8146 (mtt90) cc_final: 0.6943 (ttm170) REVERT: A 369 ASP cc_start: 0.8472 (t0) cc_final: 0.8184 (t0) REVERT: A 377 GLN cc_start: 0.8138 (tp-100) cc_final: 0.7928 (tp40) REVERT: A 386 ASP cc_start: 0.8778 (t0) cc_final: 0.8380 (t0) REVERT: A 389 ARG cc_start: 0.9083 (tpp80) cc_final: 0.8681 (tpp80) REVERT: A 449 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8721 (mmmm) REVERT: A 452 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7879 (mt-10) REVERT: A 569 GLU cc_start: 0.8673 (tt0) cc_final: 0.8153 (tm-30) REVERT: A 579 LYS cc_start: 0.8986 (mttt) cc_final: 0.8504 (mmmm) REVERT: A 593 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8793 (mt0) REVERT: A 603 ASP cc_start: 0.8233 (t0) cc_final: 0.7904 (t0) REVERT: A 621 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8350 (ttt-90) REVERT: A 728 GLU cc_start: 0.7968 (tp30) cc_final: 0.7692 (tp30) REVERT: A 729 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8021 (mpp) REVERT: A 737 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8430 (mtm-85) REVERT: A 809 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8591 (mp0) REVERT: A 838 LYS cc_start: 0.8456 (mttt) cc_final: 0.8154 (mmmm) REVERT: A 850 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: B 269 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8356 (tp30) REVERT: B 296 ARG cc_start: 0.9053 (mmm-85) cc_final: 0.8723 (mmm160) REVERT: B 297 LEU cc_start: 0.8726 (mm) cc_final: 0.8464 (mp) REVERT: B 307 VAL cc_start: 0.8676 (t) cc_final: 0.8356 (p) REVERT: B 425 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7490 (mt-10) REVERT: B 476 TYR cc_start: 0.8256 (m-10) cc_final: 0.7969 (m-10) REVERT: B 508 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8357 (tttt) REVERT: B 512 GLU cc_start: 0.8638 (tp30) cc_final: 0.8202 (tp30) REVERT: B 577 LYS cc_start: 0.8839 (tttt) cc_final: 0.8567 (ttmm) REVERT: B 653 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7893 (tm-30) REVERT: B 664 GLN cc_start: 0.8740 (mp-120) cc_final: 0.8486 (mp-120) REVERT: B 674 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 698 ASP cc_start: 0.8577 (t0) cc_final: 0.8244 (t0) REVERT: B 853 GLU cc_start: 0.8864 (tt0) cc_final: 0.8554 (pm20) REVERT: B 926 GLU cc_start: 0.8240 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 953 MET cc_start: 0.8567 (mmm) cc_final: 0.8363 (mmm) REVERT: B 1018 GLU cc_start: 0.8752 (pp20) cc_final: 0.8460 (pp20) REVERT: B 1084 LYS cc_start: 0.8699 (mttt) cc_final: 0.8318 (mmmm) REVERT: B 1091 LYS cc_start: 0.8205 (mttt) cc_final: 0.7878 (mmmm) outliers start: 60 outliers final: 39 residues processed: 429 average time/residue: 0.3062 time to fit residues: 181.8200 Evaluate side-chains 423 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 378 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 798 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1052 PHE Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13360 Z= 0.236 Angle : 0.647 12.714 18021 Z= 0.319 Chirality : 0.042 0.201 2063 Planarity : 0.005 0.057 2286 Dihedral : 6.049 125.585 1771 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.21 % Allowed : 27.07 % Favored : 68.72 % 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: -0.70 (0.22), residues: 1602 helix: 0.72 (0.19), residues: 784 sheet: -1.91 (0.37), residues: 178 loop : -1.46 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 807 HIS 0.007 0.001 HIS B 729 PHE 0.017 0.001 PHE A 551 TYR 0.032 0.002 TYR A 619 ARG 0.010 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 387 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8614 (t) cc_final: 0.8317 (p) REVERT: A 172 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7755 (mmtt) REVERT: A 192 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7805 (mp) REVERT: A 198 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7282 (mm-30) REVERT: A 226 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8115 (mm-30) REVERT: A 245 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7535 (tp) REVERT: A 260 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: A 261 MET cc_start: 0.7546 (mmp) cc_final: 0.6131 (mmp) REVERT: A 345 TRP cc_start: 0.8593 (m-10) cc_final: 0.7828 (m-10) REVERT: A 347 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8256 (mtpt) REVERT: A 351 MET cc_start: 0.8438 (ttm) cc_final: 0.8082 (ttm) REVERT: A 361 ASN cc_start: 0.8026 (m-40) cc_final: 0.7555 (m-40) REVERT: A 369 ASP cc_start: 0.8418 (t0) cc_final: 0.8140 (t0) REVERT: A 377 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7991 (tp40) REVERT: A 386 ASP cc_start: 0.8772 (t0) cc_final: 0.8364 (t0) REVERT: A 389 ARG cc_start: 0.9102 (tpp80) cc_final: 0.8677 (tpp80) REVERT: A 569 GLU cc_start: 0.8684 (tt0) cc_final: 0.8114 (tp30) REVERT: A 579 LYS cc_start: 0.9004 (mttt) cc_final: 0.8520 (mmmm) REVERT: A 593 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8816 (mt0) REVERT: A 603 ASP cc_start: 0.8220 (t0) cc_final: 0.7878 (t0) REVERT: A 701 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7878 (mt-10) REVERT: A 728 GLU cc_start: 0.8042 (tp30) cc_final: 0.7762 (tp30) REVERT: A 729 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8042 (mpp) REVERT: A 742 ASP cc_start: 0.8071 (t70) cc_final: 0.7649 (t0) REVERT: A 778 CYS cc_start: 0.8477 (t) cc_final: 0.8152 (t) REVERT: A 809 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8533 (mp0) REVERT: A 838 LYS cc_start: 0.8505 (mttt) cc_final: 0.8192 (mmmm) REVERT: A 850 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: B 242 GLN cc_start: 0.8421 (mt0) cc_final: 0.8221 (mp10) REVERT: B 269 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8151 (tp30) REVERT: B 296 ARG cc_start: 0.9054 (mmm-85) cc_final: 0.8334 (tpt90) REVERT: B 297 LEU cc_start: 0.8735 (mm) cc_final: 0.8456 (mp) REVERT: B 307 VAL cc_start: 0.8662 (t) cc_final: 0.8311 (p) REVERT: B 425 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7528 (mt-10) REVERT: B 476 TYR cc_start: 0.8321 (m-10) cc_final: 0.8064 (m-10) REVERT: B 508 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8385 (tttt) REVERT: B 512 GLU cc_start: 0.8643 (tp30) cc_final: 0.8208 (tp30) REVERT: B 541 THR cc_start: 0.8646 (m) cc_final: 0.8258 (t) REVERT: B 577 LYS cc_start: 0.8864 (tttt) cc_final: 0.8584 (ttmm) REVERT: B 653 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8102 (tm-30) REVERT: B 674 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7873 (mt-10) REVERT: B 698 ASP cc_start: 0.8599 (t0) cc_final: 0.8250 (t0) REVERT: B 798 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7478 (mm-40) REVERT: B 823 LYS cc_start: 0.8630 (tptp) cc_final: 0.8404 (tptm) REVERT: B 832 ASP cc_start: 0.8764 (t0) cc_final: 0.8463 (t0) REVERT: B 853 GLU cc_start: 0.8857 (tt0) cc_final: 0.8544 (pm20) REVERT: B 873 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: B 926 GLU cc_start: 0.8258 (tm-30) cc_final: 0.8037 (tm-30) REVERT: B 953 MET cc_start: 0.8535 (mmm) cc_final: 0.8329 (mmm) REVERT: B 1018 GLU cc_start: 0.8784 (pp20) cc_final: 0.8467 (pp20) REVERT: B 1084 LYS cc_start: 0.8724 (mttt) cc_final: 0.8311 (mmmm) REVERT: B 1091 LYS cc_start: 0.8225 (mttt) cc_final: 0.7985 (mtpp) outliers start: 61 outliers final: 39 residues processed: 428 average time/residue: 0.2763 time to fit residues: 163.9571 Evaluate side-chains 425 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 377 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 798 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1052 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 0.0270 chunk 132 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 467 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13360 Z= 0.244 Angle : 0.660 12.550 18021 Z= 0.326 Chirality : 0.043 0.263 2063 Planarity : 0.005 0.059 2286 Dihedral : 6.007 125.596 1771 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.77 % Allowed : 27.21 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1602 helix: 0.74 (0.19), residues: 782 sheet: -1.89 (0.37), residues: 178 loop : -1.47 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 807 HIS 0.014 0.001 HIS B 817 PHE 0.016 0.001 PHE B 463 TYR 0.028 0.002 TYR A 619 ARG 0.010 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 386 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8599 (t) cc_final: 0.8303 (p) REVERT: A 172 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7716 (mmtt) REVERT: A 192 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7922 (mp) REVERT: A 198 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7178 (mm-30) REVERT: A 226 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8181 (mm-30) REVERT: A 245 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7547 (tp) REVERT: A 260 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: A 345 TRP cc_start: 0.8590 (m-10) cc_final: 0.7787 (m-10) REVERT: A 351 MET cc_start: 0.8433 (ttm) cc_final: 0.8086 (ttm) REVERT: A 361 ASN cc_start: 0.8047 (m-40) cc_final: 0.7602 (m110) REVERT: A 369 ASP cc_start: 0.8374 (t0) cc_final: 0.8140 (t0) REVERT: A 377 GLN cc_start: 0.8227 (tp-100) cc_final: 0.8024 (tp40) REVERT: A 386 ASP cc_start: 0.8754 (t0) cc_final: 0.8345 (t0) REVERT: A 389 ARG cc_start: 0.9085 (tpp80) cc_final: 0.8662 (tpp80) REVERT: A 452 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: A 458 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7083 (tt) REVERT: A 469 LEU cc_start: 0.8595 (pt) cc_final: 0.8316 (pt) REVERT: A 493 GLN cc_start: 0.8743 (mt0) cc_final: 0.8480 (mp10) REVERT: A 562 GLU cc_start: 0.9056 (tp30) cc_final: 0.8739 (tm-30) REVERT: A 569 GLU cc_start: 0.8686 (tt0) cc_final: 0.8121 (tp30) REVERT: A 579 LYS cc_start: 0.9001 (mttt) cc_final: 0.8618 (mmmm) REVERT: A 603 ASP cc_start: 0.8206 (t0) cc_final: 0.7856 (t0) REVERT: A 701 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7897 (mt-10) REVERT: A 728 GLU cc_start: 0.8031 (tp30) cc_final: 0.7702 (tp30) REVERT: A 729 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8072 (mpp) REVERT: A 742 ASP cc_start: 0.8169 (t70) cc_final: 0.7724 (t0) REVERT: A 778 CYS cc_start: 0.8472 (t) cc_final: 0.8163 (t) REVERT: A 809 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8614 (mp0) REVERT: A 838 LYS cc_start: 0.8504 (mttt) cc_final: 0.8205 (mmmm) REVERT: A 850 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: B 242 GLN cc_start: 0.8425 (mt0) cc_final: 0.8221 (mp10) REVERT: B 269 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8336 (tp30) REVERT: B 296 ARG cc_start: 0.9041 (mmm-85) cc_final: 0.8714 (mmm160) REVERT: B 297 LEU cc_start: 0.8740 (mm) cc_final: 0.8479 (mp) REVERT: B 307 VAL cc_start: 0.8806 (t) cc_final: 0.8460 (p) REVERT: B 425 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 476 TYR cc_start: 0.8356 (m-10) cc_final: 0.8104 (m-10) REVERT: B 508 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8356 (tttm) REVERT: B 512 GLU cc_start: 0.8657 (tp30) cc_final: 0.8236 (tp30) REVERT: B 577 LYS cc_start: 0.8908 (tttt) cc_final: 0.8625 (ttmm) REVERT: B 632 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8253 (mttm) REVERT: B 653 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 674 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7900 (mt-10) REVERT: B 698 ASP cc_start: 0.8576 (t0) cc_final: 0.8211 (t0) REVERT: B 801 LEU cc_start: 0.8101 (mt) cc_final: 0.7886 (tp) REVERT: B 832 ASP cc_start: 0.8767 (t0) cc_final: 0.8461 (t0) REVERT: B 853 GLU cc_start: 0.8877 (tt0) cc_final: 0.8548 (pm20) REVERT: B 873 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.6413 (tm-30) REVERT: B 926 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 953 MET cc_start: 0.8498 (mmm) cc_final: 0.8297 (mmm) REVERT: B 1018 GLU cc_start: 0.8786 (pp20) cc_final: 0.8473 (pp20) REVERT: B 1084 LYS cc_start: 0.8731 (mttt) cc_final: 0.8314 (mmmm) REVERT: B 1088 HIS cc_start: 0.8446 (t70) cc_final: 0.8205 (t-90) outliers start: 69 outliers final: 44 residues processed: 430 average time/residue: 0.2693 time to fit residues: 161.1141 Evaluate side-chains 432 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 377 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1052 PHE Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.0970 chunk 93 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 0.0010 chunk 14 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 142 optimal weight: 0.1980 chunk 150 optimal weight: 0.8980 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13360 Z= 0.189 Angle : 0.661 13.093 18021 Z= 0.323 Chirality : 0.042 0.236 2063 Planarity : 0.005 0.062 2286 Dihedral : 5.872 124.026 1771 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.56 % Allowed : 28.18 % Favored : 67.27 % 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: -0.60 (0.22), residues: 1602 helix: 0.80 (0.19), residues: 778 sheet: -1.81 (0.37), residues: 179 loop : -1.42 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.016 0.001 PHE B 463 TYR 0.025 0.001 TYR A 619 ARG 0.010 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 377 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 198 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7219 (mm-30) REVERT: A 226 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7945 (mm-30) REVERT: A 245 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7482 (tp) REVERT: A 261 MET cc_start: 0.7550 (mmp) cc_final: 0.7053 (mmp) REVERT: A 345 TRP cc_start: 0.8492 (m-10) cc_final: 0.7618 (m-10) REVERT: A 351 MET cc_start: 0.8429 (ttm) cc_final: 0.8076 (ttm) REVERT: A 369 ASP cc_start: 0.8380 (t0) cc_final: 0.8142 (t0) REVERT: A 377 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7962 (tp40) REVERT: A 386 ASP cc_start: 0.8751 (t0) cc_final: 0.8345 (t0) REVERT: A 389 ARG cc_start: 0.9060 (tpp80) cc_final: 0.8617 (tpp80) REVERT: A 409 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: A 452 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: A 493 GLN cc_start: 0.8719 (mt0) cc_final: 0.8477 (mp10) REVERT: A 550 LYS cc_start: 0.7284 (mmmt) cc_final: 0.7075 (mmtp) REVERT: A 562 GLU cc_start: 0.9079 (tp30) cc_final: 0.8740 (tm-30) REVERT: A 569 GLU cc_start: 0.8659 (tt0) cc_final: 0.8074 (tp30) REVERT: A 579 LYS cc_start: 0.8933 (mttt) cc_final: 0.8456 (mmmm) REVERT: A 595 LEU cc_start: 0.9049 (tp) cc_final: 0.8807 (tt) REVERT: A 602 LEU cc_start: 0.8977 (tp) cc_final: 0.8773 (tt) REVERT: A 603 ASP cc_start: 0.8199 (t0) cc_final: 0.7813 (t0) REVERT: A 728 GLU cc_start: 0.7948 (tp30) cc_final: 0.7626 (tp30) REVERT: A 729 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8032 (mpp) REVERT: A 742 ASP cc_start: 0.8069 (t70) cc_final: 0.7601 (t0) REVERT: A 809 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8572 (mp0) REVERT: A 838 LYS cc_start: 0.8458 (mttt) cc_final: 0.8164 (mmmm) REVERT: A 850 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: B 269 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8254 (tp30) REVERT: B 296 ARG cc_start: 0.9016 (mmm-85) cc_final: 0.8660 (mmm160) REVERT: B 297 LEU cc_start: 0.8720 (mm) cc_final: 0.8457 (mp) REVERT: B 307 VAL cc_start: 0.8796 (t) cc_final: 0.8428 (p) REVERT: B 425 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 476 TYR cc_start: 0.8295 (m-10) cc_final: 0.7882 (m-10) REVERT: B 508 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8354 (tttm) REVERT: B 512 GLU cc_start: 0.8567 (tp30) cc_final: 0.8009 (tp30) REVERT: B 577 LYS cc_start: 0.8849 (tttt) cc_final: 0.8570 (ttmm) REVERT: B 632 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8178 (mttm) REVERT: B 647 HIS cc_start: 0.8430 (t70) cc_final: 0.8103 (t-170) REVERT: B 653 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8050 (tm-30) REVERT: B 659 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8458 (t) REVERT: B 674 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7856 (mt-10) REVERT: B 698 ASP cc_start: 0.8516 (t0) cc_final: 0.8145 (t0) REVERT: B 832 ASP cc_start: 0.8750 (t0) cc_final: 0.8437 (t0) REVERT: B 853 GLU cc_start: 0.8884 (tt0) cc_final: 0.8544 (pm20) REVERT: B 873 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.6404 (tm-30) REVERT: B 926 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7957 (tm-30) REVERT: B 953 MET cc_start: 0.8474 (tmm) cc_final: 0.8267 (mmm) REVERT: B 955 GLU cc_start: 0.8628 (mp0) cc_final: 0.8238 (mp0) REVERT: B 1018 GLU cc_start: 0.8727 (pp20) cc_final: 0.8398 (pp20) REVERT: B 1084 LYS cc_start: 0.8681 (mttt) cc_final: 0.8297 (mmmm) REVERT: B 1088 HIS cc_start: 0.8426 (t70) cc_final: 0.8181 (t-90) outliers start: 66 outliers final: 42 residues processed: 420 average time/residue: 0.2827 time to fit residues: 165.1386 Evaluate side-chains 424 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 371 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1052 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 114 optimal weight: 0.0070 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 138 optimal weight: 0.0270 chunk 145 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13360 Z= 0.215 Angle : 0.674 12.888 18021 Z= 0.330 Chirality : 0.042 0.188 2063 Planarity : 0.005 0.055 2286 Dihedral : 5.838 121.383 1771 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.35 % Allowed : 28.66 % Favored : 66.99 % 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: -0.62 (0.22), residues: 1602 helix: 0.76 (0.19), residues: 781 sheet: -1.78 (0.37), residues: 179 loop : -1.43 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 807 HIS 0.008 0.001 HIS B 729 PHE 0.015 0.001 PHE B 463 TYR 0.027 0.002 TYR A 619 ARG 0.010 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 377 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8594 (t) cc_final: 0.8325 (p) REVERT: A 165 TYR cc_start: 0.8515 (p90) cc_final: 0.8073 (p90) REVERT: A 192 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 198 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7221 (mm-30) REVERT: A 226 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7974 (mm-30) REVERT: A 245 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7479 (tp) REVERT: A 261 MET cc_start: 0.7559 (mmp) cc_final: 0.7050 (mmp) REVERT: A 275 LYS cc_start: 0.8883 (tppt) cc_final: 0.8572 (mmmm) REVERT: A 296 PHE cc_start: 0.8402 (p90) cc_final: 0.8187 (p90) REVERT: A 345 TRP cc_start: 0.8518 (m-10) cc_final: 0.7651 (m-10) REVERT: A 351 MET cc_start: 0.8456 (ttm) cc_final: 0.8106 (ttm) REVERT: A 361 ASN cc_start: 0.8057 (m-40) cc_final: 0.7608 (m110) REVERT: A 369 ASP cc_start: 0.8366 (t0) cc_final: 0.8149 (t0) REVERT: A 377 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7987 (tp40) REVERT: A 386 ASP cc_start: 0.8764 (t0) cc_final: 0.8360 (t0) REVERT: A 389 ARG cc_start: 0.9061 (tpp80) cc_final: 0.8624 (tpp80) REVERT: A 409 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: A 452 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: A 458 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7111 (tt) REVERT: A 550 LYS cc_start: 0.7357 (mmmt) cc_final: 0.7122 (mmtp) REVERT: A 562 GLU cc_start: 0.9092 (tp30) cc_final: 0.8760 (tm-30) REVERT: A 569 GLU cc_start: 0.8665 (tt0) cc_final: 0.8094 (tp30) REVERT: A 579 LYS cc_start: 0.8931 (mttt) cc_final: 0.8468 (mmmm) REVERT: A 603 ASP cc_start: 0.8211 (t0) cc_final: 0.7861 (t0) REVERT: A 678 TYR cc_start: 0.8726 (t80) cc_final: 0.8494 (t80) REVERT: A 728 GLU cc_start: 0.7983 (tp30) cc_final: 0.7774 (tp30) REVERT: A 729 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8023 (mpp) REVERT: A 742 ASP cc_start: 0.8215 (t70) cc_final: 0.7717 (t0) REVERT: A 778 CYS cc_start: 0.8397 (t) cc_final: 0.8066 (t) REVERT: A 798 ASN cc_start: 0.8539 (t0) cc_final: 0.8300 (t0) REVERT: A 809 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8577 (mp0) REVERT: A 838 LYS cc_start: 0.8457 (mttt) cc_final: 0.8185 (mmmm) REVERT: A 850 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: B 242 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7736 (mp10) REVERT: B 269 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8281 (tp30) REVERT: B 296 ARG cc_start: 0.9020 (mmm-85) cc_final: 0.8689 (mmm160) REVERT: B 297 LEU cc_start: 0.8718 (mm) cc_final: 0.8458 (mp) REVERT: B 307 VAL cc_start: 0.8787 (t) cc_final: 0.8425 (p) REVERT: B 425 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7541 (mt-10) REVERT: B 476 TYR cc_start: 0.8262 (m-10) cc_final: 0.7881 (m-10) REVERT: B 508 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8368 (tttm) REVERT: B 512 GLU cc_start: 0.8575 (tp30) cc_final: 0.8045 (tp30) REVERT: B 577 LYS cc_start: 0.8865 (tttt) cc_final: 0.8585 (ttmm) REVERT: B 632 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8246 (mttm) REVERT: B 653 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 674 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 698 ASP cc_start: 0.8503 (t0) cc_final: 0.8139 (t0) REVERT: B 832 ASP cc_start: 0.8754 (t0) cc_final: 0.8443 (t0) REVERT: B 853 GLU cc_start: 0.8897 (tt0) cc_final: 0.8526 (pm20) REVERT: B 873 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.6382 (tm-30) REVERT: B 917 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8544 (mt0) REVERT: B 926 GLU cc_start: 0.8215 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 955 GLU cc_start: 0.8620 (mp0) cc_final: 0.8207 (mp0) REVERT: B 1018 GLU cc_start: 0.8747 (pp20) cc_final: 0.8418 (pp20) REVERT: B 1084 LYS cc_start: 0.8693 (mttt) cc_final: 0.8307 (mmmm) REVERT: B 1088 HIS cc_start: 0.8427 (t70) cc_final: 0.8180 (t-90) outliers start: 63 outliers final: 42 residues processed: 417 average time/residue: 0.2808 time to fit residues: 162.8455 Evaluate side-chains 428 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 373 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1052 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 0.0670 chunk 94 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 0.0000 chunk 79 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 0.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13360 Z= 0.206 Angle : 0.677 13.047 18021 Z= 0.330 Chirality : 0.042 0.194 2063 Planarity : 0.005 0.059 2286 Dihedral : 5.783 118.150 1771 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.01 % Allowed : 28.80 % Favored : 67.20 % 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: -0.65 (0.22), residues: 1602 helix: 0.78 (0.19), residues: 780 sheet: -1.91 (0.36), residues: 193 loop : -1.42 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 807 HIS 0.007 0.001 HIS B 729 PHE 0.014 0.001 PHE B 463 TYR 0.021 0.002 TYR B1068 ARG 0.009 0.001 ARG A 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 372 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8587 (t) cc_final: 0.8315 (p) REVERT: A 165 TYR cc_start: 0.8529 (p90) cc_final: 0.8058 (p90) REVERT: A 192 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 198 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7219 (mm-30) REVERT: A 226 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7969 (mm-30) REVERT: A 245 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7451 (tp) REVERT: A 261 MET cc_start: 0.7560 (mmp) cc_final: 0.7040 (mmp) REVERT: A 275 LYS cc_start: 0.8876 (tppt) cc_final: 0.8565 (mmmm) REVERT: A 345 TRP cc_start: 0.8521 (m-10) cc_final: 0.7645 (m-10) REVERT: A 351 MET cc_start: 0.8457 (ttm) cc_final: 0.8091 (ttm) REVERT: A 361 ASN cc_start: 0.8067 (m-40) cc_final: 0.7631 (m110) REVERT: A 377 GLN cc_start: 0.8211 (tp-100) cc_final: 0.7993 (tp40) REVERT: A 386 ASP cc_start: 0.8766 (t0) cc_final: 0.8361 (t0) REVERT: A 389 ARG cc_start: 0.9047 (tpp80) cc_final: 0.8595 (tpp80) REVERT: A 452 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: A 550 LYS cc_start: 0.7355 (mmmt) cc_final: 0.7056 (mmtp) REVERT: A 562 GLU cc_start: 0.9092 (tp30) cc_final: 0.8763 (tm-30) REVERT: A 569 GLU cc_start: 0.8638 (tt0) cc_final: 0.8050 (tp30) REVERT: A 579 LYS cc_start: 0.8907 (mttt) cc_final: 0.8452 (mmmm) REVERT: A 595 LEU cc_start: 0.9074 (tp) cc_final: 0.8798 (tt) REVERT: A 603 ASP cc_start: 0.8185 (t0) cc_final: 0.7837 (t0) REVERT: A 728 GLU cc_start: 0.7961 (tp30) cc_final: 0.7751 (tp30) REVERT: A 729 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8050 (mpp) REVERT: A 742 ASP cc_start: 0.8236 (t70) cc_final: 0.7720 (t0) REVERT: A 778 CYS cc_start: 0.8377 (t) cc_final: 0.8044 (t) REVERT: A 798 ASN cc_start: 0.8529 (t0) cc_final: 0.8198 (t0) REVERT: A 809 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8568 (mp0) REVERT: A 838 LYS cc_start: 0.8433 (mttt) cc_final: 0.8169 (mmmm) REVERT: A 850 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: B 242 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: B 269 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8249 (tp30) REVERT: B 296 ARG cc_start: 0.9017 (mmm-85) cc_final: 0.8677 (mmm160) REVERT: B 297 LEU cc_start: 0.8719 (mm) cc_final: 0.8459 (mp) REVERT: B 307 VAL cc_start: 0.8781 (t) cc_final: 0.8406 (p) REVERT: B 425 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7531 (mt-10) REVERT: B 476 TYR cc_start: 0.8210 (m-10) cc_final: 0.7854 (m-10) REVERT: B 508 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8326 (tttm) REVERT: B 577 LYS cc_start: 0.8860 (tttt) cc_final: 0.8581 (ttmm) REVERT: B 653 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 674 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 698 ASP cc_start: 0.8496 (t0) cc_final: 0.8118 (t0) REVERT: B 832 ASP cc_start: 0.8763 (t0) cc_final: 0.8448 (t0) REVERT: B 853 GLU cc_start: 0.8902 (tt0) cc_final: 0.8527 (pm20) REVERT: B 873 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.6344 (tm-30) REVERT: B 917 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: B 926 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 955 GLU cc_start: 0.8617 (mp0) cc_final: 0.8209 (mp0) REVERT: B 1018 GLU cc_start: 0.8732 (pp20) cc_final: 0.8405 (pp20) REVERT: B 1084 LYS cc_start: 0.8700 (mttt) cc_final: 0.8297 (mmmm) REVERT: B 1088 HIS cc_start: 0.8420 (t70) cc_final: 0.8169 (t-90) outliers start: 58 outliers final: 44 residues processed: 409 average time/residue: 0.2748 time to fit residues: 156.1613 Evaluate side-chains 423 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 369 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 969 GLN Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1052 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.0040 chunk 129 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 132 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 574 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.170432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140434 restraints weight = 22864.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.144777 restraints weight = 10407.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147513 restraints weight = 5918.259| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 13360 Z= 0.205 Angle : 0.685 12.945 18021 Z= 0.333 Chirality : 0.042 0.198 2063 Planarity : 0.005 0.056 2286 Dihedral : 5.663 114.144 1769 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.63 % Allowed : 28.66 % Favored : 66.71 % 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: -0.58 (0.22), residues: 1602 helix: 0.84 (0.19), residues: 783 sheet: -1.88 (0.35), residues: 201 loop : -1.39 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 807 HIS 0.005 0.001 HIS B 729 PHE 0.013 0.001 PHE B 463 TYR 0.028 0.002 TYR A 678 ARG 0.010 0.001 ARG A 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3694.42 seconds wall clock time: 66 minutes 55.57 seconds (4015.57 seconds total)