Starting phenix.real_space_refine on Sun Mar 17 09:11:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/03_2024/6d6v_7821.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/03_2024/6d6v_7821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/03_2024/6d6v_7821.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/03_2024/6d6v_7821.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/03_2024/6d6v_7821.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/03_2024/6d6v_7821.pdb" } resolution = 4.8 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 Zn 1 6.06 5 P 177 5.49 5 S 54 5.16 5 C 10405 2.51 5 N 2948 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 394": "OE1" <-> "OE2" Residue "H TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 409": "OD1" <-> "OD2" Residue "H TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 465": "NH1" <-> "NH2" Residue "H GLU 471": "OE1" <-> "OE2" Residue "H GLU 490": "OE1" <-> "OE2" Residue "H ASP 497": "OD1" <-> "OD2" Residue "H GLU 507": "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: 17317 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 8253 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 959} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1538 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 3, 'TRANS': 181} Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 919 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "E" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1207 Classifications: {'peptide': 149} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 143} Chain: "B" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3322 Classifications: {'RNA': 159} Modifications used: {'5*END': 1, 'rna2p_pur': 18, 'rna2p_pyr': 21, 'rna3p_pur': 59, 'rna3p_pyr': 60} Link IDs: {'rna2p': 38, 'rna3p': 120} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G%rna3p_pur:plan2': 2, ' G%rna3p_pur:plan': 2, ' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 406 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 785 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'TRANS': 156} Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 157 Planarities with less than four sites: {'UNK:plan-1': 157} Unresolved non-hydrogen planarities: 157 Chain: "H" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8788 SG CYS D 575 71.318 62.077 84.962 1.00328.59 S Time building chain proxies: 9.34, per 1000 atoms: 0.54 Number of scatterers: 17317 At special positions: 0 Unit cell: (148.24, 160.48, 114.24, 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) Zn 1 29.99 S 54 16.00 P 177 15.00 O 3732 8.00 N 2948 7.00 C 10405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.52 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 575 " 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3282 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 51.5% alpha, 13.6% beta 43 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 6.77 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.583A pdb=" N GLN A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.751A pdb=" N TYR A 177 " --> pdb=" O CYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 301 through 320 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 386 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 394 through 411 removed outlier: 4.371A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.679A pdb=" N ASN A 439 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 440 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS A 441 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 467 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 493 through 505 Processing helix chain 'A' and resid 506 through 509 removed outlier: 4.321A pdb=" N GLU A 509 " --> pdb=" O LYS A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 506 through 509' Processing helix chain 'A' and resid 551 through 579 removed outlier: 3.670A pdb=" N LYS A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 607 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 711 through 717 removed outlier: 3.970A pdb=" N LEU A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 753 removed outlier: 3.836A pdb=" N ILE A 745 " --> pdb=" O THR A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 805 removed outlier: 3.686A pdb=" N GLU A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 840 Processing helix chain 'A' and resid 856 through 865 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 911 through 921 removed outlier: 4.249A pdb=" N ASN A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 965 removed outlier: 3.639A pdb=" N LEU A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) Proline residue: A 959 - end of helix Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 983 through 1003 removed outlier: 3.750A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1040 Processing helix chain 'A' and resid 1043 through 1075 removed outlier: 4.742A pdb=" N LYS A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'A' and resid 1099 through 1108 Proline residue: A1105 - end of helix Processing helix chain 'D' and resid 516 through 526 Processing helix chain 'D' and resid 604 through 613 Processing helix chain 'D' and resid 619 through 621 No H-bonds generated for 'chain 'D' and resid 619 through 621' Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 635 through 646 removed outlier: 3.602A pdb=" N LEU D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 693 removed outlier: 3.816A pdb=" N SER D 684 " --> pdb=" O ILE D 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 removed outlier: 5.904A pdb=" N ALA F 19 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 removed outlier: 3.534A pdb=" N TYR F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 removed outlier: 3.781A pdb=" N ILE E 39 " --> pdb=" O ASN E 35 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN E 41 " --> pdb=" O PHE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 5.566A pdb=" N GLU E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 175 removed outlier: 3.920A pdb=" N ILE E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 28 removed outlier: 3.896A pdb=" N UNK G 11 " --> pdb=" O UNK G 7 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N UNK G 13 " --> pdb=" O UNK G 9 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N UNK G 14 " --> pdb=" O UNK G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 4.133A pdb=" N UNK G 71 " --> pdb=" O UNK G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 3.627A pdb=" N UNK G 130 " --> pdb=" O UNK G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 154 Processing helix chain 'H' and resid 391 through 401 removed outlier: 3.501A pdb=" N VAL H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 479 Processing helix chain 'H' and resid 503 through 531 removed outlier: 4.041A pdb=" N PHE H 525 " --> pdb=" O PHE H 521 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN H 530 " --> pdb=" O PHE H 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 162 removed outlier: 7.938A pdb=" N PHE A 158 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 169 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 167 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 476 through 481 removed outlier: 4.615A pdb=" N LYS A 481 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN A 487 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AA5, first strand: chain 'A' and resid 613 through 618 Processing sheet with id=AA6, first strand: chain 'A' and resid 647 through 648 removed outlier: 4.202A pdb=" N ILE A 647 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 880 through 882 Processing sheet with id=AA8, first strand: chain 'D' and resid 551 through 554 removed outlier: 4.885A pdb=" N TYR D 670 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET D 601 " --> pdb=" O TYR D 670 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE D 603 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N LYS D 674 " --> pdb=" O PHE D 603 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR D 670 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU D 658 " --> pdb=" O TYR D 670 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL D 672 " --> pdb=" O GLN D 656 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLN D 656 " --> pdb=" O VAL D 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 562 through 563 removed outlier: 3.671A pdb=" N PHE D 571 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 70 through 75 removed outlier: 6.670A pdb=" N ILE F 43 " --> pdb=" O CYS F 33 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU F 44 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL F 83 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL F 55 " --> pdb=" O VAL F 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.553A pdb=" N TYR E 146 " --> pdb=" O MET E 133 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS E 135 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU E 144 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU E 144 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL E 99 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR E 146 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY E 94 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE E 85 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET E 86 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU E 76 " --> pdb=" O MET E 86 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS E 88 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 87 through 89 Processing sheet with id=AB4, first strand: chain 'H' and resid 406 through 411 removed outlier: 4.766A pdb=" N LEU H 487 " --> pdb=" O VAL H 498 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 7.24 Time building geometry restraints manager: 10.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5118 1.34 - 1.49: 6588 1.49 - 1.65: 6213 1.65 - 1.80: 63 1.80 - 1.95: 16 Bond restraints: 17998 Sorted by residual: bond pdb=" CA SER A 890 " pdb=" C SER A 890 " ideal model delta sigma weight residual 1.524 1.473 0.051 7.00e-03 2.04e+04 5.30e+01 bond pdb=" SD MET H 527 " pdb=" CE MET H 527 " ideal model delta sigma weight residual 1.791 1.952 -0.161 2.50e-02 1.60e+03 4.17e+01 bond pdb=" CG MET H 527 " pdb=" SD MET H 527 " ideal model delta sigma weight residual 1.803 1.955 -0.152 2.50e-02 1.60e+03 3.69e+01 bond pdb=" CB ASN A 648 " pdb=" CG ASN A 648 " ideal model delta sigma weight residual 1.516 1.399 0.117 2.50e-02 1.60e+03 2.21e+01 bond pdb=" CA LEU A 923 " pdb=" C LEU A 923 " ideal model delta sigma weight residual 1.523 1.440 0.083 1.80e-02 3.09e+03 2.13e+01 ... (remaining 17993 not shown) Histogram of bond angle deviations from ideal: 95.24 - 104.49: 874 104.49 - 113.74: 10414 113.74 - 122.99: 11699 122.99 - 132.24: 2064 132.24 - 141.49: 61 Bond angle restraints: 25112 Sorted by residual: angle pdb=" N ILE A 626 " pdb=" CA ILE A 626 " pdb=" C ILE A 626 " ideal model delta sigma weight residual 108.84 120.25 -11.41 1.32e+00 5.74e-01 7.47e+01 angle pdb=" C SER A 922 " pdb=" N LEU A 923 " pdb=" CA LEU A 923 " ideal model delta sigma weight residual 122.31 138.67 -16.36 2.00e+00 2.50e-01 6.69e+01 angle pdb=" N LYS A 849 " pdb=" CA LYS A 849 " pdb=" C LYS A 849 " ideal model delta sigma weight residual 108.07 118.55 -10.48 1.38e+00 5.25e-01 5.77e+01 angle pdb=" N ASP A 627 " pdb=" CA ASP A 627 " pdb=" C ASP A 627 " ideal model delta sigma weight residual 107.73 96.14 11.59 1.80e+00 3.09e-01 4.15e+01 angle pdb=" CA PRO A 934 " pdb=" C PRO A 934 " pdb=" N ASN A 935 " ideal model delta sigma weight residual 117.98 109.19 8.79 1.43e+00 4.89e-01 3.78e+01 ... (remaining 25107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 10228 35.72 - 71.44: 620 71.44 - 107.16: 88 107.16 - 142.88: 12 142.88 - 178.61: 10 Dihedral angle restraints: 10958 sinusoidal: 5916 harmonic: 5042 Sorted by residual: dihedral pdb=" CA SER A 299 " pdb=" C SER A 299 " pdb=" N CYS A 300 " pdb=" CA CYS A 300 " ideal model delta harmonic sigma weight residual -180.00 -113.29 -66.71 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA UNK G 62 " pdb=" C UNK G 62 " pdb=" N UNK G 63 " pdb=" CA UNK G 63 " ideal model delta harmonic sigma weight residual -180.00 -130.09 -49.91 0 5.00e+00 4.00e-02 9.97e+01 dihedral pdb=" CA PHE F 97 " pdb=" C PHE F 97 " pdb=" N ASP F 98 " pdb=" CA ASP F 98 " ideal model delta harmonic sigma weight residual 180.00 131.55 48.45 0 5.00e+00 4.00e-02 9.39e+01 ... (remaining 10955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 2854 0.200 - 0.400: 62 0.400 - 0.600: 6 0.600 - 0.800: 2 0.800 - 1.000: 1 Chirality restraints: 2925 Sorted by residual: chirality pdb=" C1' C B 46 " pdb=" O4' C B 46 " pdb=" C2' C B 46 " pdb=" N1 C B 46 " both_signs ideal model delta sigma weight residual False 2.46 1.46 1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CG LEU A 565 " pdb=" CB LEU A 565 " pdb=" CD1 LEU A 565 " pdb=" CD2 LEU A 565 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" C3' U B 42 " pdb=" C4' U B 42 " pdb=" O3' U B 42 " pdb=" C2' U B 42 " both_signs ideal model delta sigma weight residual False -2.48 -1.79 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 2922 not shown) Planarity restraints: 2584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 585 " 0.053 2.00e-02 2.50e+03 3.15e-02 1.99e+01 pdb=" CG TYR A 585 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR A 585 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 585 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 585 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 585 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 585 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 585 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 15 " 0.059 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" N1 DT C 15 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT C 15 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DT C 15 " -0.030 2.00e-02 2.50e+03 pdb=" N3 DT C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT C 15 " 0.012 2.00e-02 2.50e+03 pdb=" O4 DT C 15 " 0.020 2.00e-02 2.50e+03 pdb=" C5 DT C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT C 15 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT C 15 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 46 " -0.056 2.00e-02 2.50e+03 2.93e-02 1.93e+01 pdb=" N1 C B 46 " 0.050 2.00e-02 2.50e+03 pdb=" C2 C B 46 " 0.038 2.00e-02 2.50e+03 pdb=" O2 C B 46 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C B 46 " -0.010 2.00e-02 2.50e+03 pdb=" C4 C B 46 " -0.008 2.00e-02 2.50e+03 pdb=" N4 C B 46 " -0.019 2.00e-02 2.50e+03 pdb=" C5 C B 46 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C B 46 " 0.009 2.00e-02 2.50e+03 ... (remaining 2581 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 8 1.93 - 2.67: 1148 2.67 - 3.42: 26487 3.42 - 4.16: 48918 4.16 - 4.90: 75700 Nonbonded interactions: 152261 Sorted by model distance: nonbonded pdb=" OP2 G B 121 " pdb=" O LYS H 518 " model vdw 1.189 3.040 nonbonded pdb=" C5' G B 121 " pdb=" CB PHE H 521 " model vdw 1.441 3.840 nonbonded pdb=" O4' G B 121 " pdb=" O LYS H 517 " model vdw 1.447 3.040 nonbonded pdb=" CB UNK G 51 " pdb=" O UNK G 73 " model vdw 1.641 3.440 nonbonded pdb=" OE2 GLU E 65 " pdb=" O MET E 136 " model vdw 1.673 3.040 ... (remaining 152256 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: 1.000 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: 4.680 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 58.940 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.013 0.161 17998 Z= 0.838 Angle : 1.698 17.540 25112 Z= 0.888 Chirality : 0.085 1.000 2925 Planarity : 0.010 0.091 2584 Dihedral : 21.411 178.605 7676 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 25.63 Ramachandran Plot: Outliers : 0.73 % Allowed : 15.78 % Favored : 83.50 % Rotamer: Outliers : 0.97 % Allowed : 4.04 % Favored : 94.99 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 6.25 % Twisted General : 2.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.17), residues: 1515 helix: -2.30 (0.15), residues: 637 sheet: -2.50 (0.40), residues: 138 loop : -3.45 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A1030 HIS 0.015 0.004 HIS A 319 PHE 0.073 0.006 PHE A 634 TYR 0.070 0.006 TYR A 585 ARG 0.032 0.002 ARG A 727 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.796 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 ASN cc_start: 0.8434 (m-40) cc_final: 0.8145 (m-40) REVERT: A 566 MET cc_start: 0.8902 (mmt) cc_final: 0.8680 (tpp) REVERT: A 631 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9181 (mt) REVERT: A 634 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8100 (m-10) REVERT: A 701 ARG cc_start: 0.7806 (ptm160) cc_final: 0.7299 (ptt-90) REVERT: A 777 ILE cc_start: 0.9473 (pt) cc_final: 0.8937 (pt) REVERT: A 955 MET cc_start: 0.9326 (mtt) cc_final: 0.9105 (mmp) REVERT: D 586 MET cc_start: 0.6292 (tpp) cc_final: 0.6011 (tpp) REVERT: D 601 MET cc_start: 0.8037 (mtt) cc_final: 0.7480 (mtp) REVERT: H 397 LEU cc_start: 0.8459 (tp) cc_final: 0.8123 (pp) outliers start: 14 outliers final: 8 residues processed: 137 average time/residue: 0.3168 time to fit residues: 63.3952 Evaluate side-chains 91 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 40.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 105 ASN A 141 ASN A 163 GLN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 317 ASN A 319 HIS A 320 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 361 ASN A 475 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 574 ASN A 590 ASN A 633 ASN A 648 ASN A 697 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN A 804 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 839 ASN A 896 GLN A 900 ASN A 918 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 GLN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 482 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17998 Z= 0.250 Angle : 0.877 18.738 25112 Z= 0.457 Chirality : 0.050 0.853 2925 Planarity : 0.005 0.066 2584 Dihedral : 25.115 176.587 4350 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.07 % Favored : 86.80 % Rotamer: Outliers : 0.07 % Allowed : 2.30 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.94 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.20), residues: 1515 helix: -0.96 (0.18), residues: 656 sheet: -1.99 (0.41), residues: 149 loop : -3.11 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 604 HIS 0.006 0.002 HIS A 234 PHE 0.048 0.003 PHE A 634 TYR 0.028 0.002 TYR A1061 ARG 0.010 0.001 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.810 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 THR cc_start: 0.8390 (m) cc_final: 0.8074 (p) REVERT: A 139 LEU cc_start: 0.9679 (mt) cc_final: 0.9351 (mt) REVERT: A 179 SER cc_start: 0.6941 (p) cc_final: 0.6424 (p) REVERT: A 565 LEU cc_start: 0.9501 (mm) cc_final: 0.9270 (mm) REVERT: A 811 MET cc_start: 0.8690 (tmm) cc_final: 0.8099 (ppp) REVERT: A 912 LEU cc_start: 0.9205 (tp) cc_final: 0.8690 (tp) REVERT: D 586 MET cc_start: 0.6973 (tpp) cc_final: 0.6476 (tpp) REVERT: D 601 MET cc_start: 0.8494 (mtt) cc_final: 0.7890 (ttm) REVERT: F 59 TYR cc_start: 0.9056 (t80) cc_final: 0.8585 (t80) REVERT: F 61 ARG cc_start: 0.8572 (ttt-90) cc_final: 0.7479 (tmm160) REVERT: E 146 TYR cc_start: 0.9070 (t80) cc_final: 0.7992 (t80) REVERT: E 162 ASP cc_start: 0.9377 (m-30) cc_final: 0.9043 (m-30) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.3235 time to fit residues: 64.3790 Evaluate side-chains 89 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 165 optimal weight: 40.0000 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 30.0000 chunk 164 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 overall best weight: 5.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 GLN ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN D 656 GLN E 49 ASN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 HIS ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17998 Z= 0.373 Angle : 0.972 18.190 25112 Z= 0.505 Chirality : 0.052 0.857 2925 Planarity : 0.006 0.056 2584 Dihedral : 25.179 178.734 4350 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 36.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.96 % Favored : 82.90 % Rotamer: Outliers : 0.42 % Allowed : 5.29 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.94 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.20), residues: 1515 helix: -1.05 (0.18), residues: 675 sheet: -2.66 (0.39), residues: 147 loop : -2.98 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 604 HIS 0.007 0.002 HIS A 234 PHE 0.051 0.003 PHE A 634 TYR 0.041 0.003 TYR D 565 ARG 0.010 0.001 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.885 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: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9711 (mt) cc_final: 0.9478 (mt) REVERT: A 593 ILE cc_start: 0.9404 (tt) cc_final: 0.8872 (mt) REVERT: A 811 MET cc_start: 0.8801 (tmm) cc_final: 0.8285 (ppp) REVERT: A 912 LEU cc_start: 0.9520 (tp) cc_final: 0.9184 (tp) REVERT: D 586 MET cc_start: 0.6935 (tpp) cc_final: 0.6590 (tpp) REVERT: F 59 TYR cc_start: 0.9246 (t80) cc_final: 0.8881 (t80) REVERT: F 61 ARG cc_start: 0.8803 (ttt-90) cc_final: 0.7846 (tmm160) REVERT: E 86 MET cc_start: 0.8312 (tpp) cc_final: 0.8058 (tpp) REVERT: E 162 ASP cc_start: 0.9342 (m-30) cc_final: 0.9074 (m-30) REVERT: H 463 MET cc_start: 0.8644 (ptt) cc_final: 0.8372 (ptt) outliers start: 6 outliers final: 3 residues processed: 106 average time/residue: 0.2944 time to fit residues: 48.4561 Evaluate side-chains 72 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 30.0000 chunk 124 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 79 optimal weight: 0.0010 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 chunk 175 optimal weight: 40.0000 chunk 86 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17998 Z= 0.206 Angle : 0.784 17.305 25112 Z= 0.409 Chirality : 0.048 0.910 2925 Planarity : 0.005 0.057 2584 Dihedral : 24.755 178.251 4350 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.86 % Favored : 86.01 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -2.48 (0.21), residues: 1515 helix: -0.37 (0.19), residues: 664 sheet: -2.40 (0.39), residues: 149 loop : -2.79 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 604 HIS 0.004 0.001 HIS A 234 PHE 0.043 0.002 PHE A 634 TYR 0.033 0.002 TYR A 650 ARG 0.012 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.811 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 139 LEU cc_start: 0.9667 (mt) cc_final: 0.9377 (mt) REVERT: A 565 LEU cc_start: 0.9519 (mm) cc_final: 0.9265 (mm) REVERT: A 566 MET cc_start: 0.8731 (tpt) cc_final: 0.8089 (tpt) REVERT: A 595 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8898 (mt-10) REVERT: A 811 MET cc_start: 0.8719 (tmm) cc_final: 0.8301 (ppp) REVERT: A 954 VAL cc_start: 0.9396 (t) cc_final: 0.9130 (t) REVERT: D 586 MET cc_start: 0.6681 (tpp) cc_final: 0.5828 (tpp) REVERT: F 59 TYR cc_start: 0.9145 (t80) cc_final: 0.8880 (t80) REVERT: F 61 ARG cc_start: 0.8740 (ttt-90) cc_final: 0.8032 (ttp80) REVERT: E 86 MET cc_start: 0.8278 (tpp) cc_final: 0.7988 (tpp) REVERT: E 136 MET cc_start: 0.9099 (mmp) cc_final: 0.8815 (mmp) REVERT: E 146 TYR cc_start: 0.9129 (t80) cc_final: 0.8454 (t80) REVERT: E 162 ASP cc_start: 0.9403 (m-30) cc_final: 0.9007 (m-30) REVERT: H 463 MET cc_start: 0.8651 (ptt) cc_final: 0.8338 (ptt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2748 time to fit residues: 49.3090 Evaluate side-chains 79 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 150 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 HIS A 904 ASN A 918 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17998 Z= 0.300 Angle : 0.849 17.683 25112 Z= 0.444 Chirality : 0.048 0.858 2925 Planarity : 0.005 0.049 2584 Dihedral : 24.783 177.888 4350 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 32.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.25 % Favored : 84.69 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -2.64 (0.21), residues: 1515 helix: -0.51 (0.19), residues: 675 sheet: -2.60 (0.37), residues: 159 loop : -2.86 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 604 HIS 0.012 0.001 HIS A 949 PHE 0.032 0.003 PHE A 819 TYR 0.029 0.002 TYR A 650 ARG 0.011 0.001 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.755 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 139 LEU cc_start: 0.9702 (mt) cc_final: 0.9464 (mt) REVERT: A 566 MET cc_start: 0.8884 (tpt) cc_final: 0.7955 (tpt) REVERT: A 811 MET cc_start: 0.8887 (tmm) cc_final: 0.8317 (ppp) REVERT: A 912 LEU cc_start: 0.9340 (tp) cc_final: 0.9019 (tp) REVERT: F 59 TYR cc_start: 0.9236 (t80) cc_final: 0.8971 (t80) REVERT: E 86 MET cc_start: 0.8295 (tpp) cc_final: 0.8082 (tpp) REVERT: E 136 MET cc_start: 0.9094 (mmp) cc_final: 0.8849 (mmp) REVERT: E 146 TYR cc_start: 0.9163 (t80) cc_final: 0.8461 (t80) REVERT: E 162 ASP cc_start: 0.9354 (m-30) cc_final: 0.9031 (m-30) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2922 time to fit residues: 40.4109 Evaluate side-chains 62 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 103 optimal weight: 0.0470 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 overall best weight: 2.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 HIS ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 HIS ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17998 Z= 0.227 Angle : 0.782 17.112 25112 Z= 0.408 Chirality : 0.047 0.876 2925 Planarity : 0.004 0.048 2584 Dihedral : 24.596 178.010 4350 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.26 % Favored : 85.68 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -2.45 (0.21), residues: 1515 helix: -0.23 (0.19), residues: 670 sheet: -2.62 (0.38), residues: 160 loop : -2.86 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 604 HIS 0.004 0.001 HIS A 234 PHE 0.033 0.002 PHE A 819 TYR 0.026 0.002 TYR D 565 ARG 0.012 0.001 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9724 (mt) cc_final: 0.9454 (mt) REVERT: A 179 SER cc_start: 0.7386 (p) cc_final: 0.7137 (p) REVERT: A 562 ASN cc_start: 0.8473 (t0) cc_final: 0.7942 (t0) REVERT: A 566 MET cc_start: 0.8799 (tpt) cc_final: 0.8024 (tpt) REVERT: A 811 MET cc_start: 0.8824 (tmm) cc_final: 0.8298 (ppp) REVERT: A 912 LEU cc_start: 0.9301 (tp) cc_final: 0.8928 (tp) REVERT: A 916 LEU cc_start: 0.9313 (mt) cc_final: 0.9111 (mt) REVERT: D 586 MET cc_start: 0.7026 (tpp) cc_final: 0.5923 (tpp) REVERT: D 693 HIS cc_start: 0.8010 (m-70) cc_final: 0.7809 (m-70) REVERT: F 59 TYR cc_start: 0.9212 (t80) cc_final: 0.8745 (t80) REVERT: F 61 ARG cc_start: 0.8715 (ttt-90) cc_final: 0.7795 (tmm160) REVERT: E 136 MET cc_start: 0.9032 (mmp) cc_final: 0.8818 (mmp) REVERT: E 146 TYR cc_start: 0.9058 (t80) cc_final: 0.8651 (t80) REVERT: E 162 ASP cc_start: 0.9330 (m-30) cc_final: 0.8977 (m-30) REVERT: H 463 MET cc_start: 0.8448 (ptt) cc_final: 0.8067 (ptt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2656 time to fit residues: 40.5162 Evaluate side-chains 68 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 175 optimal weight: 40.0000 chunk 109 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17998 Z= 0.198 Angle : 0.744 16.775 25112 Z= 0.387 Chirality : 0.046 0.888 2925 Planarity : 0.004 0.054 2584 Dihedral : 24.342 177.282 4350 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.26 % Favored : 85.68 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.20 (0.21), residues: 1515 helix: 0.12 (0.20), residues: 659 sheet: -2.53 (0.39), residues: 156 loop : -2.84 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 604 HIS 0.005 0.001 HIS A 234 PHE 0.032 0.002 PHE A 819 TYR 0.031 0.002 TYR D 565 ARG 0.011 0.001 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.698 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 139 LEU cc_start: 0.9709 (mt) cc_final: 0.9418 (mt) REVERT: A 140 LEU cc_start: 0.9470 (tp) cc_final: 0.9269 (tt) REVERT: A 179 SER cc_start: 0.7360 (p) cc_final: 0.7139 (p) REVERT: A 562 ASN cc_start: 0.8283 (t0) cc_final: 0.7575 (m-40) REVERT: A 566 MET cc_start: 0.8813 (tpt) cc_final: 0.8155 (tpt) REVERT: A 811 MET cc_start: 0.8756 (tmm) cc_final: 0.8288 (ppp) REVERT: A 830 LEU cc_start: 0.9171 (mp) cc_final: 0.8937 (mt) REVERT: A 912 LEU cc_start: 0.9297 (tp) cc_final: 0.9046 (tp) REVERT: D 586 MET cc_start: 0.6964 (tpp) cc_final: 0.5841 (tpp) REVERT: F 59 TYR cc_start: 0.9167 (t80) cc_final: 0.8752 (t80) REVERT: F 61 ARG cc_start: 0.8673 (ttt-90) cc_final: 0.7838 (tmm160) REVERT: E 146 TYR cc_start: 0.9119 (t80) cc_final: 0.8717 (t80) REVERT: E 162 ASP cc_start: 0.9274 (m-30) cc_final: 0.8959 (m-30) REVERT: H 463 MET cc_start: 0.8378 (ptt) cc_final: 0.8029 (ptt) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2679 time to fit residues: 44.5731 Evaluate side-chains 70 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN A 343 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 HIS ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17998 Z= 0.174 Angle : 0.714 16.361 25112 Z= 0.369 Chirality : 0.046 0.902 2925 Planarity : 0.004 0.055 2584 Dihedral : 24.062 176.443 4350 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.14 % Favored : 86.80 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.95 (0.21), residues: 1515 helix: 0.36 (0.20), residues: 663 sheet: -2.17 (0.42), residues: 142 loop : -2.82 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 604 HIS 0.004 0.001 HIS A 234 PHE 0.033 0.001 PHE A 819 TYR 0.033 0.002 TYR D 565 ARG 0.009 0.001 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9725 (mt) cc_final: 0.9428 (mt) REVERT: A 140 LEU cc_start: 0.9438 (tp) cc_final: 0.9206 (tt) REVERT: A 179 SER cc_start: 0.7076 (p) cc_final: 0.6826 (p) REVERT: A 562 ASN cc_start: 0.8037 (t0) cc_final: 0.7606 (t0) REVERT: A 569 GLN cc_start: 0.9108 (tt0) cc_final: 0.8447 (tp-100) REVERT: A 811 MET cc_start: 0.8648 (tmm) cc_final: 0.8092 (ppp) REVERT: D 586 MET cc_start: 0.6801 (tpp) cc_final: 0.6006 (tpp) REVERT: F 59 TYR cc_start: 0.9124 (t80) cc_final: 0.8727 (t80) REVERT: F 61 ARG cc_start: 0.8561 (ttt-90) cc_final: 0.7753 (tmm160) REVERT: E 86 MET cc_start: 0.8010 (tpt) cc_final: 0.7494 (tmm) REVERT: E 136 MET cc_start: 0.9095 (mmp) cc_final: 0.8871 (mmp) REVERT: E 146 TYR cc_start: 0.9172 (t80) cc_final: 0.8860 (t80) REVERT: E 162 ASP cc_start: 0.9208 (m-30) cc_final: 0.8923 (m-30) REVERT: H 463 MET cc_start: 0.8442 (ptt) cc_final: 0.8177 (ptt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2902 time to fit residues: 48.5701 Evaluate side-chains 71 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 20.0000 chunk 168 optimal weight: 30.0000 chunk 153 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 147 optimal weight: 30.0000 chunk 154 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 overall best weight: 7.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 662 GLN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 17998 Z= 0.454 Angle : 0.987 18.293 25112 Z= 0.514 Chirality : 0.052 0.850 2925 Planarity : 0.006 0.055 2584 Dihedral : 24.732 176.167 4350 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 42.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 15.71 % Favored : 84.09 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -2.75 (0.20), residues: 1515 helix: -0.51 (0.19), residues: 665 sheet: -2.66 (0.41), residues: 135 loop : -3.02 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 604 HIS 0.010 0.002 HIS A 949 PHE 0.032 0.003 PHE A 634 TYR 0.072 0.003 TYR A 650 ARG 0.010 0.001 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9733 (mt) cc_final: 0.9528 (mt) REVERT: A 562 ASN cc_start: 0.8271 (t0) cc_final: 0.7602 (m-40) REVERT: A 811 MET cc_start: 0.8597 (tmm) cc_final: 0.8246 (ppp) REVERT: D 586 MET cc_start: 0.7094 (tpp) cc_final: 0.6310 (tpp) REVERT: F 59 TYR cc_start: 0.9236 (t80) cc_final: 0.8996 (t80) REVERT: F 61 ARG cc_start: 0.8932 (ttt-90) cc_final: 0.8404 (tmm160) REVERT: E 86 MET cc_start: 0.8347 (tpt) cc_final: 0.7411 (tmm) REVERT: E 136 MET cc_start: 0.9187 (mmp) cc_final: 0.8903 (mmp) REVERT: E 162 ASP cc_start: 0.9292 (m-30) cc_final: 0.8991 (m-30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2779 time to fit residues: 36.1406 Evaluate side-chains 56 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17998 Z= 0.274 Angle : 0.821 17.400 25112 Z= 0.426 Chirality : 0.048 0.810 2925 Planarity : 0.005 0.058 2584 Dihedral : 24.562 173.371 4350 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 32.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.18 % Favored : 84.69 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.57 (0.21), residues: 1515 helix: -0.25 (0.19), residues: 664 sheet: -2.81 (0.39), residues: 153 loop : -2.95 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 604 HIS 0.018 0.002 HIS A 948 PHE 0.021 0.002 PHE A 588 TYR 0.046 0.003 TYR A 650 ARG 0.011 0.001 ARG F 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9729 (mt) cc_final: 0.9479 (mt) REVERT: A 562 ASN cc_start: 0.7961 (t0) cc_final: 0.7353 (m-40) REVERT: A 811 MET cc_start: 0.8557 (tmm) cc_final: 0.8170 (ppp) REVERT: D 586 MET cc_start: 0.6765 (tpp) cc_final: 0.6153 (tpp) REVERT: F 18 MET cc_start: 0.9570 (mmp) cc_final: 0.9340 (mmm) REVERT: F 59 TYR cc_start: 0.9227 (t80) cc_final: 0.8881 (t80) REVERT: F 61 ARG cc_start: 0.8813 (ttt-90) cc_final: 0.8128 (ttp80) REVERT: E 86 MET cc_start: 0.8249 (tpt) cc_final: 0.7276 (tmm) REVERT: E 136 MET cc_start: 0.9020 (mmp) cc_final: 0.8652 (mmp) REVERT: E 162 ASP cc_start: 0.9338 (m-30) cc_final: 0.9016 (m-30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2704 time to fit residues: 36.0814 Evaluate side-chains 60 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 148 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN A 343 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.046809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.034799 restraints weight = 215505.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.035669 restraints weight = 147468.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.036340 restraints weight = 111826.059| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17998 Z= 0.189 Angle : 0.725 14.778 25112 Z= 0.377 Chirality : 0.045 0.655 2925 Planarity : 0.004 0.051 2584 Dihedral : 24.144 169.175 4350 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.18 (0.21), residues: 1515 helix: 0.16 (0.20), residues: 665 sheet: -2.64 (0.38), residues: 165 loop : -2.84 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 604 HIS 0.005 0.001 HIS A 949 PHE 0.018 0.002 PHE A 588 TYR 0.034 0.002 TYR D 565 ARG 0.011 0.001 ARG F 12 =============================================================================== Job complete usr+sys time: 2553.29 seconds wall clock time: 48 minutes 18.89 seconds (2898.89 seconds total)