Starting phenix.real_space_refine (version: dev) on Tue Dec 13 21:16:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/12_2022/6d6v_7821.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/12_2022/6d6v_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_7821/12_2022/6d6v_7821.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/12_2022/6d6v_7821.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/12_2022/6d6v_7821.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/12_2022/6d6v_7821.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Convert atoms to be neutral 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-4807/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: 24 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: 10.76, per 1000 atoms: 0.62 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: 9.05 Conformation dependent library (CDL) restraints added in 2.1 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: 5.59 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: 6.84 Time building geometry restraints manager: 9.60 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: 10004 35.72 - 71.44: 418 71.44 - 107.16: 60 107.16 - 142.88: 12 142.88 - 178.61: 10 Dihedral angle restraints: 10504 sinusoidal: 5462 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 10501 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 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. 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: 0.610 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: 5.370 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.150 Process input model: 56.880 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 1.697 17.540 25112 Z= 0.888 Chirality : 0.085 1.000 2925 Planarity : 0.010 0.091 2584 Dihedral : 19.433 178.605 7222 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.73 % Allowed : 15.78 % Favored : 83.50 % Rotamer Outliers : 0.97 % 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 *********************** 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 : 1.869 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 outliers start: 14 outliers final: 8 residues processed: 137 average time/residue: 0.3372 time to fit residues: 68.6398 Evaluate side-chains 87 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2547 time to fit residues: 5.4428 ------------------------------------------------------------------------------- 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: 10.0000 chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 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 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN 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 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: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 17998 Z= 0.238 Angle : 0.885 18.830 25112 Z= 0.459 Chirality : 0.050 0.843 2925 Planarity : 0.005 0.067 2584 Dihedral : 22.591 176.223 3896 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.94 % Favored : 86.93 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 1.07 % 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: -3.07 (0.20), residues: 1515 helix: -0.97 (0.18), residues: 655 sheet: -2.09 (0.41), residues: 151 loop : -3.12 (0.21), residues: 709 *********************** 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 134 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.891 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 outliers start: 3 outliers final: 2 residues processed: 133 average time/residue: 0.3228 time to fit residues: 65.1889 Evaluate side-chains 88 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.830 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1697 time to fit residues: 2.9648 ------------------------------------------------------------------------------- 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: 6.9990 chunk 51 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 165 optimal weight: 40.0000 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 30.0000 chunk 164 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 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** A 987 ASN ** 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 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: 0.7404 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 17998 Z= 0.393 Angle : 1.001 18.488 25112 Z= 0.517 Chirality : 0.053 0.868 2925 Planarity : 0.006 0.056 2584 Dihedral : 22.725 177.972 3896 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 37.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.77 % Favored : 83.10 % Rotamer Outliers : 0.42 % 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: -3.16 (0.20), residues: 1515 helix: -1.07 (0.18), residues: 666 sheet: -2.70 (0.39), residues: 143 loop : -3.01 (0.22), residues: 706 *********************** 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 102 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 1.680 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 outliers start: 6 outliers final: 1 residues processed: 102 average time/residue: 0.2844 time to fit residues: 45.5414 Evaluate side-chains 64 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.731 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1534 time to fit residues: 2.6219 ------------------------------------------------------------------------------- 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: 20.0000 chunk 124 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 79 optimal weight: 0.0470 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- 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 648 ASN ** 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** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 HIS ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** 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 ** 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: 0.7234 moved from start: 0.3569 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 : 0.794 17.197 25112 Z= 0.411 Chirality : 0.048 0.902 2925 Planarity : 0.005 0.074 2584 Dihedral : 22.203 177.894 3896 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.66 % Favored : 86.20 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.49 (0.21), residues: 1515 helix: -0.36 (0.19), residues: 663 sheet: -2.41 (0.39), residues: 158 loop : -2.81 (0.23), residues: 694 *********************** 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 108 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 1.827 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 outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 0.2803 time to fit residues: 48.2882 Evaluate side-chains 80 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4470 time to fit residues: 3.2362 ------------------------------------------------------------------------------- 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: 10.0000 chunk 99 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 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 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** ** 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 ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 17998 Z= 0.334 Angle : 0.883 17.820 25112 Z= 0.459 Chirality : 0.049 0.849 2925 Planarity : 0.005 0.057 2584 Dihedral : 22.297 177.350 3896 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 34.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.11 % Favored : 83.76 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -0.61 (0.19), residues: 680 sheet: -2.70 (0.36), residues: 171 loop : -2.89 (0.23), residues: 664 *********************** 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 95 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.716 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 outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.2790 time to fit residues: 41.8202 Evaluate side-chains 61 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1673 ------------------------------------------------------------------------------- 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: 10.0000 chunk 158 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** 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 824 GLN A 839 ASN A 918 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 HIS ** 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: 0.7302 moved from start: 0.4148 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= 0.242 Angle : 0.799 17.345 25112 Z= 0.415 Chirality : 0.047 0.854 2925 Planarity : 0.004 0.060 2584 Dihedral : 22.109 176.769 3896 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.32 % Favored : 85.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -0.29 (0.19), residues: 676 sheet: -2.67 (0.38), residues: 160 loop : -2.83 (0.23), residues: 679 *********************** 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 97 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2868 time to fit residues: 46.0027 Evaluate side-chains 63 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8394 ------------------------------------------------------------------------------- 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: 9.9990 chunk 19 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 chunk 175 optimal weight: 40.0000 chunk 109 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 569 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 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 776 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** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 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 629 ASN D 656 GLN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 17998 Z= 0.192 Angle : 0.755 16.784 25112 Z= 0.389 Chirality : 0.047 0.862 2925 Planarity : 0.004 0.070 2584 Dihedral : 21.772 172.357 3896 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 24.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.13 % Favored : 85.81 % Rotamer Outliers : 0.00 % 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: -2.15 (0.21), residues: 1515 helix: 0.16 (0.19), residues: 669 sheet: -2.67 (0.38), residues: 166 loop : -2.80 (0.23), residues: 680 *********************** 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 105 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.934 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 outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2960 time to fit residues: 49.2159 Evaluate side-chains 70 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2083 ------------------------------------------------------------------------------- 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: 0.2980 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 33 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 0.0570 chunk 137 optimal weight: 5.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 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** ** 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 609 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.5099 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= 0.180 Angle : 0.723 13.737 25112 Z= 0.373 Chirality : 0.044 0.624 2925 Planarity : 0.004 0.066 2584 Dihedral : 21.440 168.798 3896 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.53 % Favored : 86.40 % Rotamer Outliers : 0.00 % 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: -1.90 (0.21), residues: 1515 helix: 0.36 (0.20), residues: 668 sheet: -2.12 (0.43), residues: 144 loop : -2.78 (0.22), residues: 703 *********************** 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 100 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.874 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 outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2990 time to fit residues: 47.0004 Evaluate side-chains 66 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3303 ------------------------------------------------------------------------------- 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: 4.9990 chunk 128 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 147 optimal weight: 30.0000 chunk 154 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** 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 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 662 GLN ** A 697 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 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 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** ** 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 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.081 17998 Z= 0.488 Angle : 1.051 17.152 25112 Z= 0.545 Chirality : 0.052 0.434 2925 Planarity : 0.006 0.065 2584 Dihedral : 22.232 171.096 3896 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 45.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 16.30 % Favored : 83.50 % Rotamer Outliers : 0.00 % 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: -2.97 (0.20), residues: 1515 helix: -0.75 (0.18), residues: 673 sheet: -2.72 (0.39), residues: 146 loop : -3.09 (0.21), residues: 696 *********************** 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 82 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2907 time to fit residues: 39.2692 Evaluate side-chains 52 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3998 ------------------------------------------------------------------------------- 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: 0.9980 chunk 172 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 556 ASN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A 697 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 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 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 656 GLN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 HIS ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 17998 Z= 0.208 Angle : 0.775 13.129 25112 Z= 0.400 Chirality : 0.045 0.468 2925 Planarity : 0.004 0.054 2584 Dihedral : 21.733 167.610 3896 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 28.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.26 % Favored : 85.74 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.34 (0.21), residues: 1515 helix: -0.05 (0.19), residues: 674 sheet: -2.27 (0.42), residues: 142 loop : -2.99 (0.22), residues: 699 ********************** 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 94 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.2790 time to fit residues: 42.4466 Evaluate side-chains 63 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1707 time to fit residues: 2.6856 ------------------------------------------------------------------------------- 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: 0.0170 chunk 153 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 144 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 343 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** 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 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN ** 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 612 ASN D 656 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.047413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.035490 restraints weight = 213769.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036291 restraints weight = 145570.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.036940 restraints weight = 110640.995| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 17998 Z= 0.177 Angle : 0.709 11.265 25112 Z= 0.369 Chirality : 0.043 0.423 2925 Planarity : 0.004 0.058 2584 Dihedral : 21.264 169.370 3896 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.81 % Favored : 87.19 % Rotamer Outliers : 0.00 % 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: -1.94 (0.21), residues: 1515 helix: 0.41 (0.20), residues: 667 sheet: -2.44 (0.36), residues: 188 loop : -2.78 (0.23), residues: 660 =============================================================================== Job complete usr+sys time: 2399.11 seconds wall clock time: 45 minutes 51.83 seconds (2751.83 seconds total)