Starting phenix.real_space_refine (version: dev) on Wed Feb 22 10:53:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/02_2023/6d6v_7821.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/02_2023/6d6v_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_7821/02_2023/6d6v_7821.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/02_2023/6d6v_7821.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/02_2023/6d6v_7821.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6v_7821/02_2023/6d6v_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 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-4877/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: 10.15, per 1000 atoms: 0.59 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: 8.28 Conformation dependent library (CDL) restraints added in 1.9 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: 5.40 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: 6.90 Time building geometry restraints manager: 8.75 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: 1.210 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: 5.350 Check model and map are aligned: 0.270 Process input model: 54.780 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.150 ------------------------------------------------------------------------------- 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 : 25.63 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 : 1.885 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 137 average time/residue: 0.3397 time to fit residues: 68.2458 Evaluate side-chains 87 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2629 time to fit residues: 5.3462 ------------------------------------------------------------------------------- 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: 8.9990 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 : 25.69 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 : 1.962 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: 0.3512 time to fit residues: 69.8739 Evaluate side-chains 88 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5373 time to fit residues: 3.8636 ------------------------------------------------------------------------------- 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: 0.8980 chunk 51 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 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: 8.9990 chunk 132 optimal weight: 20.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 767 GLN ** A 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** 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 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 17998 Z= 0.372 Angle : 0.967 18.381 25112 Z= 0.501 Chirality : 0.052 0.864 2925 Planarity : 0.005 0.058 2584 Dihedral : 22.654 178.252 3896 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 35.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.50 % Favored : 83.37 % Rotamer Outliers : 0.28 % 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: -3.07 (0.20), residues: 1515 helix: -1.00 (0.18), residues: 666 sheet: -2.65 (0.39), residues: 143 loop : -2.97 (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: 4 poor density : 98 time to evaluate : 1.742 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 outliers start: 4 outliers final: 2 residues processed: 102 average time/residue: 0.3006 time to fit residues: 47.4486 Evaluate side-chains 67 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2067 time to fit residues: 2.9166 ------------------------------------------------------------------------------- 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: 4.9990 chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 0.0470 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 overall best weight: 0.9680 ------------------------------------------------------------------------------- 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 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 804 ASN A 824 GLN A 853 ASN 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 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 17998 Z= 0.193 Angle : 0.776 16.979 25112 Z= 0.401 Chirality : 0.048 0.899 2925 Planarity : 0.004 0.074 2584 Dihedral : 22.090 177.830 3896 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.20 % Favored : 86.67 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.40 (0.21), residues: 1515 helix: -0.26 (0.19), residues: 663 sheet: -2.27 (0.39), residues: 158 loop : -2.81 (0.22), 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 120 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 1.901 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 outliers start: 2 outliers final: 0 residues processed: 120 average time/residue: 0.3194 time to fit residues: 58.3294 Evaluate side-chains 86 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3215 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 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: 9.9990 chunk 44 optimal weight: 0.1980 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** 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 ** 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 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 804 ASN A 824 GLN A 865 HIS ** 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 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** 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: 0.7382 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 17998 Z= 0.381 Angle : 0.927 18.089 25112 Z= 0.481 Chirality : 0.050 0.845 2925 Planarity : 0.005 0.055 2584 Dihedral : 22.338 177.417 3896 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 36.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.24 % Favored : 83.70 % 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: -2.75 (0.20), residues: 1515 helix: -0.60 (0.19), residues: 670 sheet: -2.56 (0.37), residues: 169 loop : -2.92 (0.23), residues: 676 *********************** 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 : 1.639 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: 86 average time/residue: 0.3262 time to fit residues: 44.2033 Evaluate side-chains 58 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3734 ------------------------------------------------------------------------------- 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: 7.9990 chunk 43 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 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 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 839 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** ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 17998 Z= 0.261 Angle : 0.825 17.747 25112 Z= 0.427 Chirality : 0.048 0.854 2925 Planarity : 0.004 0.060 2584 Dihedral : 22.201 176.742 3896 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 29.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.79 % Favored : 85.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -2.55 (0.21), residues: 1515 helix: -0.37 (0.19), residues: 674 sheet: -2.54 (0.39), residues: 158 loop : -2.88 (0.23), residues: 683 *********************** 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 92 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.959 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: 92 average time/residue: 0.2883 time to fit residues: 42.5242 Evaluate side-chains 68 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.782 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3072 ------------------------------------------------------------------------------- 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: 2.9990 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 98 optimal weight: 0.4980 chunk 175 optimal weight: 50.0000 chunk 109 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN A 904 ASN A 918 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 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 629 ASN 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** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 17998 Z= 0.191 Angle : 0.744 16.118 25112 Z= 0.382 Chirality : 0.046 0.836 2925 Planarity : 0.004 0.074 2584 Dihedral : 21.663 169.861 3896 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 22.22 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 : 0.27 % 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: -2.03 (0.21), residues: 1515 helix: 0.25 (0.20), residues: 667 sheet: -2.03 (0.42), residues: 146 loop : -2.88 (0.22), residues: 702 *********************** 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 110 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.834 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: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3016 time to fit residues: 51.9958 Evaluate side-chains 67 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.712 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2441 ------------------------------------------------------------------------------- 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: 5.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 611 GLN ** 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 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN ** A 927 GLN ** 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 ** 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: 0.7242 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 17998 Z= 0.230 Angle : 0.768 14.424 25112 Z= 0.395 Chirality : 0.045 0.634 2925 Planarity : 0.004 0.062 2584 Dihedral : 21.658 169.117 3896 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 27.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.73 % Favored : 86.20 % 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: -2.09 (0.21), residues: 1515 helix: 0.21 (0.20), residues: 666 sheet: -2.33 (0.40), residues: 158 loop : -2.85 (0.22), residues: 691 *********************** 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 90 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.762 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: 90 average time/residue: 0.2845 time to fit residues: 41.4689 Evaluate side-chains 66 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2924 ------------------------------------------------------------------------------- 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: 0.0770 chunk 71 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 147 optimal weight: 30.0000 chunk 154 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 overall best weight: 5.0144 ------------------------------------------------------------------------------- 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 569 GLN ** A 581 GLN ** 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 776 ASN ** 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** ** 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 606 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: 0.7350 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 17998 Z= 0.328 Angle : 0.868 13.674 25112 Z= 0.448 Chirality : 0.047 0.489 2925 Planarity : 0.005 0.059 2584 Dihedral : 21.956 169.153 3896 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 33.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.64 % Favored : 84.29 % 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: -2.40 (0.21), residues: 1515 helix: -0.09 (0.19), residues: 660 sheet: -2.43 (0.41), residues: 146 loop : -2.96 (0.22), residues: 709 *********************** 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 83 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.677 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: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2943 time to fit residues: 39.3820 Evaluate side-chains 56 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2577 ------------------------------------------------------------------------------- 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: 2.9990 chunk 172 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 0.0270 chunk 181 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 14 optimal weight: 0.0060 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.8058 ------------------------------------------------------------------------------- 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 556 ASN ** 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 804 ASN A 839 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 17998 Z= 0.183 Angle : 0.730 11.481 25112 Z= 0.374 Chirality : 0.045 0.499 2925 Planarity : 0.004 0.062 2584 Dihedral : 21.439 167.688 3896 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.61 % Favored : 87.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.94 (0.21), residues: 1515 helix: 0.35 (0.20), residues: 663 sheet: -2.03 (0.41), residues: 154 loop : -2.84 (0.22), residues: 698 ********************** 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 96 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.663 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: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3112 time to fit residues: 46.4775 Evaluate side-chains 69 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.953 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1668 ------------------------------------------------------------------------------- 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: 3.9990 chunk 153 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 18 optimal weight: 0.0370 chunk 26 optimal weight: 0.0870 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 804 ASN ** 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 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.046858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034900 restraints weight = 216422.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.035734 restraints weight = 148188.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036413 restraints weight = 112837.098| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 17998 Z= 0.201 Angle : 0.723 11.025 25112 Z= 0.373 Chirality : 0.043 0.435 2925 Planarity : 0.004 0.056 2584 Dihedral : 21.376 168.789 3896 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.40 % Favored : 86.60 % 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: -1.91 (0.21), residues: 1515 helix: 0.38 (0.20), residues: 668 sheet: -2.22 (0.41), residues: 154 loop : -2.79 (0.22), residues: 693 =============================================================================== Job complete usr+sys time: 2467.41 seconds wall clock time: 47 minutes 2.84 seconds (2822.84 seconds total)