Starting phenix.real_space_refine on Sat Dec 9 14:08:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsp_33430/12_2023/7xsp_33430.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsp_33430/12_2023/7xsp_33430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsp_33430/12_2023/7xsp_33430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsp_33430/12_2023/7xsp_33430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsp_33430/12_2023/7xsp_33430.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsp_33430/12_2023/7xsp_33430.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 50 5.49 5 S 33 5.16 5 C 6991 2.51 5 N 1979 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B ASP 148": "OD1" <-> "OD2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B ASP 171": "OD1" <-> "OD2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B ASP 463": "OD1" <-> "OD2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B ASP 542": "OD1" <-> "OD2" Residue "B ASP 547": "OD1" <-> "OD2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B ASP 644": "OD1" <-> "OD2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B GLU 656": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 671": "OE1" <-> "OE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B ASP 698": "OD1" <-> "OD2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "B GLU 763": "OE1" <-> "OE2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B ASP 788": "OD1" <-> "OD2" Residue "B ASP 793": "OD1" <-> "OD2" Residue "B PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 847": "OD1" <-> "OD2" Residue "B ASP 874": "OD1" <-> "OD2" Residue "B ASP 875": "OD1" <-> "OD2" Residue "B GLU 878": "OE1" <-> "OE2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 936": "OE1" <-> "OE2" Residue "B ASP 938": "OD1" <-> "OD2" Residue "B GLU 947": "OE1" <-> "OE2" Residue "B PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 995": "OE1" <-> "OE2" Residue "B PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1024": "OE1" <-> "OE2" Residue "B ASP 1025": "OD1" <-> "OD2" Residue "B GLU 1437": "OE1" <-> "OE2" Residue "B GLU 1451": "OE1" <-> "OE2" Residue "B GLU 1460": "OE1" <-> "OE2" Residue "B ASP 1471": "OD1" <-> "OD2" Residue "B GLU 1525": "OE1" <-> "OE2" Residue "B GLU 1529": "OE1" <-> "OE2" Residue "B ASP 1565": "OD1" <-> "OD2" Residue "B PHE 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1586": "OD1" <-> "OD2" Residue "B GLU 1589": "OE1" <-> "OE2" Residue "B GLU 1600": "OE1" <-> "OE2" Residue "B ASP 1623": "OD1" <-> "OD2" Residue "B ASP 1636": "OD1" <-> "OD2" Residue "B GLU 1640": "OE1" <-> "OE2" Residue "B GLU 1650": "OE1" <-> "OE2" Residue "B GLU 1651": "OE1" <-> "OE2" Residue "B GLU 1657": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11317 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 10247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1271, 10247 Classifications: {'peptide': 1271} Link IDs: {'PTRANS': 60, 'TRANS': 1210} Chain breaks: 6 Chain: "A" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 3, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 15} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 676 SG CYS B 88 77.713 23.479 19.824 1.00 50.66 S ATOM 947 SG CYS B 121 81.097 22.783 17.534 1.00 58.82 S ATOM 993 SG CYS B 127 80.389 26.879 19.183 1.00 46.40 S ATOM 1017 SG CYS B 130 81.082 24.013 21.266 1.00 43.14 S ATOM 3604 SG CYS B 491 55.166 29.174 45.413 1.00 50.01 S ATOM 3672 SG CYS B 501 56.555 28.034 42.294 1.00 44.90 S ATOM 3686 SG CYS B 503 54.360 30.892 41.958 1.00 44.09 S ATOM 3708 SG CYS B 506 58.143 31.814 42.708 1.00 43.59 S ATOM 5679 SG CYS B 750 40.765 34.293 72.491 1.00 55.83 S ATOM 5692 SG CYS B 752 38.920 37.986 71.151 1.00 51.95 S ATOM 5714 SG CYS B 755 42.536 38.002 70.638 1.00 48.48 S ATOM 7692 SG CYS B1018 41.070 58.721 102.197 1.00 40.83 S ATOM 7908 SG CYS B1406 41.835 55.177 100.983 1.00 41.16 S ATOM 7959 SG CYS B1414 37.793 57.007 100.502 1.00 40.43 S ATOM 7976 SG CYS B1417 40.582 57.625 98.336 1.00 36.21 S Time building chain proxies: 6.31, per 1000 atoms: 0.56 Number of scatterers: 11317 At special positions: 0 Unit cell: (111.15, 113.715, 138.51, 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 4 29.99 S 33 16.00 P 50 15.00 O 2260 8.00 N 1979 7.00 C 6991 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: 4.55 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 88 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 130 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 121 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 506 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 491 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 503 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 501 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 752 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 755 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 750 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1406 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1417 " Number of angles added : 21 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 18 sheets defined 27.6% alpha, 23.4% beta 8 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.805A pdb=" N MET B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.746A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.567A pdb=" N GLN B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 303 removed outlier: 4.247A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 354 through 375 removed outlier: 4.214A pdb=" N LEU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 488 removed outlier: 3.562A pdb=" N LEU B 475 " --> pdb=" O PRO B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 637 removed outlier: 3.787A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.696A pdb=" N HIS B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 759 Processing helix chain 'B' and resid 776 through 780 removed outlier: 3.895A pdb=" N PHE B 780 " --> pdb=" O GLY B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 848 Processing helix chain 'B' and resid 855 through 859 Processing helix chain 'B' and resid 873 through 881 Processing helix chain 'B' and resid 999 through 1016 removed outlier: 3.716A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1486 through 1493 removed outlier: 3.842A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) Processing helix chain 'B' and resid 1493 through 1499 Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.555A pdb=" N ILE B1587 " --> pdb=" O PRO B1583 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 removed outlier: 3.685A pdb=" N VAL B1618 " --> pdb=" O GLN B1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1615 through 1618' Processing helix chain 'B' and resid 1619 through 1629 Processing helix chain 'B' and resid 1662 through 1667 removed outlier: 3.566A pdb=" N LEU B1666 " --> pdb=" O THR B1662 " (cutoff:3.500A) Processing helix chain 'B' and resid 1673 through 1681 Processing sheet with id=AA1, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.795A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG B 19 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N TRP B 44 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL B 21 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N TRP B 46 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 9.773A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 13.786A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG B 180 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR B 191 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 178 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG B 193 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG B 176 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP B 195 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N SER B 174 " --> pdb=" O TRP B 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.864A pdb=" N LEU B 167 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR B 9 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.625A pdb=" N VAL B 85 " --> pdb=" O TRP B 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.075A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.698A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY B 600 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.698A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.944A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AB1, first strand: chain 'B' and resid 533 through 534 removed outlier: 3.740A pdb=" N THR B 539 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 703 through 704 removed outlier: 6.061A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 703 through 704 removed outlier: 6.061A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 699 through 700 removed outlier: 7.043A pdb=" N ALA B 699 " --> pdb=" O TYR B 808 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 803 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 920 through 921 Processing sheet with id=AB6, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.906A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.906A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL B1517 " --> pdb=" O THR B 960 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N THR B 960 " --> pdb=" O VAL B1517 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER B1519 " --> pdb=" O LEU B 958 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 958 " --> pdb=" O SER B1519 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP B1521 " --> pdb=" O CYS B 956 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS B 956 " --> pdb=" O ASP B1521 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARG B1523 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 954 " --> pdb=" O ARG B1523 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU B1525 " --> pdb=" O GLY B 952 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY B 952 " --> pdb=" O GLU B1525 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B 957 " --> pdb=" O ILE B1564 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE B1564 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU B 959 " --> pdb=" O ILE B1562 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE B1562 " --> pdb=" O GLU B 959 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 985 through 986 removed outlier: 6.533A pdb=" N LYS B 985 " --> pdb=" O THR B1508 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLU B1510 " --> pdb=" O LYS B 985 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 5.90 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3048 1.33 - 1.45: 2347 1.45 - 1.57: 6143 1.57 - 1.69: 94 1.69 - 1.81: 45 Bond restraints: 11677 Sorted by residual: bond pdb=" O3' U D -2 " pdb=" P A D -1 " ideal model delta sigma weight residual 1.607 1.507 0.100 1.50e-02 4.44e+03 4.43e+01 bond pdb=" O3' A D -1 " pdb=" P C D 0 " ideal model delta sigma weight residual 1.607 1.537 0.070 1.50e-02 4.44e+03 2.19e+01 bond pdb=" O3' C D 15 " pdb=" P G D 16 " ideal model delta sigma weight residual 1.607 1.543 0.064 1.50e-02 4.44e+03 1.80e+01 bond pdb=" P A D -1 " pdb=" OP1 A D -1 " ideal model delta sigma weight residual 1.485 1.424 0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" O3' G D 16 " pdb=" P G D 17 " ideal model delta sigma weight residual 1.607 1.561 0.046 1.50e-02 4.44e+03 9.36e+00 ... (remaining 11672 not shown) Histogram of bond angle deviations from ideal: 96.17 - 103.84: 288 103.84 - 111.50: 4985 111.50 - 119.17: 4592 119.17 - 126.83: 5824 126.83 - 134.50: 293 Bond angle restraints: 15982 Sorted by residual: angle pdb=" O3' A D -1 " pdb=" C3' A D -1 " pdb=" C2' A D -1 " ideal model delta sigma weight residual 109.50 97.00 12.50 1.50e+00 4.44e-01 6.94e+01 angle pdb=" O2' G D 16 " pdb=" C2' G D 16 " pdb=" C1' G D 16 " ideal model delta sigma weight residual 108.40 96.17 12.23 1.50e+00 4.44e-01 6.65e+01 angle pdb=" O2' A D -1 " pdb=" C2' A D -1 " pdb=" C1' A D -1 " ideal model delta sigma weight residual 111.80 121.65 -9.85 1.50e+00 4.44e-01 4.31e+01 angle pdb=" C4' A D -1 " pdb=" C3' A D -1 " pdb=" O3' A D -1 " ideal model delta sigma weight residual 109.40 101.33 8.07 1.50e+00 4.44e-01 2.89e+01 angle pdb=" C ASP B1470 " pdb=" N ASP B1471 " pdb=" CA ASP B1471 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 ... (remaining 15977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 6702 35.56 - 71.13: 286 71.13 - 106.69: 26 106.69 - 142.26: 1 142.26 - 177.82: 3 Dihedral angle restraints: 7018 sinusoidal: 3392 harmonic: 3626 Sorted by residual: dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 40.72 159.28 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U D -13 " pdb=" C1' U D -13 " pdb=" N1 U D -13 " pdb=" C2 U D -13 " ideal model delta sinusoidal sigma weight residual -160.00 -27.30 -132.70 1 1.50e+01 4.44e-03 7.16e+01 dihedral pdb=" O4' U D -8 " pdb=" C1' U D -8 " pdb=" N1 U D -8 " pdb=" C2 U D -8 " ideal model delta sinusoidal sigma weight residual -128.00 49.82 -177.82 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1707 0.160 - 0.321: 17 0.321 - 0.481: 2 0.481 - 0.642: 0 0.642 - 0.802: 1 Chirality restraints: 1727 Sorted by residual: chirality pdb=" C2' A D -1 " pdb=" C3' A D -1 " pdb=" O2' A D -1 " pdb=" C1' A D -1 " both_signs ideal model delta sigma weight residual False -2.52 -1.72 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C1' A D -1 " pdb=" O4' A D -1 " pdb=" C2' A D -1 " pdb=" N9 A D -1 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" C3' A D -1 " pdb=" C4' A D -1 " pdb=" O3' A D -1 " pdb=" C2' A D -1 " both_signs ideal model delta sigma weight residual False -2.74 -3.07 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 1724 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D -1 " 0.063 2.00e-02 2.50e+03 3.03e-02 2.53e+01 pdb=" N9 A D -1 " -0.073 2.00e-02 2.50e+03 pdb=" C8 A D -1 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A D -1 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A D -1 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A D -1 " 0.012 2.00e-02 2.50e+03 pdb=" N6 A D -1 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A D -1 " 0.015 2.00e-02 2.50e+03 pdb=" C2 A D -1 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A D -1 " -0.016 2.00e-02 2.50e+03 pdb=" C4 A D -1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 962 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO B 963 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 963 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 963 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 426 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO B 427 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 427 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 427 " 0.042 5.00e-02 4.00e+02 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3375 2.82 - 3.34: 8781 3.34 - 3.86: 17973 3.86 - 4.38: 20992 4.38 - 4.90: 36988 Nonbonded interactions: 88109 Sorted by model distance: nonbonded pdb=" OH TYR B1663 " pdb=" OP2 C D 15 " model vdw 2.303 2.440 nonbonded pdb=" O ASN B 179 " pdb=" O2' G D -3 " model vdw 2.308 2.440 nonbonded pdb=" OH TYR B1645 " pdb=" OP1 C D 14 " model vdw 2.313 2.440 nonbonded pdb=" O PHE B 104 " pdb=" O2' G D -9 " model vdw 2.341 2.440 nonbonded pdb=" OG SER B 680 " pdb=" O GLY B 859 " model vdw 2.346 2.440 ... (remaining 88104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 3.470 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 38.780 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.006 0.100 11677 Z= 0.391 Angle : 0.853 13.733 15982 Z= 0.490 Chirality : 0.058 0.802 1727 Planarity : 0.008 0.084 1884 Dihedral : 18.514 177.820 4698 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 3.42 % Allowed : 14.59 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.85 (0.19), residues: 1257 helix: -2.18 (0.21), residues: 300 sheet: -0.15 (0.35), residues: 192 loop : -2.35 (0.17), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS B 727 PHE 0.027 0.003 PHE B1691 TYR 0.018 0.002 TYR B 860 ARG 0.005 0.001 ARG B1452 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 264 time to evaluate : 1.353 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 14 residues processed: 288 average time/residue: 1.2448 time to fit residues: 387.3153 Evaluate side-chains 225 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 211 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 0.1521 time to fit residues: 3.1310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 0.0040 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN B 112 GLN B 114 GLN B 276 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN B 350 ASN B 365 ASN B 433 GLN B 871 ASN ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1404 HIS B1621 HIS B1649 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11677 Z= 0.165 Angle : 0.528 5.883 15982 Z= 0.281 Chirality : 0.042 0.252 1727 Planarity : 0.005 0.053 1884 Dihedral : 16.648 179.553 2103 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 4.50 % Allowed : 19.37 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.46 (0.20), residues: 1257 helix: 0.40 (0.28), residues: 308 sheet: -0.12 (0.34), residues: 190 loop : -1.88 (0.18), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS B 915 PHE 0.015 0.001 PHE B1691 TYR 0.011 0.001 TYR B 149 ARG 0.007 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 232 time to evaluate : 1.229 Fit side-chains outliers start: 50 outliers final: 20 residues processed: 255 average time/residue: 1.3248 time to fit residues: 364.2964 Evaluate side-chains 227 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 8 average time/residue: 0.5884 time to fit residues: 7.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 0.0570 chunk 32 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN B 673 GLN B 917 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11677 Z= 0.167 Angle : 0.512 6.736 15982 Z= 0.271 Chirality : 0.042 0.225 1727 Planarity : 0.005 0.050 1884 Dihedral : 16.528 178.841 2103 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 3.87 % Allowed : 20.72 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1257 helix: 1.41 (0.29), residues: 308 sheet: 0.24 (0.35), residues: 192 loop : -1.60 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS B 727 PHE 0.016 0.001 PHE B1570 TYR 0.019 0.001 TYR B1595 ARG 0.008 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 217 time to evaluate : 1.274 Fit side-chains outliers start: 43 outliers final: 21 residues processed: 240 average time/residue: 1.2704 time to fit residues: 329.7678 Evaluate side-chains 231 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.3622 time to fit residues: 4.4359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 778 ASN B1485 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11677 Z= 0.344 Angle : 0.603 7.632 15982 Z= 0.316 Chirality : 0.047 0.273 1727 Planarity : 0.006 0.055 1884 Dihedral : 16.642 179.361 2103 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.09 % Favored : 94.75 % Rotamer: Outliers : 4.77 % Allowed : 20.45 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1257 helix: 1.57 (0.30), residues: 308 sheet: 0.55 (0.35), residues: 197 loop : -1.59 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.009 0.001 HIS B 727 PHE 0.022 0.002 PHE B1691 TYR 0.016 0.002 TYR B 149 ARG 0.007 0.001 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 223 time to evaluate : 1.326 Fit side-chains outliers start: 53 outliers final: 30 residues processed: 252 average time/residue: 1.3097 time to fit residues: 356.4127 Evaluate side-chains 246 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 18 residues processed: 12 average time/residue: 0.3111 time to fit residues: 6.6322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 433 GLN B 993 ASN B1485 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11677 Z= 0.183 Angle : 0.535 8.224 15982 Z= 0.279 Chirality : 0.042 0.246 1727 Planarity : 0.005 0.056 1884 Dihedral : 16.550 179.155 2103 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 4.68 % Allowed : 22.52 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1257 helix: 1.96 (0.30), residues: 308 sheet: 0.58 (0.35), residues: 192 loop : -1.46 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS B 727 PHE 0.019 0.001 PHE B1570 TYR 0.011 0.001 TYR B 149 ARG 0.009 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 214 time to evaluate : 1.203 Fit side-chains outliers start: 52 outliers final: 33 residues processed: 244 average time/residue: 1.3174 time to fit residues: 348.0111 Evaluate side-chains 243 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 210 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 24 residues processed: 11 average time/residue: 0.3405 time to fit residues: 6.4475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 433 GLN B 534 ASN B 778 ASN B 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11677 Z= 0.289 Angle : 0.586 8.537 15982 Z= 0.306 Chirality : 0.045 0.264 1727 Planarity : 0.005 0.059 1884 Dihedral : 16.571 178.868 2103 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 5.32 % Allowed : 21.98 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1257 helix: 1.91 (0.30), residues: 308 sheet: 0.71 (0.35), residues: 197 loop : -1.48 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1530 HIS 0.007 0.001 HIS B 727 PHE 0.021 0.002 PHE B1570 TYR 0.014 0.001 TYR B 149 ARG 0.009 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 215 time to evaluate : 1.095 Fit side-chains outliers start: 59 outliers final: 37 residues processed: 247 average time/residue: 1.2819 time to fit residues: 342.2387 Evaluate side-chains 248 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 22 residues processed: 17 average time/residue: 0.6494 time to fit residues: 14.4385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 76 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 328 HIS B 433 GLN B 786 HIS B 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11677 Z= 0.163 Angle : 0.523 7.420 15982 Z= 0.273 Chirality : 0.042 0.236 1727 Planarity : 0.005 0.057 1884 Dihedral : 16.499 179.605 2103 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 4.68 % Allowed : 22.61 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.22), residues: 1257 helix: 2.19 (0.30), residues: 310 sheet: 0.73 (0.36), residues: 190 loop : -1.42 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 727 PHE 0.021 0.001 PHE B1570 TYR 0.009 0.001 TYR B 149 ARG 0.010 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 220 time to evaluate : 1.190 Fit side-chains outliers start: 52 outliers final: 30 residues processed: 249 average time/residue: 1.2279 time to fit residues: 330.5892 Evaluate side-chains 246 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 20 residues processed: 10 average time/residue: 0.5540 time to fit residues: 8.2267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 433 GLN B 534 ASN B 778 ASN B 955 ASN B 993 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11677 Z= 0.346 Angle : 0.613 8.814 15982 Z= 0.320 Chirality : 0.047 0.271 1727 Planarity : 0.006 0.067 1884 Dihedral : 16.595 178.716 2103 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 4.23 % Allowed : 23.33 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.22), residues: 1257 helix: 1.93 (0.29), residues: 310 sheet: 0.77 (0.35), residues: 201 loop : -1.48 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1530 HIS 0.007 0.001 HIS B 727 PHE 0.024 0.002 PHE B1570 TYR 0.015 0.002 TYR B 149 ARG 0.009 0.001 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 218 time to evaluate : 1.388 Fit side-chains outliers start: 47 outliers final: 37 residues processed: 244 average time/residue: 1.2885 time to fit residues: 341.2316 Evaluate side-chains 257 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 22 residues processed: 15 average time/residue: 0.3850 time to fit residues: 8.9541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11677 Z= 0.163 Angle : 0.530 7.549 15982 Z= 0.276 Chirality : 0.042 0.233 1727 Planarity : 0.005 0.062 1884 Dihedral : 16.489 179.609 2103 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 3.06 % Allowed : 25.05 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1257 helix: 2.26 (0.30), residues: 310 sheet: 0.72 (0.35), residues: 199 loop : -1.38 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS B 727 PHE 0.024 0.001 PHE B1570 TYR 0.010 0.001 TYR B 578 ARG 0.009 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 1.243 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 27 residues processed: 241 average time/residue: 1.3085 time to fit residues: 340.7143 Evaluate side-chains 239 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 5 average time/residue: 0.6729 time to fit residues: 5.5836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 433 GLN B 534 ASN B 778 ASN B 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11677 Z= 0.224 Angle : 0.561 8.343 15982 Z= 0.290 Chirality : 0.043 0.245 1727 Planarity : 0.005 0.064 1884 Dihedral : 16.494 179.456 2103 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.57 % Favored : 94.35 % Rotamer: Outliers : 2.88 % Allowed : 24.95 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1257 helix: 2.18 (0.29), residues: 310 sheet: 0.80 (0.35), residues: 204 loop : -1.41 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1530 HIS 0.006 0.001 HIS B 727 PHE 0.025 0.002 PHE B1570 TYR 0.013 0.001 TYR B 149 ARG 0.009 0.000 ARG B 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 1.320 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 26 residues processed: 240 average time/residue: 1.3156 time to fit residues: 340.8899 Evaluate side-chains 240 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 214 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 5 average time/residue: 0.8094 time to fit residues: 6.1626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 433 GLN B 534 ASN B 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098432 restraints weight = 15268.715| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.84 r_work: 0.3087 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11677 Z= 0.244 Angle : 0.577 9.974 15982 Z= 0.298 Chirality : 0.044 0.250 1727 Planarity : 0.005 0.063 1884 Dihedral : 16.508 178.823 2103 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 2.70 % Allowed : 25.50 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1257 helix: 2.15 (0.29), residues: 310 sheet: 0.78 (0.35), residues: 201 loop : -1.41 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1530 HIS 0.005 0.001 HIS B 727 PHE 0.025 0.002 PHE B1570 TYR 0.013 0.001 TYR B 149 ARG 0.010 0.000 ARG B 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5408.75 seconds wall clock time: 96 minutes 8.80 seconds (5768.80 seconds total)