Starting phenix.real_space_refine on Fri Feb 16 05:01:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/02_2024/8f5b_28864_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/02_2024/8f5b_28864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/02_2024/8f5b_28864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/02_2024/8f5b_28864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/02_2024/8f5b_28864_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/02_2024/8f5b_28864_updated.pdb" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 293 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 73 5.16 5 C 9121 2.51 5 N 2378 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1679": "OD1" <-> "OD2" Residue "A TYR 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14152 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1924, 13954 Classifications: {'peptide': 1924} Incomplete info: {'truncation_to_alanine': 350} Link IDs: {'PTRANS': 98, 'TRANS': 1825} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1440 Unresolved non-hydrogen angles: 1823 Unresolved non-hydrogen dihedrals: 1221 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 21, 'ASP:plan': 37, 'TYR:plan': 13, 'ASN:plan1': 21, 'TRP:plan': 9, 'HIS:plan': 9, 'PHE:plan': 22, 'GLU:plan': 54, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 998 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {' MG': 2, 'ANP': 2, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.17, per 1000 atoms: 0.58 Number of scatterers: 14152 At special positions: 0 Unit cell: (80.7751, 94.4125, 217.149, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 73 16.00 P 6 15.00 Mg 2 11.99 O 2572 8.00 N 2378 7.00 C 9121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1455 " distance=2.03 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 504 " " NAG A2303 " - " ASN A1662 " " NAG A2306 " - " ASN A 444 " " NAG B 1 " - " ASN A 415 " Time building additional restraints: 6.22 Conformation dependent library (CDL) restraints added in 2.8 seconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 51.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 Processing helix chain 'A' and resid 22 through 44 Proline residue: A 32 - end of helix removed outlier: 4.175A pdb=" N LEU A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 75 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 117 through 136 Processing helix chain 'A' and resid 276 through 289 Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.540A pdb=" N PHE A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 385 through 395 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 405 through 444 removed outlier: 3.890A pdb=" N SER A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N THR A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 457 through 466 removed outlier: 4.383A pdb=" N VAL A 460 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 507 through 519 Processing helix chain 'A' and resid 531 through 543 Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 602 through 606 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 646 through 648 No H-bonds generated for 'chain 'A' and resid 646 through 648' Processing helix chain 'A' and resid 650 through 679 removed outlier: 5.063A pdb=" N PHE A 655 " --> pdb=" O ASN A 652 " (cutoff:3.500A) Proline residue: A 656 - end of helix removed outlier: 3.900A pdb=" N TRP A 663 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR A 665 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 693 through 722 Processing helix chain 'A' and resid 733 through 754 Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.591A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Proline residue: A 775 - end of helix Processing helix chain 'A' and resid 788 through 796 removed outlier: 4.068A pdb=" N LEU A 796 " --> pdb=" O LYS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 814 Processing helix chain 'A' and resid 836 through 860 removed outlier: 4.004A pdb=" N GLN A 859 " --> pdb=" O TRP A 855 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 969 through 975 Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1020 through 1031 removed outlier: 4.146A pdb=" N LYS A1031 " --> pdb=" O TYR A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1049 Processing helix chain 'A' and resid 1064 through 1076 Processing helix chain 'A' and resid 1094 through 1108 removed outlier: 3.786A pdb=" N SER A1099 " --> pdb=" O TYR A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1126 Processing helix chain 'A' and resid 1144 through 1150 Processing helix chain 'A' and resid 1206 through 1215 Processing helix chain 'A' and resid 1242 through 1252 Processing helix chain 'A' and resid 1269 through 1280 Processing helix chain 'A' and resid 1348 through 1368 Processing helix chain 'A' and resid 1370 through 1391 removed outlier: 4.438A pdb=" N LEU A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Proline residue: A1380 - end of helix Processing helix chain 'A' and resid 1407 through 1409 No H-bonds generated for 'chain 'A' and resid 1407 through 1409' Processing helix chain 'A' and resid 1425 through 1436 Processing helix chain 'A' and resid 1468 through 1476 Processing helix chain 'A' and resid 1531 through 1546 Proline residue: A1539 - end of helix Processing helix chain 'A' and resid 1574 through 1587 Processing helix chain 'A' and resid 1593 through 1609 removed outlier: 4.320A pdb=" N GLU A1601 " --> pdb=" O GLU A1597 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A1602 " --> pdb=" O ALA A1598 " (cutoff:3.500A) Proline residue: A1603 - end of helix removed outlier: 3.700A pdb=" N HIS A1608 " --> pdb=" O ASP A1604 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A1609 " --> pdb=" O PHE A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1638 Processing helix chain 'A' and resid 1669 through 1706 WARNING: missing atoms! Proline residue: A1694 - end of helix removed outlier: 4.920A pdb=" N PHE A1697 " --> pdb=" O VAL A1693 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL A1698 " --> pdb=" O PRO A1694 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A1699 " --> pdb=" O ALA A1695 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR A1700 " --> pdb=" O SER A1696 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A1701 " --> pdb=" O PHE A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1714 Processing helix chain 'A' and resid 1720 through 1749 Processing helix chain 'A' and resid 1752 through 1755 No H-bonds generated for 'chain 'A' and resid 1752 through 1755' Processing helix chain 'A' and resid 1757 through 1783 Proline residue: A1761 - end of helix Proline residue: A1776 - end of helix Proline residue: A1780 - end of helix removed outlier: 4.641A pdb=" N PHE A1783 " --> pdb=" O TYR A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1816 Processing helix chain 'A' and resid 1823 through 1827 Processing helix chain 'A' and resid 1837 through 1861 Processing helix chain 'A' and resid 1876 through 1899 Processing helix chain 'A' and resid 1920 through 1930 Processing helix chain 'A' and resid 1978 through 1986 Processing helix chain 'A' and resid 2007 through 2013 removed outlier: 3.754A pdb=" N ASN A2013 " --> pdb=" O GLU A2009 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2040 Processing helix chain 'A' and resid 2044 through 2058 removed outlier: 3.583A pdb=" N ILE A2047 " --> pdb=" O ALA A2044 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLU A2048 " --> pdb=" O GLU A2045 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A2056 " --> pdb=" O TRP A2053 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A2058 " --> pdb=" O ILE A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2073 through 2084 Processing helix chain 'A' and resid 2103 through 2119 removed outlier: 3.688A pdb=" N ARG A2107 " --> pdb=" O PRO A2103 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A2108 " --> pdb=" O GLN A2104 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2136 Processing helix chain 'A' and resid 2154 through 2160 Processing helix chain 'A' and resid 2187 through 2192 Processing helix chain 'A' and resid 2215 through 2225 Processing helix chain 'A' and resid 2241 through 2252 Processing sheet with id= A, first strand: chain 'A' and resid 550 through 552 removed outlier: 6.017A pdb=" N GLY A1653 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N TYR A 569 " --> pdb=" O GLY A1653 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR A1655 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE A 571 " --> pdb=" O THR A1655 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE A1657 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N MET A 573 " --> pdb=" O ILE A1657 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN A1659 " --> pdb=" O MET A 573 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 632 through 636 removed outlier: 7.124A pdb=" N ILE A1615 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N GLN A 635 " --> pdb=" O ILE A1615 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A1617 " --> pdb=" O GLN A 635 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 930 through 932 Processing sheet with id= D, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 5.971A pdb=" N THR A 959 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ARG A1129 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU A 962 " --> pdb=" O ARG A1129 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A1131 " --> pdb=" O LEU A 962 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 1155 through 1157 Processing sheet with id= F, first strand: chain 'A' and resid 1967 through 1970 removed outlier: 6.807A pdb=" N VAL A2123 " --> pdb=" O PHE A1968 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU A1970 " --> pdb=" O VAL A2123 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A2125 " --> pdb=" O LEU A1970 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 2165 through 2170 Processing sheet with id= H, first strand: chain 'A' and resid 2140 through 2144 removed outlier: 3.734A pdb=" N CYS A2150 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A2144 " --> pdb=" O PHE A2148 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N PHE A2148 " --> pdb=" O VAL A2144 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4522 1.34 - 1.46: 3241 1.46 - 1.58: 6588 1.58 - 1.70: 7 1.70 - 1.82: 114 Bond restraints: 14472 Sorted by residual: bond pdb=" O3A ANP A2304 " pdb=" PB ANP A2304 " ideal model delta sigma weight residual 1.700 1.548 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" O3A ANP A2305 " pdb=" PB ANP A2305 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" N3B ANP A2304 " pdb=" PG ANP A2304 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" N3B ANP A2305 " pdb=" PG ANP A2305 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" O5' ANP A2304 " pdb=" PA ANP A2304 " ideal model delta sigma weight residual 1.655 1.574 0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 14467 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.89: 399 105.89 - 112.93: 8061 112.93 - 119.96: 4680 119.96 - 127.00: 6453 127.00 - 134.04: 208 Bond angle restraints: 19801 Sorted by residual: angle pdb=" PB ANP A2304 " pdb=" N3B ANP A2304 " pdb=" PG ANP A2304 " ideal model delta sigma weight residual 126.95 108.46 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" PB ANP A2305 " pdb=" N3B ANP A2305 " pdb=" PG ANP A2305 " ideal model delta sigma weight residual 126.95 108.85 18.10 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C ASN A 444 " pdb=" CA ASN A 444 " pdb=" CB ASN A 444 " ideal model delta sigma weight residual 110.09 101.94 8.15 1.67e+00 3.59e-01 2.38e+01 angle pdb=" C TYR A 97 " pdb=" CA TYR A 97 " pdb=" CB TYR A 97 " ideal model delta sigma weight residual 111.82 106.62 5.20 1.28e+00 6.10e-01 1.65e+01 angle pdb=" N ASN A 444 " pdb=" CA ASN A 444 " pdb=" CB ASN A 444 " ideal model delta sigma weight residual 110.49 116.24 -5.75 1.48e+00 4.57e-01 1.51e+01 ... (remaining 19796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 8161 24.81 - 49.62: 421 49.62 - 74.44: 70 74.44 - 99.25: 26 99.25 - 124.06: 16 Dihedral angle restraints: 8694 sinusoidal: 3131 harmonic: 5563 Sorted by residual: dihedral pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " pdb=" SG CYS A 324 " pdb=" CB CYS A 324 " ideal model delta sinusoidal sigma weight residual -86.00 -8.32 -77.68 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CA ASN A 98 " pdb=" C ASN A 98 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CB CYS A 370 " pdb=" SG CYS A 370 " pdb=" SG CYS A 519 " pdb=" CB CYS A 519 " ideal model delta sinusoidal sigma weight residual 93.00 48.59 44.41 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 8691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2001 0.057 - 0.114: 355 0.114 - 0.170: 26 0.170 - 0.227: 3 0.227 - 0.284: 6 Chirality restraints: 2391 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.87e+00 chirality pdb=" C3' ANP A2304 " pdb=" C2' ANP A2304 " pdb=" C4' ANP A2304 " pdb=" O3' ANP A2304 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2388 not shown) Planarity restraints: 2499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 444 " -0.007 2.00e-02 2.50e+03 3.28e-02 1.35e+01 pdb=" CG ASN A 444 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN A 444 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 444 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG A2306 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 444 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" CG ASN A 444 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 444 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 444 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.021 2.00e-02 2.50e+03 1.96e-02 4.81e+00 pdb=" CG ASN A 98 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.015 2.00e-02 2.50e+03 pdb=" C1 NAG A2301 " -0.018 2.00e-02 2.50e+03 ... (remaining 2496 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 180 2.57 - 3.16: 12828 3.16 - 3.74: 23966 3.74 - 4.32: 28766 4.32 - 4.90: 46859 Nonbonded interactions: 112599 Sorted by model distance: nonbonded pdb=" O1G ANP A2305 " pdb="MG MG A2307 " model vdw 1.993 2.170 nonbonded pdb=" OE1 GLN A2019 " pdb="MG MG A2307 " model vdw 2.007 2.170 nonbonded pdb=" N3B ANP A2304 " pdb="MG MG A2308 " model vdw 2.017 2.250 nonbonded pdb=" OG1 THR A 970 " pdb="MG MG A2308 " model vdw 2.025 2.170 nonbonded pdb=" O2A ANP A2304 " pdb="MG MG A2308 " model vdw 2.033 2.170 ... (remaining 112594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 10.190 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 43.000 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.004 0.152 14472 Z= 0.287 Angle : 0.715 18.492 19801 Z= 0.336 Chirality : 0.044 0.284 2391 Planarity : 0.004 0.041 2494 Dihedral : 16.735 124.061 5074 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.07 % Allowed : 0.22 % Favored : 99.70 % 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: 0.29 (0.20), residues: 1904 helix: 1.70 (0.17), residues: 1021 sheet: -0.24 (0.48), residues: 139 loop : -1.98 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 31 HIS 0.006 0.001 HIS A 52 PHE 0.023 0.001 PHE A 655 TYR 0.026 0.001 TYR A1735 ARG 0.002 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.627 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 1018 LEU cc_start: 0.8813 (tp) cc_final: 0.8547 (tp) REVERT: A 1115 MET cc_start: 0.6220 (ppp) cc_final: 0.5970 (ppp) REVERT: A 1679 ASP cc_start: 0.8855 (m-30) cc_final: 0.8591 (m-30) REVERT: A 1733 MET cc_start: 0.8877 (tmm) cc_final: 0.8367 (tmm) REVERT: A 1770 TYR cc_start: 0.9118 (t80) cc_final: 0.8764 (t80) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.2044 time to fit residues: 52.5159 Evaluate side-chains 126 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1670 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 0.0370 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1727 ASN A1799 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14472 Z= 0.190 Angle : 0.617 8.611 19801 Z= 0.297 Chirality : 0.041 0.226 2391 Planarity : 0.004 0.040 2494 Dihedral : 11.592 96.165 2288 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.12 % Allowed : 10.72 % Favored : 88.16 % 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: 0.08 (0.20), residues: 1904 helix: 1.51 (0.17), residues: 1025 sheet: -0.75 (0.45), residues: 146 loop : -1.97 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 31 HIS 0.007 0.001 HIS A1023 PHE 0.022 0.001 PHE A1026 TYR 0.028 0.001 TYR A2016 ARG 0.003 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.727 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 1026 PHE cc_start: 0.7933 (m-80) cc_final: 0.7645 (m-80) REVERT: A 1115 MET cc_start: 0.6249 (ppp) cc_final: 0.5992 (ppp) REVERT: A 1690 MET cc_start: 0.8075 (mmt) cc_final: 0.7691 (mmt) REVERT: A 1733 MET cc_start: 0.8901 (tmm) cc_final: 0.8344 (tmm) outliers start: 15 outliers final: 9 residues processed: 145 average time/residue: 0.2068 time to fit residues: 49.8714 Evaluate side-chains 133 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 0.0770 chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 0.0770 chunk 155 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1727 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14472 Z= 0.174 Angle : 0.613 9.804 19801 Z= 0.289 Chirality : 0.042 0.199 2391 Planarity : 0.004 0.039 2494 Dihedral : 9.451 77.898 2288 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.34 % Allowed : 15.41 % Favored : 83.25 % 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: 0.09 (0.20), residues: 1904 helix: 1.52 (0.17), residues: 1024 sheet: -0.76 (0.45), residues: 146 loop : -1.96 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 31 HIS 0.005 0.001 HIS A 52 PHE 0.013 0.001 PHE A 734 TYR 0.017 0.001 TYR A1735 ARG 0.002 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.801 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 61 MET cc_start: 0.9013 (tpp) cc_final: 0.8802 (tpp) REVERT: A 74 PHE cc_start: 0.9119 (t80) cc_final: 0.8800 (t80) REVERT: A 769 TYR cc_start: 0.8939 (t80) cc_final: 0.8736 (t80) REVERT: A 1115 MET cc_start: 0.6249 (ppp) cc_final: 0.5965 (ppp) REVERT: A 1690 MET cc_start: 0.8033 (mmt) cc_final: 0.7669 (mmt) REVERT: A 1733 MET cc_start: 0.8960 (tmm) cc_final: 0.8398 (tmm) REVERT: A 1735 TYR cc_start: 0.7634 (t80) cc_final: 0.7363 (t80) REVERT: A 2130 MET cc_start: 0.6915 (ptm) cc_final: 0.6663 (ptp) REVERT: A 2169 MET cc_start: 0.8976 (tpt) cc_final: 0.8067 (mpp) outliers start: 18 outliers final: 13 residues processed: 147 average time/residue: 0.2031 time to fit residues: 49.4692 Evaluate side-chains 136 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 185 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1426 GLN A1727 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14472 Z= 0.207 Angle : 0.617 9.814 19801 Z= 0.295 Chirality : 0.042 0.288 2391 Planarity : 0.004 0.037 2494 Dihedral : 7.733 74.582 2288 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.01 % Allowed : 18.47 % Favored : 79.52 % 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: 0.02 (0.20), residues: 1904 helix: 1.47 (0.16), residues: 1031 sheet: -0.86 (0.45), residues: 146 loop : -2.02 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 31 HIS 0.005 0.001 HIS A1711 PHE 0.012 0.001 PHE A 734 TYR 0.019 0.001 TYR A2036 ARG 0.002 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.592 Fit side-chains REVERT: A 660 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8983 (p) REVERT: A 746 MET cc_start: 0.8789 (tpp) cc_final: 0.8182 (tpp) REVERT: A 1115 MET cc_start: 0.6420 (ppp) cc_final: 0.6081 (ppp) REVERT: A 1209 MET cc_start: 0.9340 (ptt) cc_final: 0.9022 (ppp) REVERT: A 1690 MET cc_start: 0.7934 (mmt) cc_final: 0.7571 (mmt) REVERT: A 1700 TYR cc_start: 0.8035 (t80) cc_final: 0.7523 (t80) REVERT: A 1733 MET cc_start: 0.9013 (tmm) cc_final: 0.8443 (tmm) REVERT: A 2169 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8145 (mpp) outliers start: 27 outliers final: 15 residues processed: 153 average time/residue: 0.2018 time to fit residues: 51.1028 Evaluate side-chains 144 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14472 Z= 0.173 Angle : 0.621 11.609 19801 Z= 0.291 Chirality : 0.042 0.283 2391 Planarity : 0.004 0.039 2494 Dihedral : 7.246 77.488 2285 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.01 % Allowed : 19.73 % Favored : 78.26 % 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: 0.05 (0.20), residues: 1904 helix: 1.50 (0.16), residues: 1032 sheet: -1.14 (0.43), residues: 158 loop : -1.96 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1772 HIS 0.005 0.001 HIS A 52 PHE 0.019 0.001 PHE A1026 TYR 0.022 0.001 TYR A 769 ARG 0.001 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.648 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 746 MET cc_start: 0.8722 (tpp) cc_final: 0.8411 (tpp) REVERT: A 1115 MET cc_start: 0.6370 (ppp) cc_final: 0.6046 (ppp) REVERT: A 1209 MET cc_start: 0.9319 (ptt) cc_final: 0.9034 (ppp) REVERT: A 1690 MET cc_start: 0.8077 (mmt) cc_final: 0.7675 (mmt) REVERT: A 1700 TYR cc_start: 0.8061 (t80) cc_final: 0.7523 (t80) REVERT: A 1733 MET cc_start: 0.8988 (tmm) cc_final: 0.8441 (tmm) REVERT: A 2169 MET cc_start: 0.9039 (tpt) cc_final: 0.8137 (mpp) outliers start: 27 outliers final: 20 residues processed: 149 average time/residue: 0.2049 time to fit residues: 50.7861 Evaluate side-chains 144 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.2980 chunk 167 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 0.0470 overall best weight: 1.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14472 Z= 0.186 Angle : 0.620 12.042 19801 Z= 0.292 Chirality : 0.042 0.271 2391 Planarity : 0.004 0.037 2494 Dihedral : 6.978 78.541 2285 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.94 % Allowed : 21.30 % Favored : 76.77 % 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: 0.04 (0.20), residues: 1904 helix: 1.51 (0.17), residues: 1030 sheet: -1.18 (0.43), residues: 158 loop : -1.97 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1772 HIS 0.005 0.001 HIS A 52 PHE 0.016 0.001 PHE A1026 TYR 0.016 0.001 TYR A 769 ARG 0.001 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.679 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 61 MET cc_start: 0.9069 (tpp) cc_final: 0.8841 (tpp) REVERT: A 1115 MET cc_start: 0.6434 (ppp) cc_final: 0.6084 (ppp) REVERT: A 1209 MET cc_start: 0.9358 (ptt) cc_final: 0.9079 (ppp) REVERT: A 1690 MET cc_start: 0.8083 (mmt) cc_final: 0.7650 (mmt) REVERT: A 1700 TYR cc_start: 0.8070 (t80) cc_final: 0.7559 (t80) REVERT: A 1733 MET cc_start: 0.8968 (tmm) cc_final: 0.8462 (tmm) REVERT: A 2169 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8172 (mpp) outliers start: 26 outliers final: 21 residues processed: 145 average time/residue: 0.1929 time to fit residues: 46.6298 Evaluate side-chains 151 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1731 ASP Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 185 optimal weight: 0.6980 chunk 115 optimal weight: 0.0060 chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14472 Z= 0.157 Angle : 0.635 13.325 19801 Z= 0.290 Chirality : 0.042 0.298 2391 Planarity : 0.004 0.037 2494 Dihedral : 6.789 80.739 2285 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.01 % Allowed : 21.82 % Favored : 76.17 % 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: 0.05 (0.20), residues: 1904 helix: 1.50 (0.17), residues: 1029 sheet: -1.10 (0.43), residues: 158 loop : -1.96 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1772 HIS 0.005 0.001 HIS A 52 PHE 0.010 0.001 PHE A1026 TYR 0.014 0.001 TYR A1779 ARG 0.001 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 746 MET cc_start: 0.8689 (tpp) cc_final: 0.8329 (tpp) REVERT: A 1115 MET cc_start: 0.6372 (ppp) cc_final: 0.6058 (ppp) REVERT: A 1209 MET cc_start: 0.9337 (ptt) cc_final: 0.9068 (ppp) REVERT: A 1690 MET cc_start: 0.8137 (mmt) cc_final: 0.7670 (mmt) REVERT: A 1700 TYR cc_start: 0.8081 (t80) cc_final: 0.7780 (t80) REVERT: A 1733 MET cc_start: 0.8961 (tmm) cc_final: 0.8438 (tmm) REVERT: A 2169 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8180 (mpp) outliers start: 27 outliers final: 21 residues processed: 152 average time/residue: 0.2052 time to fit residues: 51.9878 Evaluate side-chains 154 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1731 ASP Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14472 Z= 0.163 Angle : 0.641 14.354 19801 Z= 0.294 Chirality : 0.041 0.312 2391 Planarity : 0.004 0.036 2494 Dihedral : 6.669 80.716 2285 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.94 % Allowed : 22.49 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1904 helix: 1.54 (0.17), residues: 1028 sheet: -1.00 (0.44), residues: 158 loop : -1.96 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1772 HIS 0.005 0.001 HIS A 52 PHE 0.010 0.001 PHE A 734 TYR 0.015 0.001 TYR A1779 ARG 0.006 0.000 ARG A2217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 61 MET cc_start: 0.9037 (tpp) cc_final: 0.8773 (tpp) REVERT: A 746 MET cc_start: 0.8725 (tpp) cc_final: 0.8319 (tpp) REVERT: A 1115 MET cc_start: 0.6402 (ppp) cc_final: 0.6079 (ppp) REVERT: A 1209 MET cc_start: 0.9346 (ptt) cc_final: 0.9076 (ppp) REVERT: A 1690 MET cc_start: 0.8140 (mmt) cc_final: 0.7662 (mmt) REVERT: A 1700 TYR cc_start: 0.8096 (t80) cc_final: 0.7788 (t80) REVERT: A 1733 MET cc_start: 0.8967 (tmm) cc_final: 0.8489 (tmm) REVERT: A 2169 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8165 (mpp) outliers start: 26 outliers final: 22 residues processed: 150 average time/residue: 0.2090 time to fit residues: 51.9605 Evaluate side-chains 158 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1373 PHE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1731 ASP Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14472 Z= 0.204 Angle : 0.650 12.920 19801 Z= 0.302 Chirality : 0.042 0.325 2391 Planarity : 0.004 0.035 2494 Dihedral : 6.658 81.470 2285 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.01 % Allowed : 22.71 % Favored : 75.28 % 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: 0.08 (0.20), residues: 1904 helix: 1.54 (0.17), residues: 1028 sheet: -1.09 (0.44), residues: 158 loop : -1.94 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 925 HIS 0.005 0.001 HIS A 52 PHE 0.011 0.001 PHE A 734 TYR 0.015 0.001 TYR A1779 ARG 0.003 0.000 ARG A2217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 61 MET cc_start: 0.9036 (tpp) cc_final: 0.8757 (tpp) REVERT: A 573 MET cc_start: 0.7410 (ptm) cc_final: 0.7064 (ptm) REVERT: A 746 MET cc_start: 0.8740 (tpp) cc_final: 0.8310 (tpp) REVERT: A 1115 MET cc_start: 0.6494 (ppp) cc_final: 0.6111 (ppp) REVERT: A 1209 MET cc_start: 0.9347 (ptt) cc_final: 0.9072 (ppp) REVERT: A 1690 MET cc_start: 0.8075 (mmt) cc_final: 0.7371 (mmt) REVERT: A 1700 TYR cc_start: 0.8119 (t80) cc_final: 0.7804 (t80) REVERT: A 1733 MET cc_start: 0.9009 (tmm) cc_final: 0.8485 (tmm) REVERT: A 1770 TYR cc_start: 0.8978 (t80) cc_final: 0.8422 (t80) REVERT: A 2169 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8185 (mpp) outliers start: 27 outliers final: 25 residues processed: 153 average time/residue: 0.2052 time to fit residues: 52.1534 Evaluate side-chains 161 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1373 PHE Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1731 ASP Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1807 SER Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 4.9990 chunk 111 optimal weight: 0.0270 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 191 optimal weight: 0.0870 chunk 176 optimal weight: 0.0980 chunk 152 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 117 optimal weight: 40.0000 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14472 Z= 0.158 Angle : 0.652 13.803 19801 Z= 0.296 Chirality : 0.042 0.340 2391 Planarity : 0.004 0.036 2494 Dihedral : 6.572 83.701 2285 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 1.71 % Allowed : 23.16 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1904 helix: 1.55 (0.17), residues: 1026 sheet: -1.00 (0.44), residues: 158 loop : -1.95 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1772 HIS 0.005 0.001 HIS A 52 PHE 0.015 0.001 PHE A1982 TYR 0.015 0.001 TYR A1779 ARG 0.003 0.000 ARG A2217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.612 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 61 MET cc_start: 0.9007 (tpp) cc_final: 0.8781 (tpp) REVERT: A 66 MET cc_start: 0.8552 (mmp) cc_final: 0.8040 (mmt) REVERT: A 746 MET cc_start: 0.8776 (tpp) cc_final: 0.8377 (tpp) REVERT: A 1115 MET cc_start: 0.6396 (ppp) cc_final: 0.6086 (ppp) REVERT: A 1209 MET cc_start: 0.9332 (ptt) cc_final: 0.9040 (ppp) REVERT: A 1690 MET cc_start: 0.7938 (mmt) cc_final: 0.7448 (mmt) REVERT: A 1700 TYR cc_start: 0.8124 (t80) cc_final: 0.7791 (t80) REVERT: A 1733 MET cc_start: 0.8973 (tmm) cc_final: 0.8459 (tmm) REVERT: A 2169 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8170 (mpp) outliers start: 23 outliers final: 20 residues processed: 157 average time/residue: 0.1940 time to fit residues: 50.8565 Evaluate side-chains 165 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1373 PHE Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1731 ASP Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.064930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.053660 restraints weight = 106661.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.054878 restraints weight = 67582.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055655 restraints weight = 49547.907| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14472 Z= 0.167 Angle : 0.651 13.662 19801 Z= 0.296 Chirality : 0.041 0.326 2391 Planarity : 0.004 0.035 2494 Dihedral : 6.483 83.204 2285 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.56 % Allowed : 23.38 % Favored : 75.06 % 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: 0.09 (0.20), residues: 1904 helix: 1.52 (0.16), residues: 1028 sheet: -0.97 (0.44), residues: 158 loop : -1.93 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 663 HIS 0.005 0.001 HIS A 52 PHE 0.023 0.001 PHE A 802 TYR 0.016 0.001 TYR A1779 ARG 0.003 0.000 ARG A2217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.69 seconds wall clock time: 47 minutes 11.53 seconds (2831.53 seconds total)