Starting phenix.real_space_refine on Thu Jul 31 12:31:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6i_29770/07_2025/8g6i_29770_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6i_29770/07_2025/8g6i_29770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6i_29770/07_2025/8g6i_29770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6i_29770/07_2025/8g6i_29770.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6i_29770/07_2025/8g6i_29770_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6i_29770/07_2025/8g6i_29770_neut.cif" } resolution = 4.23 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= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 8485 2.51 5 N 2259 2.21 5 O 2480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13287 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1239, 10005 Classifications: {'peptide': 1239} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1177} Chain breaks: 7 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1614 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1612 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.76, per 1000 atoms: 0.66 Number of scatterers: 13287 At special positions: 0 Unit cell: (84.316, 116.624, 204.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2480 8.00 N 2259 7.00 C 8485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A1832 " - pdb=" SG CYS A1858 " distance=2.03 Simple disulfide: pdb=" SG CYS A2021 " - pdb=" SG CYS A2169 " distance=2.02 Simple disulfide: pdb=" SG CYS A2174 " - pdb=" SG CYS A2326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG D 1 " - " ASN A 240 " " NAG E 1 " - " ASN A1810 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3108 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 23 sheets defined 7.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.703A pdb=" N GLN A 410 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 411 " --> pdb=" O LYS A 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 411' Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.919A pdb=" N ASP A 519 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 520 " --> pdb=" O VAL A 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 516 through 520' Processing helix chain 'A' and resid 538 through 546 removed outlier: 3.553A pdb=" N LEU A 543 " --> pdb=" O MET A 539 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ALA A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 595 removed outlier: 4.235A pdb=" N GLN A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.920A pdb=" N GLY A 600 " --> pdb=" O ASN A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 removed outlier: 3.740A pdb=" N GLN A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1754 Processing helix chain 'A' and resid 1820 through 1824 removed outlier: 3.666A pdb=" N MET A1823 " --> pdb=" O GLN A1820 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A1824 " --> pdb=" O HIS A1821 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1820 through 1824' Processing helix chain 'A' and resid 1913 through 1917 Processing helix chain 'A' and resid 1949 through 1953 removed outlier: 3.680A pdb=" N ASN A1952 " --> pdb=" O SER A1949 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A1953 " --> pdb=" O ASN A1950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1949 through 1953' Processing helix chain 'A' and resid 2002 through 2007 Processing helix chain 'A' and resid 2047 through 2051 removed outlier: 3.950A pdb=" N LEU A2050 " --> pdb=" O ALA A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2190 removed outlier: 3.667A pdb=" N GLN A2189 " --> pdb=" O SER A2186 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A2190 " --> pdb=" O ASP A2187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2186 through 2190' Processing helix chain 'A' and resid 2204 through 2208 removed outlier: 3.539A pdb=" N ALA A2208 " --> pdb=" O PRO A2205 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 removed outlier: 4.125A pdb=" N LEU B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 189 removed outlier: 3.954A pdb=" N HIS B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 189 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.693A pdb=" N VAL A 51 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 10 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 86 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 5 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 88 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 90 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 9 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 85 " --> pdb=" O TRP A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 80 removed outlier: 3.799A pdb=" N CYS A 180 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 203 removed outlier: 4.335A pdb=" N MET A 232 " --> pdb=" O PHE A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 248 removed outlier: 3.993A pdb=" N GLY A 248 " --> pdb=" O ARG A 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 260 Processing sheet with id=AA6, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.220A pdb=" N TYR A 533 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A 549 " --> pdb=" O TYR A 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 649 through 650 removed outlier: 3.665A pdb=" N LEU A 649 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1701 through 1706 removed outlier: 4.198A pdb=" N VAL A1703 " --> pdb=" O VAL A1734 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A1734 " --> pdb=" O VAL A1703 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1773 through 1774 removed outlier: 3.855A pdb=" N VAL A1773 " --> pdb=" O TYR A1815 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1836 through 1837 removed outlier: 3.620A pdb=" N GLY A1853 " --> pdb=" O TYR A1837 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1877 through 1878 removed outlier: 4.408A pdb=" N LEU A1878 " --> pdb=" O TYR A1943 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A1964 " --> pdb=" O GLU A1987 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1933 through 1934 removed outlier: 4.142A pdb=" N MET A1934 " --> pdb=" O LEU A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 2071 through 2074 removed outlier: 3.966A pdb=" N ILE A2071 " --> pdb=" O LEU A2151 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A2151 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A2149 " --> pdb=" O VAL A2073 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A2148 " --> pdb=" O SER A2106 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A2106 " --> pdb=" O TYR A2148 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS A2152 " --> pdb=" O ILE A2102 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A2102 " --> pdb=" O HIS A2152 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR A2154 " --> pdb=" O GLN A2100 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLN A2100 " --> pdb=" O THR A2154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2071 through 2074 removed outlier: 3.966A pdb=" N ILE A2071 " --> pdb=" O LEU A2151 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A2151 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A2149 " --> pdb=" O VAL A2073 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A2148 " --> pdb=" O SER A2106 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A2106 " --> pdb=" O TYR A2148 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS A2152 " --> pdb=" O ILE A2102 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A2102 " --> pdb=" O HIS A2152 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR A2154 " --> pdb=" O GLN A2100 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLN A2100 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A2101 " --> pdb=" O PHE A2126 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A2126 " --> pdb=" O PHE A2101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2144 through 2145 removed outlier: 3.865A pdb=" N HIS A2082 " --> pdb=" O MET A2167 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N MET A2167 " --> pdb=" O HIS A2082 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE A2084 " --> pdb=" O GLU A2165 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU A2165 " --> pdb=" O ILE A2084 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2089 through 2091 Processing sheet with id=AB8, first strand: chain 'A' and resid 2293 through 2294 Processing sheet with id=AB9, first strand: chain 'A' and resid 2260 through 2265 removed outlier: 4.114A pdb=" N LEU A2261 " --> pdb=" O HIS A2309 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A2309 " --> pdb=" O LEU A2261 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A2263 " --> pdb=" O ARG A2307 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A2307 " --> pdb=" O SER A2263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.753A pdb=" N ILE B 2 " --> pdb=" O THR B 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 20 through 21 removed outlier: 3.756A pdb=" N ILE B 21 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 73 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.876A pdb=" N LEU B 89 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 36 through 37 Processing sheet with id=AC5, first strand: chain 'C' and resid 5 through 6 94 hydrogen bonds defined for protein. 195 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: 3.42 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4246 1.34 - 1.46: 3373 1.46 - 1.58: 5919 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 13638 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" CA ASN A1915 " pdb=" C ASN A1915 " ideal model delta sigma weight residual 1.522 1.546 -0.023 1.38e-02 5.25e+03 2.89e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" CA PHE A1743 " pdb=" CB PHE A1743 " ideal model delta sigma weight residual 1.525 1.545 -0.020 1.36e-02 5.41e+03 2.25e+00 bond pdb=" CA ILE A 553 " pdb=" CB ILE A 553 " ideal model delta sigma weight residual 1.532 1.548 -0.016 1.08e-02 8.57e+03 2.22e+00 ... (remaining 13633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 17913 1.72 - 3.43: 488 3.43 - 5.15: 86 5.15 - 6.87: 17 6.87 - 8.59: 2 Bond angle restraints: 18506 Sorted by residual: angle pdb=" N LYS A 124 " pdb=" CA LYS A 124 " pdb=" C LYS A 124 " ideal model delta sigma weight residual 112.72 108.62 4.10 1.14e+00 7.69e-01 1.29e+01 angle pdb=" C PHE A 697 " pdb=" N ARG A 698 " pdb=" CA ARG A 698 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" N ILE A 553 " pdb=" CA ILE A 553 " pdb=" C ILE A 553 " ideal model delta sigma weight residual 106.42 111.47 -5.05 1.51e+00 4.39e-01 1.12e+01 angle pdb=" C VAL A1767 " pdb=" N GLU A1768 " pdb=" CA GLU A1768 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" N VAL C 167 " pdb=" CA VAL C 167 " pdb=" C VAL C 167 " ideal model delta sigma weight residual 113.39 108.73 4.66 1.47e+00 4.63e-01 1.00e+01 ... (remaining 18501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7419 17.83 - 35.67: 585 35.67 - 53.50: 95 53.50 - 71.33: 22 71.33 - 89.16: 12 Dihedral angle restraints: 8133 sinusoidal: 3293 harmonic: 4840 Sorted by residual: dihedral pdb=" CB CYS C 144 " pdb=" SG CYS C 144 " pdb=" SG CYS C 200 " pdb=" CB CYS C 200 " ideal model delta sinusoidal sigma weight residual 93.00 173.01 -80.01 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS A2021 " pdb=" SG CYS A2021 " pdb=" SG CYS A2169 " pdb=" CB CYS A2169 " ideal model delta sinusoidal sigma weight residual -86.00 -15.81 -70.19 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CA GLU C 46 " pdb=" C GLU C 46 " pdb=" N TRP C 47 " pdb=" CA TRP C 47 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 8130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1771 0.070 - 0.140: 244 0.140 - 0.210: 4 0.210 - 0.280: 0 0.280 - 0.350: 3 Chirality restraints: 2022 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 240 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A1810 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB ILE A 553 " pdb=" CA ILE A 553 " pdb=" CG1 ILE A 553 " pdb=" CG2 ILE A 553 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 2019 not shown) Planarity restraints: 2358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A2077 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO A2078 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A2078 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2078 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 415 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 416 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 416 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 416 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1929 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A1930 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1930 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1930 " -0.026 5.00e-02 4.00e+02 ... (remaining 2355 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 400 2.69 - 3.25: 12686 3.25 - 3.80: 18716 3.80 - 4.35: 23523 4.35 - 4.90: 37592 Nonbonded interactions: 92917 Sorted by model distance: nonbonded pdb=" O ARG A 17 " pdb=" NH1 ARG A 17 " model vdw 2.143 3.120 nonbonded pdb=" O TRP A1996 " pdb=" OG1 THR A2013 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR B 87 " pdb=" O ALA C 43 " model vdw 2.181 3.040 nonbonded pdb=" O LYS A1845 " pdb=" OG SER A1849 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU A1704 " pdb=" OH TYR A1890 " model vdw 2.232 3.040 ... (remaining 92912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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: 3.820 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.320 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4372 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 : 0.003 0.140 13653 Z= 0.149 Angle : 0.689 10.156 18540 Z= 0.365 Chirality : 0.046 0.350 2022 Planarity : 0.005 0.055 2356 Dihedral : 13.130 89.164 4992 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.30 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: -3.49 (0.18), residues: 1645 helix: -3.17 (0.43), residues: 76 sheet: -1.69 (0.45), residues: 139 loop : -2.61 (0.14), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 139 HIS 0.007 0.001 HIS C 35 PHE 0.009 0.001 PHE A2014 TYR 0.017 0.002 TYR A 487 ARG 0.004 0.001 ARG A1813 Details of bonding type rmsd link_NAG-ASN : bond 0.01161 ( 2) link_NAG-ASN : angle 6.27109 ( 6) link_BETA1-4 : bond 0.00674 ( 2) link_BETA1-4 : angle 1.61653 ( 6) hydrogen bonds : bond 0.30881 ( 91) hydrogen bonds : angle 12.18001 ( 195) SS BOND : bond 0.00290 ( 11) SS BOND : angle 0.75410 ( 22) covalent geometry : bond 0.00292 (13638) covalent geometry : angle 0.67911 (18506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 HIS cc_start: 0.6855 (t70) cc_final: 0.5919 (p-80) REVERT: A 308 LEU cc_start: 0.8588 (tp) cc_final: 0.8372 (tp) REVERT: A 519 ASP cc_start: 0.8436 (t70) cc_final: 0.8140 (p0) REVERT: A 589 GLU cc_start: 0.7027 (tt0) cc_final: 0.6816 (mp0) REVERT: A 665 GLU cc_start: 0.6052 (tm-30) cc_final: 0.5538 (pm20) REVERT: A 682 MET cc_start: 0.5048 (tmm) cc_final: 0.4046 (tpt) REVERT: A 1926 MET cc_start: 0.2790 (mtp) cc_final: 0.2318 (mmp) REVERT: A 2018 SER cc_start: 0.7109 (m) cc_final: 0.6788 (t) REVERT: A 2118 ASN cc_start: 0.8415 (t0) cc_final: 0.8205 (t0) REVERT: A 2222 GLN cc_start: 0.9052 (pt0) cc_final: 0.8770 (pt0) REVERT: A 2254 SER cc_start: 0.7907 (p) cc_final: 0.7552 (t) REVERT: B 78 LEU cc_start: 0.7066 (tt) cc_final: 0.6120 (tt) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2551 time to fit residues: 91.2143 Evaluate side-chains 161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0970 chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 121 GLN A 145 ASN A 233 HIS A 257 HIS A 318 HIS A 626 GLN ** A1777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1894 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1957 HIS A2005 HIS A2152 HIS A2284 GLN A2311 GLN B 37 GLN B 199 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.164105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.147400 restraints weight = 85951.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.147217 restraints weight = 90514.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.147403 restraints weight = 85279.337| |-----------------------------------------------------------------------------| r_work (final): 0.4634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4909 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13653 Z= 0.122 Angle : 0.626 9.672 18540 Z= 0.315 Chirality : 0.046 0.277 2022 Planarity : 0.005 0.064 2356 Dihedral : 5.158 55.225 1892 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.42 % Favored : 90.33 % Rotamer: Outliers : 0.14 % Allowed : 4.18 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.18), residues: 1645 helix: -2.70 (0.44), residues: 85 sheet: -1.74 (0.41), residues: 155 loop : -2.48 (0.15), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 256 HIS 0.005 0.001 HIS A 100 PHE 0.021 0.001 PHE A1743 TYR 0.017 0.001 TYR A2105 ARG 0.011 0.001 ARG A1749 Details of bonding type rmsd link_NAG-ASN : bond 0.01807 ( 2) link_NAG-ASN : angle 5.68110 ( 6) link_BETA1-4 : bond 0.00601 ( 2) link_BETA1-4 : angle 1.61462 ( 6) hydrogen bonds : bond 0.03627 ( 91) hydrogen bonds : angle 8.79404 ( 195) SS BOND : bond 0.00340 ( 11) SS BOND : angle 2.29260 ( 22) covalent geometry : bond 0.00267 (13638) covalent geometry : angle 0.61285 (18506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.4723 (m-10) cc_final: 0.4511 (m-80) REVERT: A 46 LEU cc_start: 0.8095 (mt) cc_final: 0.7894 (mp) REVERT: A 232 MET cc_start: 0.6054 (pmm) cc_final: 0.5731 (mpp) REVERT: A 282 HIS cc_start: 0.6014 (t70) cc_final: 0.5588 (t-90) REVERT: A 519 ASP cc_start: 0.8496 (t70) cc_final: 0.8261 (p0) REVERT: A 589 GLU cc_start: 0.7088 (tt0) cc_final: 0.6829 (mp0) REVERT: A 702 MET cc_start: 0.2485 (ptp) cc_final: 0.1569 (ptp) REVERT: A 1711 MET cc_start: -0.2048 (mmt) cc_final: -0.2434 (mmt) REVERT: A 1926 MET cc_start: 0.2692 (mtp) cc_final: 0.2343 (mmp) REVERT: A 1972 LYS cc_start: 0.7412 (tptt) cc_final: 0.7120 (mtpt) REVERT: A 2118 ASN cc_start: 0.8655 (t0) cc_final: 0.8249 (t0) REVERT: B 70 ASP cc_start: 0.8114 (m-30) cc_final: 0.7816 (m-30) outliers start: 2 outliers final: 0 residues processed: 199 average time/residue: 0.2548 time to fit residues: 74.7052 Evaluate side-chains 141 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 0.0970 chunk 123 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 143 optimal weight: 40.0000 chunk 113 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 0.0870 chunk 95 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN A1777 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.165450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.147098 restraints weight = 86682.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.146911 restraints weight = 86694.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.147377 restraints weight = 87742.945| |-----------------------------------------------------------------------------| r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5031 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13653 Z= 0.110 Angle : 0.610 9.745 18540 Z= 0.307 Chirality : 0.045 0.292 2022 Planarity : 0.005 0.054 2356 Dihedral : 4.803 51.080 1892 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.69 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.18), residues: 1645 helix: -2.38 (0.48), residues: 85 sheet: -1.64 (0.44), residues: 143 loop : -2.42 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 256 HIS 0.015 0.001 HIS C 35 PHE 0.021 0.001 PHE C 109 TYR 0.022 0.001 TYR A1976 ARG 0.005 0.000 ARG A 698 Details of bonding type rmsd link_NAG-ASN : bond 0.01470 ( 2) link_NAG-ASN : angle 5.70027 ( 6) link_BETA1-4 : bond 0.00644 ( 2) link_BETA1-4 : angle 1.81650 ( 6) hydrogen bonds : bond 0.03310 ( 91) hydrogen bonds : angle 7.95741 ( 195) SS BOND : bond 0.00208 ( 11) SS BOND : angle 2.16311 ( 22) covalent geometry : bond 0.00246 (13638) covalent geometry : angle 0.59645 (18506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.5260 (m-10) cc_final: 0.4941 (m-80) REVERT: A 89 LEU cc_start: 0.7801 (pt) cc_final: 0.7278 (tp) REVERT: A 232 MET cc_start: 0.6163 (pmm) cc_final: 0.5767 (mpp) REVERT: A 282 HIS cc_start: 0.6008 (t70) cc_final: 0.5520 (t-90) REVERT: A 589 GLU cc_start: 0.7175 (tt0) cc_final: 0.6874 (mp0) REVERT: A 665 GLU cc_start: 0.7638 (pp20) cc_final: 0.6145 (pm20) REVERT: A 682 MET cc_start: 0.4311 (tmm) cc_final: 0.2537 (tpt) REVERT: A 1711 MET cc_start: -0.1906 (mmt) cc_final: -0.2255 (mmt) REVERT: A 1926 MET cc_start: 0.2737 (mtp) cc_final: 0.2513 (mmp) REVERT: A 1973 MET cc_start: 0.7491 (pmm) cc_final: 0.6868 (pmm) REVERT: A 2118 ASN cc_start: 0.8662 (t0) cc_final: 0.8249 (t0) REVERT: A 2167 MET cc_start: 0.6020 (tmm) cc_final: 0.5270 (tmm) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2586 time to fit residues: 70.2267 Evaluate side-chains 144 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 141 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN A 693 HIS A1770 ASN A1778 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2031 HIS ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.150515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.130718 restraints weight = 77349.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.131449 restraints weight = 69639.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.131795 restraints weight = 64059.603| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5360 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 13653 Z= 0.259 Angle : 0.857 10.587 18540 Z= 0.445 Chirality : 0.053 0.328 2022 Planarity : 0.007 0.075 2356 Dihedral : 6.180 50.520 1892 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.58 % Favored : 87.17 % Rotamer: Outliers : 0.14 % Allowed : 7.41 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: -3.57 (0.18), residues: 1645 helix: -2.46 (0.45), residues: 84 sheet: -2.35 (0.36), residues: 201 loop : -2.62 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP A 256 HIS 0.014 0.002 HIS A1755 PHE 0.048 0.003 PHE A2274 TYR 0.041 0.003 TYR A 395 ARG 0.014 0.001 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.01427 ( 2) link_NAG-ASN : angle 6.76980 ( 6) link_BETA1-4 : bond 0.00791 ( 2) link_BETA1-4 : angle 1.47622 ( 6) hydrogen bonds : bond 0.04449 ( 91) hydrogen bonds : angle 8.94970 ( 195) SS BOND : bond 0.00820 ( 11) SS BOND : angle 1.78449 ( 22) covalent geometry : bond 0.00570 (13638) covalent geometry : angle 0.84596 (18506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8171 (mt) cc_final: 0.7813 (mp) REVERT: A 89 LEU cc_start: 0.8081 (pt) cc_final: 0.7618 (tt) REVERT: A 232 MET cc_start: 0.6049 (pmm) cc_final: 0.5510 (mpp) REVERT: A 282 HIS cc_start: 0.6518 (t70) cc_final: 0.5978 (t70) REVERT: A 308 LEU cc_start: 0.8635 (tp) cc_final: 0.8347 (tp) REVERT: A 696 ASP cc_start: 0.7547 (p0) cc_final: 0.7235 (p0) REVERT: A 1711 MET cc_start: -0.2231 (mmt) cc_final: -0.2558 (mmt) REVERT: A 1851 LEU cc_start: 0.7492 (mt) cc_final: 0.7246 (mt) REVERT: A 2118 ASN cc_start: 0.8611 (t0) cc_final: 0.8247 (t0) outliers start: 2 outliers final: 2 residues processed: 169 average time/residue: 0.2516 time to fit residues: 63.2058 Evaluate side-chains 129 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN A 632 HIS A 660 HIS A 693 HIS A1778 GLN A1822 HIS A1870 GLN A1950 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2152 HIS ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2286 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.144922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.126562 restraints weight = 90360.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.127209 restraints weight = 84122.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.127935 restraints weight = 74803.962| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5516 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 13653 Z= 0.277 Angle : 0.908 12.267 18540 Z= 0.471 Chirality : 0.055 0.366 2022 Planarity : 0.007 0.071 2356 Dihedral : 6.932 54.049 1892 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 27.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.29 % Favored : 85.41 % Rotamer: Outliers : 0.21 % Allowed : 6.58 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: -4.02 (0.17), residues: 1645 helix: -2.99 (0.42), residues: 91 sheet: -2.57 (0.36), residues: 183 loop : -2.95 (0.14), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A1942 HIS 0.010 0.002 HIS A1697 PHE 0.034 0.003 PHE A2274 TYR 0.048 0.003 TYR A 395 ARG 0.013 0.001 ARG A 531 Details of bonding type rmsd link_NAG-ASN : bond 0.01761 ( 2) link_NAG-ASN : angle 6.01469 ( 6) link_BETA1-4 : bond 0.00657 ( 2) link_BETA1-4 : angle 1.46230 ( 6) hydrogen bonds : bond 0.04566 ( 91) hydrogen bonds : angle 9.32934 ( 195) SS BOND : bond 0.00812 ( 11) SS BOND : angle 2.08733 ( 22) covalent geometry : bond 0.00591 (13638) covalent geometry : angle 0.89862 (18506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8204 (pt) cc_final: 0.7878 (tt) REVERT: A 232 MET cc_start: 0.5807 (pmm) cc_final: 0.5468 (pmm) REVERT: A 273 GLU cc_start: 0.8760 (pp20) cc_final: 0.7941 (mp0) REVERT: A 282 HIS cc_start: 0.6737 (t70) cc_final: 0.6220 (t-90) REVERT: A 308 LEU cc_start: 0.9008 (tp) cc_final: 0.8222 (tp) REVERT: A 658 PHE cc_start: 0.5058 (p90) cc_final: 0.4809 (p90) REVERT: A 696 ASP cc_start: 0.7624 (p0) cc_final: 0.6924 (p0) REVERT: A 1711 MET cc_start: -0.1199 (mmt) cc_final: -0.1513 (mmt) REVERT: A 1926 MET cc_start: 0.1729 (mtt) cc_final: 0.0823 (mtt) REVERT: A 1973 MET cc_start: 0.7359 (pmm) cc_final: 0.7021 (pmm) REVERT: A 2118 ASN cc_start: 0.8540 (t0) cc_final: 0.8160 (t0) outliers start: 3 outliers final: 3 residues processed: 166 average time/residue: 0.2409 time to fit residues: 60.2172 Evaluate side-chains 124 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 58 optimal weight: 8.9990 chunk 161 optimal weight: 0.5980 chunk 146 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 164 optimal weight: 30.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 316 HIS ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS A1778 GLN A1870 GLN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2031 HIS A2129 ASN ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.151133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.130542 restraints weight = 87183.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.130914 restraints weight = 79281.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.130927 restraints weight = 74056.548| |-----------------------------------------------------------------------------| r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5533 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13653 Z= 0.130 Angle : 0.708 10.400 18540 Z= 0.359 Chirality : 0.049 0.410 2022 Planarity : 0.005 0.067 2356 Dihedral : 6.083 50.670 1892 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.85 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: -3.90 (0.17), residues: 1645 helix: -2.73 (0.44), residues: 90 sheet: -2.73 (0.34), residues: 181 loop : -2.84 (0.14), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A2229 HIS 0.013 0.001 HIS A1954 PHE 0.024 0.002 PHE A2274 TYR 0.024 0.002 TYR A 395 ARG 0.004 0.000 ARG A2307 Details of bonding type rmsd link_NAG-ASN : bond 0.01471 ( 2) link_NAG-ASN : angle 6.40544 ( 6) link_BETA1-4 : bond 0.01057 ( 2) link_BETA1-4 : angle 1.51378 ( 6) hydrogen bonds : bond 0.03045 ( 91) hydrogen bonds : angle 8.13981 ( 195) SS BOND : bond 0.00380 ( 11) SS BOND : angle 1.85252 ( 22) covalent geometry : bond 0.00290 (13638) covalent geometry : angle 0.69524 (18506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8334 (pt) cc_final: 0.7966 (tp) REVERT: A 92 MET cc_start: 0.3314 (mpp) cc_final: 0.3109 (mpp) REVERT: A 232 MET cc_start: 0.5840 (pmm) cc_final: 0.5600 (pmm) REVERT: A 273 GLU cc_start: 0.8928 (pp20) cc_final: 0.8024 (mp0) REVERT: A 282 HIS cc_start: 0.6619 (t70) cc_final: 0.6211 (p-80) REVERT: A 308 LEU cc_start: 0.9065 (tp) cc_final: 0.8027 (tp) REVERT: A 428 PHE cc_start: 0.7719 (t80) cc_final: 0.7281 (t80) REVERT: A 682 MET cc_start: 0.5077 (tmm) cc_final: 0.4190 (tpt) REVERT: A 1711 MET cc_start: -0.1531 (mmt) cc_final: -0.1796 (mmt) REVERT: A 1921 ILE cc_start: 0.4650 (mp) cc_final: 0.4449 (mm) REVERT: A 1973 MET cc_start: 0.7661 (pmm) cc_final: 0.7279 (pmm) REVERT: A 2118 ASN cc_start: 0.8319 (t0) cc_final: 0.8057 (t0) REVERT: A 2167 MET cc_start: 0.6475 (tmm) cc_final: 0.5781 (tmm) REVERT: A 2199 MET cc_start: 0.6326 (pmm) cc_final: 0.6063 (pmm) REVERT: C 18 LEU cc_start: 0.8322 (mm) cc_final: 0.7621 (pp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2397 time to fit residues: 59.5194 Evaluate side-chains 122 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1755 HIS A1778 GLN A1870 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2284 GLN ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.149032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.128878 restraints weight = 87321.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.129310 restraints weight = 81227.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.129678 restraints weight = 76501.433| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13653 Z= 0.151 Angle : 0.712 10.584 18540 Z= 0.358 Chirality : 0.048 0.344 2022 Planarity : 0.005 0.064 2356 Dihedral : 5.904 49.887 1892 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.46 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: -3.85 (0.17), residues: 1645 helix: -2.59 (0.45), residues: 90 sheet: -2.82 (0.31), residues: 214 loop : -2.77 (0.15), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 110 HIS 0.011 0.001 HIS A1954 PHE 0.020 0.002 PHE A2274 TYR 0.024 0.002 TYR A 395 ARG 0.006 0.000 ARG A 531 Details of bonding type rmsd link_NAG-ASN : bond 0.01431 ( 2) link_NAG-ASN : angle 6.74326 ( 6) link_BETA1-4 : bond 0.00862 ( 2) link_BETA1-4 : angle 1.82468 ( 6) hydrogen bonds : bond 0.03068 ( 91) hydrogen bonds : angle 7.99116 ( 195) SS BOND : bond 0.00434 ( 11) SS BOND : angle 2.26915 ( 22) covalent geometry : bond 0.00340 (13638) covalent geometry : angle 0.69755 (18506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8533 (pt) cc_final: 0.8121 (tp) REVERT: A 92 MET cc_start: 0.3774 (mpp) cc_final: 0.3359 (mpp) REVERT: A 232 MET cc_start: 0.6127 (pmm) cc_final: 0.5723 (pmm) REVERT: A 273 GLU cc_start: 0.8929 (pp20) cc_final: 0.7993 (mp0) REVERT: A 282 HIS cc_start: 0.6659 (t70) cc_final: 0.6185 (p-80) REVERT: A 308 LEU cc_start: 0.9195 (tp) cc_final: 0.8221 (tp) REVERT: A 428 PHE cc_start: 0.8000 (t80) cc_final: 0.7356 (t80) REVERT: A 682 MET cc_start: 0.5087 (tmm) cc_final: 0.4153 (tpt) REVERT: A 707 LYS cc_start: 0.8224 (tttt) cc_final: 0.7796 (mtmm) REVERT: A 1711 MET cc_start: -0.1764 (mmt) cc_final: -0.1972 (mmt) REVERT: A 1973 MET cc_start: 0.7735 (pmm) cc_final: 0.7207 (pmm) REVERT: A 2118 ASN cc_start: 0.8283 (t0) cc_final: 0.8033 (t0) REVERT: A 2167 MET cc_start: 0.6692 (tmm) cc_final: 0.5849 (tmm) REVERT: A 2199 MET cc_start: 0.6626 (pmm) cc_final: 0.6375 (pmm) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2494 time to fit residues: 58.5614 Evaluate side-chains 123 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 134 optimal weight: 40.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 693 HIS A1778 GLN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.148807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.131018 restraints weight = 89801.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.131927 restraints weight = 76264.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.132743 restraints weight = 67221.380| |-----------------------------------------------------------------------------| r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5302 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13653 Z= 0.135 Angle : 0.687 10.631 18540 Z= 0.346 Chirality : 0.048 0.352 2022 Planarity : 0.005 0.065 2356 Dihedral : 5.581 30.488 1892 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.46 % Favored : 87.17 % Rotamer: Outliers : 0.07 % Allowed : 2.06 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: -3.76 (0.18), residues: 1645 helix: -2.51 (0.46), residues: 90 sheet: -2.59 (0.33), residues: 205 loop : -2.74 (0.15), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1707 HIS 0.013 0.001 HIS A 693 PHE 0.017 0.002 PHE A2274 TYR 0.018 0.002 TYR A1924 ARG 0.005 0.000 ARG A2052 Details of bonding type rmsd link_NAG-ASN : bond 0.02181 ( 2) link_NAG-ASN : angle 6.66242 ( 6) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 1.67587 ( 6) hydrogen bonds : bond 0.03033 ( 91) hydrogen bonds : angle 7.62467 ( 195) SS BOND : bond 0.00373 ( 11) SS BOND : angle 1.77834 ( 22) covalent geometry : bond 0.00302 (13638) covalent geometry : angle 0.67351 (18506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8206 (pt) cc_final: 0.7939 (tp) REVERT: A 92 MET cc_start: 0.2479 (mpp) cc_final: 0.2199 (mpp) REVERT: A 232 MET cc_start: 0.5874 (pmm) cc_final: 0.5530 (pmm) REVERT: A 273 GLU cc_start: 0.8670 (pp20) cc_final: 0.7879 (mp0) REVERT: A 282 HIS cc_start: 0.6775 (t70) cc_final: 0.6355 (p-80) REVERT: A 308 LEU cc_start: 0.8887 (tp) cc_final: 0.7842 (tp) REVERT: A 428 PHE cc_start: 0.7447 (t80) cc_final: 0.6981 (t80) REVERT: A 665 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6416 (pm20) REVERT: A 682 MET cc_start: 0.5345 (tmm) cc_final: 0.4401 (tpt) REVERT: A 707 LYS cc_start: 0.8107 (tttt) cc_final: 0.7814 (mtmm) REVERT: A 1711 MET cc_start: -0.1355 (mmt) cc_final: -0.1611 (mmt) REVERT: A 1926 MET cc_start: 0.1963 (mtt) cc_final: 0.1043 (mtm) REVERT: A 1973 MET cc_start: 0.7183 (pmm) cc_final: 0.6780 (pmm) REVERT: A 2167 MET cc_start: 0.6725 (tmm) cc_final: 0.6040 (tmm) REVERT: A 2199 MET cc_start: 0.6817 (pmm) cc_final: 0.6600 (pmm) outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.2679 time to fit residues: 64.8829 Evaluate side-chains 124 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 52 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS A1820 GLN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2031 HIS ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.148342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.129356 restraints weight = 86900.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.129742 restraints weight = 83176.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.129931 restraints weight = 78776.310| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13653 Z= 0.138 Angle : 0.695 12.401 18540 Z= 0.348 Chirality : 0.048 0.355 2022 Planarity : 0.005 0.063 2356 Dihedral : 5.505 27.217 1892 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.95 % Favored : 86.69 % Rotamer: Outliers : 0.07 % Allowed : 0.75 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: -3.70 (0.18), residues: 1645 helix: -2.45 (0.47), residues: 90 sheet: -2.47 (0.37), residues: 181 loop : -2.73 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 110 HIS 0.011 0.001 HIS A1954 PHE 0.022 0.002 PHE A 52 TYR 0.018 0.001 TYR A 395 ARG 0.005 0.001 ARG A 531 Details of bonding type rmsd link_NAG-ASN : bond 0.01586 ( 2) link_NAG-ASN : angle 6.33234 ( 6) link_BETA1-4 : bond 0.00767 ( 2) link_BETA1-4 : angle 1.45526 ( 6) hydrogen bonds : bond 0.03014 ( 91) hydrogen bonds : angle 7.42965 ( 195) SS BOND : bond 0.00383 ( 11) SS BOND : angle 1.65728 ( 22) covalent geometry : bond 0.00308 (13638) covalent geometry : angle 0.68343 (18506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8488 (pt) cc_final: 0.8069 (tp) REVERT: A 92 MET cc_start: 0.3719 (mpp) cc_final: 0.3073 (mpp) REVERT: A 232 MET cc_start: 0.6089 (pmm) cc_final: 0.5639 (pmm) REVERT: A 273 GLU cc_start: 0.8833 (pp20) cc_final: 0.7972 (mp0) REVERT: A 282 HIS cc_start: 0.6748 (t70) cc_final: 0.6342 (p-80) REVERT: A 308 LEU cc_start: 0.9172 (tp) cc_final: 0.8140 (tp) REVERT: A 428 PHE cc_start: 0.7795 (t80) cc_final: 0.7277 (t80) REVERT: A 682 MET cc_start: 0.4990 (tmm) cc_final: 0.4199 (tpt) REVERT: A 707 LYS cc_start: 0.8248 (tttt) cc_final: 0.8041 (mtmt) REVERT: A 1711 MET cc_start: -0.1546 (mmt) cc_final: -0.1765 (mmt) REVERT: A 1926 MET cc_start: 0.1250 (mtt) cc_final: 0.0479 (mtm) REVERT: A 2167 MET cc_start: 0.6688 (tmm) cc_final: 0.5904 (tmm) REVERT: A 2199 MET cc_start: 0.6862 (pmm) cc_final: 0.6614 (pmm) outliers start: 1 outliers final: 1 residues processed: 164 average time/residue: 0.2249 time to fit residues: 55.8437 Evaluate side-chains 125 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 93 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 139 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1778 GLN ** A1936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1950 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2031 HIS ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.147688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.130591 restraints weight = 88268.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.131439 restraints weight = 79044.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.131713 restraints weight = 72036.398| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13653 Z= 0.139 Angle : 0.698 13.760 18540 Z= 0.349 Chirality : 0.049 0.395 2022 Planarity : 0.005 0.063 2356 Dihedral : 5.502 27.722 1892 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.01 % Favored : 86.63 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: -3.77 (0.18), residues: 1645 helix: -2.62 (0.44), residues: 96 sheet: -2.51 (0.36), residues: 191 loop : -2.76 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 14 HIS 0.011 0.001 HIS A1954 PHE 0.018 0.002 PHE A 52 TYR 0.029 0.002 TYR A 16 ARG 0.005 0.001 ARG A 531 Details of bonding type rmsd link_NAG-ASN : bond 0.01775 ( 2) link_NAG-ASN : angle 7.35716 ( 6) link_BETA1-4 : bond 0.01154 ( 2) link_BETA1-4 : angle 1.43679 ( 6) hydrogen bonds : bond 0.02918 ( 91) hydrogen bonds : angle 7.31487 ( 195) SS BOND : bond 0.00377 ( 11) SS BOND : angle 1.61175 ( 22) covalent geometry : bond 0.00311 (13638) covalent geometry : angle 0.68275 (18506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8281 (pt) cc_final: 0.8006 (tp) REVERT: A 92 MET cc_start: 0.3004 (mpp) cc_final: 0.2426 (mpp) REVERT: A 232 MET cc_start: 0.5961 (pmm) cc_final: 0.5525 (pmm) REVERT: A 261 MET cc_start: 0.6650 (mmm) cc_final: 0.6185 (tmm) REVERT: A 273 GLU cc_start: 0.8749 (pp20) cc_final: 0.7983 (mp0) REVERT: A 282 HIS cc_start: 0.6806 (t70) cc_final: 0.6390 (p-80) REVERT: A 308 LEU cc_start: 0.9056 (tp) cc_final: 0.8065 (tp) REVERT: A 428 PHE cc_start: 0.7719 (t80) cc_final: 0.7192 (t80) REVERT: A 665 GLU cc_start: 0.7451 (tm-30) cc_final: 0.6456 (pm20) REVERT: A 682 MET cc_start: 0.5362 (tmm) cc_final: 0.4522 (tpt) REVERT: A 1926 MET cc_start: 0.0918 (mtt) cc_final: 0.0206 (mtm) REVERT: A 2167 MET cc_start: 0.6813 (tmm) cc_final: 0.6018 (tmm) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3567 time to fit residues: 83.3665 Evaluate side-chains 123 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.0060 chunk 6 optimal weight: 0.2980 chunk 14 optimal weight: 0.0050 chunk 143 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 5 optimal weight: 0.0050 overall best weight: 0.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1778 GLN A1950 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.153418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.135725 restraints weight = 87006.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.135223 restraints weight = 95387.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.135317 restraints weight = 94807.026| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13653 Z= 0.113 Angle : 0.684 13.056 18540 Z= 0.334 Chirality : 0.047 0.344 2022 Planarity : 0.005 0.066 2356 Dihedral : 4.949 25.905 1892 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.43 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: -3.63 (0.18), residues: 1645 helix: -2.60 (0.45), residues: 97 sheet: -2.38 (0.37), residues: 180 loop : -2.66 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A1942 HIS 0.008 0.001 HIS A1954 PHE 0.015 0.001 PHE A 52 TYR 0.022 0.001 TYR A 157 ARG 0.004 0.000 ARG A2052 Details of bonding type rmsd link_NAG-ASN : bond 0.01236 ( 2) link_NAG-ASN : angle 7.40922 ( 6) link_BETA1-4 : bond 0.00701 ( 2) link_BETA1-4 : angle 2.03239 ( 6) hydrogen bonds : bond 0.02582 ( 91) hydrogen bonds : angle 6.62994 ( 195) SS BOND : bond 0.00159 ( 11) SS BOND : angle 1.64398 ( 22) covalent geometry : bond 0.00250 (13638) covalent geometry : angle 0.66834 (18506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5888.43 seconds wall clock time: 106 minutes 22.34 seconds (6382.34 seconds total)