Starting phenix.real_space_refine on Sat Mar 16 00:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6i_29770/03_2024/8g6i_29770_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6i_29770/03_2024/8g6i_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6i_29770/03_2024/8g6i_29770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6i_29770/03_2024/8g6i_29770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6i_29770/03_2024/8g6i_29770_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6i_29770/03_2024/8g6i_29770_neut.pdb" } 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 Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.19, per 1000 atoms: 0.54 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 - 3.50 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 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: 5.16 Conformation dependent library (CDL) restraints added in 2.5 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: 1.46 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: 3.83 Time building geometry restraints manager: 5.66 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: 99.51 - 106.41: 438 106.41 - 113.32: 7271 113.32 - 120.23: 4518 120.23 - 127.13: 6103 127.13 - 134.04: 176 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 2.520 nonbonded pdb=" O TRP A1996 " pdb=" OG1 THR A2013 " model vdw 2.180 2.440 nonbonded pdb=" OH TYR B 87 " pdb=" O ALA C 43 " model vdw 2.181 2.440 nonbonded pdb=" O LYS A1845 " pdb=" OG SER A1849 " model vdw 2.219 2.440 nonbonded pdb=" OE2 GLU A1704 " pdb=" OH TYR A1890 " model vdw 2.232 2.440 ... (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 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: 3.250 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: 10.430 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 36.700 Find NCS groups from input model: 0.400 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.870 ------------------------------------------------------------------------------- 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 13638 Z= 0.200 Angle : 0.679 8.585 18506 Z= 0.363 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.196 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: 0.2682 time to fit residues: 95.4423 Evaluate side-chains 161 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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: 0.0010 chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 overall best weight: 2.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 HIS A 257 HIS A 318 HIS A 626 GLN A1770 ASN ** A1777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1778 GLN A1870 GLN ** A1894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1954 HIS A1957 HIS A2005 HIS A2152 HIS A2311 GLN B 37 GLN B 79 GLN B 199 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4646 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13638 Z= 0.228 Angle : 0.632 8.790 18506 Z= 0.323 Chirality : 0.047 0.376 2022 Planarity : 0.005 0.064 2356 Dihedral : 5.262 56.703 1892 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.33 % Favored : 89.36 % Rotamer: Outliers : 0.21 % Allowed : 4.94 % Favored : 94.86 % 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: -3.39 (0.18), residues: 1645 helix: -2.63 (0.45), residues: 84 sheet: -2.15 (0.39), residues: 172 loop : -2.49 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 256 HIS 0.008 0.001 HIS A 100 PHE 0.022 0.002 PHE A1743 TYR 0.017 0.002 TYR A 395 ARG 0.006 0.001 ARG A1859 *********************** 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 198 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 1.367 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: A 46 LEU cc_start: 0.7848 (mt) cc_final: 0.7636 (mp) REVERT: A 232 MET cc_start: 0.5835 (pmm) cc_final: 0.5434 (mpp) REVERT: A 282 HIS cc_start: 0.6363 (t70) cc_final: 0.5958 (t-90) REVERT: A 308 LEU cc_start: 0.8555 (tp) cc_final: 0.8313 (tp) REVERT: A 589 GLU cc_start: 0.7307 (tt0) cc_final: 0.6921 (mp0) REVERT: A 696 ASP cc_start: 0.7414 (p0) cc_final: 0.7145 (p0) REVERT: A 702 MET cc_start: 0.2014 (ptp) cc_final: 0.0232 (ptp) REVERT: A 1711 MET cc_start: -0.1749 (mmt) cc_final: -0.2211 (mmt) REVERT: A 1926 MET cc_start: 0.2958 (mtp) cc_final: 0.2602 (mmp) REVERT: A 1973 MET cc_start: 0.6707 (pmm) cc_final: 0.6492 (pmm) REVERT: A 2118 ASN cc_start: 0.8408 (t0) cc_final: 0.8111 (t0) REVERT: A 2195 TYR cc_start: 0.8575 (p90) cc_final: 0.8370 (p90) outliers start: 3 outliers final: 0 residues processed: 198 average time/residue: 0.2556 time to fit residues: 73.8448 Evaluate side-chains 145 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 0.0040 chunk 102 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 150 optimal weight: 9.9990 chunk 162 optimal weight: 0.1980 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** A1777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1870 GLN ** A1894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2311 GLN B 79 GLN C 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4580 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13638 Z= 0.155 Angle : 0.578 8.663 18506 Z= 0.290 Chirality : 0.045 0.314 2022 Planarity : 0.004 0.054 2356 Dihedral : 6.814 117.496 1892 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.15 % Favored : 89.54 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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: -3.30 (0.18), residues: 1645 helix: -2.33 (0.48), residues: 84 sheet: -2.04 (0.39), residues: 175 loop : -2.45 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 256 HIS 0.013 0.001 HIS C 35 PHE 0.013 0.001 PHE A1743 TYR 0.017 0.001 TYR B 140 ARG 0.003 0.000 ARG A1749 *********************** 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 183 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.452 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: A 89 LEU cc_start: 0.7746 (pt) cc_final: 0.7380 (tp) REVERT: A 232 MET cc_start: 0.6007 (pmm) cc_final: 0.5467 (mpp) REVERT: A 282 HIS cc_start: 0.6342 (t70) cc_final: 0.5894 (t-90) REVERT: A 308 LEU cc_start: 0.8544 (tp) cc_final: 0.8319 (tp) REVERT: A 589 GLU cc_start: 0.7353 (tt0) cc_final: 0.6985 (mp0) REVERT: A 1711 MET cc_start: -0.1813 (mmt) cc_final: -0.2263 (mmt) REVERT: A 1926 MET cc_start: 0.3104 (mtp) cc_final: 0.2762 (mmm) REVERT: A 2118 ASN cc_start: 0.8454 (t0) cc_final: 0.8142 (t0) REVERT: A 2124 MET cc_start: 0.1818 (pmm) cc_final: 0.1212 (ptt) REVERT: A 2167 MET cc_start: 0.6526 (tmm) cc_final: 0.5975 (tmm) REVERT: A 2180 MET cc_start: 0.6911 (mmm) cc_final: 0.6231 (mmm) REVERT: A 2222 GLN cc_start: 0.9181 (pt0) cc_final: 0.8907 (pt0) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2361 time to fit residues: 64.3802 Evaluate side-chains 139 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 615 HIS A 626 GLN A 660 HIS A 693 HIS ** A1777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1870 GLN ** A1894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2286 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5289 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 13638 Z= 0.482 Angle : 0.985 10.544 18506 Z= 0.518 Chirality : 0.057 0.352 2022 Planarity : 0.008 0.086 2356 Dihedral : 8.555 117.109 1892 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 39.13 Ramachandran Plot: Outliers : 0.36 % Allowed : 15.56 % Favored : 84.07 % Rotamer: Outliers : 0.27 % Allowed : 9.95 % Favored : 89.78 % 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: -4.04 (0.17), residues: 1645 helix: -2.81 (0.44), residues: 86 sheet: -2.67 (0.35), residues: 183 loop : -2.97 (0.14), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP A 256 HIS 0.012 0.002 HIS A1755 PHE 0.034 0.004 PHE A2274 TYR 0.055 0.004 TYR A 395 ARG 0.013 0.002 ARG A1997 *********************** 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 171 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.555 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: A 89 LEU cc_start: 0.8151 (pt) cc_final: 0.7830 (tt) REVERT: A 92 MET cc_start: 0.2492 (mpp) cc_final: 0.2200 (mpp) REVERT: A 232 MET cc_start: 0.5731 (pmm) cc_final: 0.5359 (pmm) REVERT: A 282 HIS cc_start: 0.6739 (t70) cc_final: 0.6241 (t-90) REVERT: A 308 LEU cc_start: 0.8716 (tp) cc_final: 0.8451 (tp) REVERT: A 1711 MET cc_start: -0.1672 (mmt) cc_final: -0.2059 (mmt) REVERT: A 1851 LEU cc_start: 0.7699 (mt) cc_final: 0.7310 (mt) REVERT: A 1942 TRP cc_start: 0.7307 (m100) cc_final: 0.7004 (m100) REVERT: A 1973 MET cc_start: 0.7604 (pmm) cc_final: 0.6854 (pmm) REVERT: A 1986 VAL cc_start: 0.8016 (p) cc_final: 0.7501 (p) REVERT: A 2118 ASN cc_start: 0.8374 (t0) cc_final: 0.7979 (t0) REVERT: A 2284 GLN cc_start: 0.6620 (tp40) cc_final: 0.6263 (tp40) outliers start: 4 outliers final: 2 residues processed: 171 average time/residue: 0.2415 time to fit residues: 61.0090 Evaluate side-chains 134 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 0.0060 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 136 optimal weight: 40.0000 chunk 110 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 50.0000 chunk 40 optimal weight: 0.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1936 GLN A1950 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1977 ASN ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2211 HIS A2222 GLN B 3 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5047 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13638 Z= 0.212 Angle : 0.687 9.353 18506 Z= 0.349 Chirality : 0.048 0.338 2022 Planarity : 0.005 0.060 2356 Dihedral : 7.352 105.335 1892 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.16 % Favored : 87.48 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -3.97 (0.17), residues: 1645 helix: -2.88 (0.41), residues: 96 sheet: -2.54 (0.34), residues: 187 loop : -2.92 (0.14), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 139 HIS 0.007 0.001 HIS A 162 PHE 0.030 0.002 PHE A1743 TYR 0.023 0.002 TYR A 255 ARG 0.003 0.000 ARG C 38 *********************** 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 173 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.671 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 162 HIS cc_start: 0.6046 (m90) cc_final: 0.5038 (m-70) REVERT: A 232 MET cc_start: 0.5683 (pmm) cc_final: 0.5277 (pmm) REVERT: A 282 HIS cc_start: 0.6674 (t70) cc_final: 0.6260 (t-90) REVERT: A 308 LEU cc_start: 0.8666 (tp) cc_final: 0.8362 (tp) REVERT: A 428 PHE cc_start: 0.7211 (t80) cc_final: 0.6837 (t80) REVERT: A 665 GLU cc_start: 0.8159 (pp20) cc_final: 0.6010 (pm20) REVERT: A 682 MET cc_start: 0.5579 (tmm) cc_final: 0.5309 (tpt) REVERT: A 696 ASP cc_start: 0.7736 (p0) cc_final: 0.7177 (p0) REVERT: A 1711 MET cc_start: -0.1524 (mmt) cc_final: -0.1851 (mmt) REVERT: A 1926 MET cc_start: 0.1624 (mtt) cc_final: 0.0749 (mtm) REVERT: A 2118 ASN cc_start: 0.8316 (t0) cc_final: 0.8105 (t0) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2364 time to fit residues: 61.1394 Evaluate side-chains 137 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 40.0000 chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 0.3980 chunk 39 optimal weight: 0.0270 chunk 159 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1755 HIS ** A1777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2129 ASN A2152 HIS A2222 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4898 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13638 Z= 0.168 Angle : 0.626 8.375 18506 Z= 0.317 Chirality : 0.046 0.310 2022 Planarity : 0.005 0.061 2356 Dihedral : 6.888 105.512 1892 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.12 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % 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: -3.78 (0.18), residues: 1645 helix: -2.70 (0.44), residues: 90 sheet: -2.46 (0.34), residues: 192 loop : -2.77 (0.15), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2229 HIS 0.011 0.001 HIS A 693 PHE 0.022 0.001 PHE A1743 TYR 0.016 0.001 TYR C 53 ARG 0.005 0.000 ARG A2307 *********************** 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 179 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.504 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: A 89 LEU cc_start: 0.7429 (pp) cc_final: 0.7091 (tp) REVERT: A 92 MET cc_start: 0.1623 (mpp) cc_final: 0.1294 (mpp) REVERT: A 232 MET cc_start: 0.5722 (pmm) cc_final: 0.5321 (pmm) REVERT: A 282 HIS cc_start: 0.6666 (t70) cc_final: 0.6265 (t-90) REVERT: A 308 LEU cc_start: 0.8647 (tp) cc_final: 0.8326 (tp) REVERT: A 428 PHE cc_start: 0.7091 (t80) cc_final: 0.6886 (t80) REVERT: A 504 LEU cc_start: 0.8366 (tp) cc_final: 0.8153 (tt) REVERT: A 665 GLU cc_start: 0.8016 (pp20) cc_final: 0.6037 (pm20) REVERT: A 682 MET cc_start: 0.5453 (tmm) cc_final: 0.4693 (tpt) REVERT: A 1711 MET cc_start: -0.1556 (mmt) cc_final: -0.1831 (mmt) REVERT: A 1926 MET cc_start: 0.1772 (mtt) cc_final: 0.1017 (mtm) REVERT: A 2167 MET cc_start: 0.6531 (tmm) cc_final: 0.5832 (tmm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2354 time to fit residues: 63.4703 Evaluate side-chains 143 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 159 optimal weight: 0.0870 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN A1755 HIS ** A1894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1936 GLN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2222 GLN A2311 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4951 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13638 Z= 0.170 Angle : 0.616 11.325 18506 Z= 0.308 Chirality : 0.047 0.401 2022 Planarity : 0.005 0.056 2356 Dihedral : 6.788 107.070 1892 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.43 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: -3.71 (0.18), residues: 1645 helix: -2.60 (0.45), residues: 90 sheet: -2.51 (0.31), residues: 216 loop : -2.70 (0.15), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 139 HIS 0.003 0.001 HIS A2309 PHE 0.017 0.001 PHE A1743 TYR 0.013 0.001 TYR A 395 ARG 0.003 0.000 ARG C 38 *********************** 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 170 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.465 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 89 LEU cc_start: 0.7305 (pp) cc_final: 0.7020 (tp) REVERT: A 232 MET cc_start: 0.5694 (pmm) cc_final: 0.5274 (pmm) REVERT: A 282 HIS cc_start: 0.6750 (t70) cc_final: 0.6314 (t-90) REVERT: A 308 LEU cc_start: 0.8632 (tp) cc_final: 0.8304 (tp) REVERT: A 504 LEU cc_start: 0.8379 (tp) cc_final: 0.8168 (tt) REVERT: A 665 GLU cc_start: 0.8157 (pp20) cc_final: 0.6056 (pm20) REVERT: A 682 MET cc_start: 0.5437 (tmm) cc_final: 0.4649 (tpt) REVERT: A 707 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8001 (mtmt) REVERT: A 1711 MET cc_start: -0.1448 (mmt) cc_final: -0.1728 (mmt) REVERT: A 1921 ILE cc_start: 0.4303 (mp) cc_final: 0.4057 (mm) REVERT: A 1926 MET cc_start: 0.1615 (mtt) cc_final: 0.0885 (mtm) REVERT: A 2167 MET cc_start: 0.6706 (tmm) cc_final: 0.5888 (tmm) REVERT: A 2255 MET cc_start: 0.3245 (ptm) cc_final: 0.2997 (ptp) REVERT: A 2284 GLN cc_start: 0.6436 (tp40) cc_final: 0.5798 (tp40) REVERT: C 89 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8977 (mm-30) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2325 time to fit residues: 59.6734 Evaluate side-chains 140 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 144 optimal weight: 0.4980 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1778 GLN ** A1894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2222 GLN ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5161 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13638 Z= 0.249 Angle : 0.698 11.790 18506 Z= 0.355 Chirality : 0.048 0.368 2022 Planarity : 0.005 0.055 2356 Dihedral : 7.233 107.931 1892 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.25 % Favored : 86.44 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % 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: -3.80 (0.18), residues: 1645 helix: -2.82 (0.42), residues: 98 sheet: -2.44 (0.35), residues: 192 loop : -2.78 (0.15), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 139 HIS 0.007 0.001 HIS A 100 PHE 0.052 0.002 PHE A2274 TYR 0.026 0.002 TYR A 395 ARG 0.013 0.001 ARG A2052 *********************** 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 162 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.7383 (pp) cc_final: 0.7111 (tp) REVERT: A 232 MET cc_start: 0.5588 (pmm) cc_final: 0.5185 (pmm) REVERT: A 273 GLU cc_start: 0.8120 (pp20) cc_final: 0.7769 (mp0) REVERT: A 282 HIS cc_start: 0.6814 (t70) cc_final: 0.6396 (t-90) REVERT: A 308 LEU cc_start: 0.8752 (tp) cc_final: 0.7725 (tp) REVERT: A 428 PHE cc_start: 0.7408 (t80) cc_final: 0.7033 (t80) REVERT: A 665 GLU cc_start: 0.8444 (pp20) cc_final: 0.8221 (pp20) REVERT: A 707 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7999 (mtmt) REVERT: A 1711 MET cc_start: -0.1538 (mmt) cc_final: -0.1815 (mmt) REVERT: A 1921 ILE cc_start: 0.4425 (mp) cc_final: 0.4184 (mm) REVERT: A 1926 MET cc_start: 0.1510 (mtt) cc_final: 0.0693 (mtm) REVERT: A 2255 MET cc_start: 0.3272 (ptm) cc_final: 0.3015 (ptp) REVERT: A 2284 GLN cc_start: 0.6613 (tp40) cc_final: 0.6284 (tp40) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2182 time to fit residues: 54.1294 Evaluate side-chains 136 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.9990 chunk 139 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 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 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1936 GLN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2031 HIS A2222 GLN ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2311 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5143 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13638 Z= 0.212 Angle : 0.689 12.366 18506 Z= 0.346 Chirality : 0.048 0.341 2022 Planarity : 0.005 0.057 2356 Dihedral : 7.236 107.622 1892 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.89 % Favored : 86.81 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -3.80 (0.18), residues: 1645 helix: -2.57 (0.45), residues: 90 sheet: -2.76 (0.32), residues: 203 loop : -2.74 (0.15), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 139 HIS 0.008 0.001 HIS A 162 PHE 0.029 0.002 PHE A2274 TYR 0.016 0.002 TYR A1976 ARG 0.005 0.001 ARG A2052 *********************** 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 164 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.5648 (pmm) cc_final: 0.5265 (pmm) REVERT: A 273 GLU cc_start: 0.8084 (pp20) cc_final: 0.7775 (mp0) REVERT: A 282 HIS cc_start: 0.6828 (t70) cc_final: 0.6389 (p-80) REVERT: A 308 LEU cc_start: 0.8751 (tp) cc_final: 0.7616 (tp) REVERT: A 428 PHE cc_start: 0.7423 (t80) cc_final: 0.7039 (t80) REVERT: A 682 MET cc_start: 0.5760 (tmm) cc_final: 0.5467 (tpt) REVERT: A 707 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8106 (mtmt) REVERT: A 1711 MET cc_start: -0.1663 (mmt) cc_final: -0.1952 (mmt) REVERT: A 1856 LEU cc_start: 0.7641 (tt) cc_final: 0.6457 (mp) REVERT: A 1926 MET cc_start: 0.1465 (mtt) cc_final: 0.0677 (mtm) REVERT: A 2255 MET cc_start: 0.3222 (ptm) cc_final: 0.3012 (ptp) REVERT: A 2284 GLN cc_start: 0.6635 (tp40) cc_final: 0.6364 (tp40) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2201 time to fit residues: 54.7195 Evaluate side-chains 128 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 50.0000 chunk 95 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A1894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1950 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2222 GLN ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5143 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13638 Z= 0.206 Angle : 0.681 12.461 18506 Z= 0.342 Chirality : 0.048 0.337 2022 Planarity : 0.005 0.057 2356 Dihedral : 7.212 107.741 1892 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.74 % Favored : 85.96 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -3.81 (0.18), residues: 1645 helix: -2.55 (0.45), residues: 90 sheet: -2.80 (0.33), residues: 193 loop : -2.76 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1942 HIS 0.004 0.001 HIS A1755 PHE 0.027 0.002 PHE A 52 TYR 0.019 0.002 TYR A 16 ARG 0.005 0.001 ARG A2052 ********************** 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 163 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.2755 (mpp) cc_final: 0.2434 (mpp) REVERT: A 273 GLU cc_start: 0.8012 (pp20) cc_final: 0.7738 (mp0) REVERT: A 282 HIS cc_start: 0.6871 (t70) cc_final: 0.6444 (p-80) REVERT: A 308 LEU cc_start: 0.8760 (tp) cc_final: 0.7546 (tp) REVERT: A 428 PHE cc_start: 0.7449 (t80) cc_final: 0.7127 (t80) REVERT: A 682 MET cc_start: 0.5563 (tmm) cc_final: 0.5319 (tpt) REVERT: A 707 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8109 (mtmt) REVERT: A 1711 MET cc_start: -0.1788 (mmt) cc_final: -0.2066 (mmt) REVERT: A 1926 MET cc_start: 0.1086 (mtt) cc_final: 0.0262 (mtm) REVERT: A 1988 MET cc_start: 0.0960 (ptt) cc_final: 0.0640 (ptt) REVERT: A 2284 GLN cc_start: 0.6680 (tp40) cc_final: 0.6131 (tp40) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2159 time to fit residues: 53.5058 Evaluate side-chains 133 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 134 optimal weight: 40.0000 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.0000 chunk 115 optimal weight: 0.7980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1950 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2222 GLN ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 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 = 0.4754 r_free = 0.4754 target = 0.148133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.129696 restraints weight = 85962.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.130721 restraints weight = 73659.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.131415 restraints weight = 65009.581| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5387 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13638 Z= 0.175 Angle : 0.656 14.032 18506 Z= 0.325 Chirality : 0.047 0.340 2022 Planarity : 0.005 0.059 2356 Dihedral : 7.050 107.648 1892 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.89 % Favored : 86.81 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -3.82 (0.18), residues: 1645 helix: -2.71 (0.42), residues: 96 sheet: -2.81 (0.32), residues: 215 loop : -2.73 (0.15), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 139 HIS 0.011 0.001 HIS A 384 PHE 0.018 0.001 PHE A 60 TYR 0.019 0.001 TYR A1762 ARG 0.003 0.000 ARG A2052 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2658.89 seconds wall clock time: 49 minutes 13.70 seconds (2953.70 seconds total)