Starting phenix.real_space_refine on Sat Apr 6 18:23:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/04_2024/8t3v_41013_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/04_2024/8t3v_41013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/04_2024/8t3v_41013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/04_2024/8t3v_41013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/04_2024/8t3v_41013_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/04_2024/8t3v_41013_neut_updated.pdb" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 52 5.16 5 C 5562 2.51 5 N 1507 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "N ARG 219": "NH1" <-> "NH2" Residue "N GLU 221": "OE1" <-> "OE2" Residue "N GLU 235": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8742 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1790 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2061 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 19, 'TRANS': 256} Chain breaks: 1 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'CLR': 1, 'HXA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.00, per 1000 atoms: 0.57 Number of scatterers: 8742 At special positions: 0 Unit cell: (86.73, 120.596, 123.9, 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 52 16.00 O 1621 8.00 N 1507 7.00 C 5562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.04 Simple disulfide: pdb=" SG CYS R 79 " - pdb=" SG CYS R 170 " 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 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.6 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 33.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 184 through 202 Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 222 through 224 No H-bonds generated for 'chain 'N' and resid 222 through 224' Processing helix chain 'R' and resid 5 through 36 Proline residue: R 21 - end of helix removed outlier: 3.810A pdb=" N LEU R 25 " --> pdb=" O PRO R 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS R 33 " --> pdb=" O GLY R 29 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 67 removed outlier: 3.740A pdb=" N SER R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Proline residue: R 60 - end of helix removed outlier: 3.817A pdb=" N GLU R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 109 Proline residue: R 80 - end of helix removed outlier: 3.774A pdb=" N VAL R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Proline residue: R 89 - end of helix removed outlier: 4.192A pdb=" N GLY R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 116 removed outlier: 3.679A pdb=" N ALA R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 144 removed outlier: 3.579A pdb=" N LEU R 135 " --> pdb=" O TRP R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 190 removed outlier: 3.583A pdb=" N GLY R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) Proline residue: R 181 - end of helix removed outlier: 3.586A pdb=" N LEU R 186 " --> pdb=" O ALA R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 211 removed outlier: 3.859A pdb=" N ARG R 211 " --> pdb=" O ARG R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 235 removed outlier: 3.649A pdb=" N VAL R 225 " --> pdb=" O ARG R 221 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA R 229 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 249 removed outlier: 3.588A pdb=" N ASN R 244 " --> pdb=" O TYR R 240 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL R 245 " --> pdb=" O ASN R 241 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE R 248 " --> pdb=" O ASN R 244 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU R 249 " --> pdb=" O VAL R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 276 removed outlier: 3.565A pdb=" N ILE R 263 " --> pdb=" O LYS R 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER R 268 " --> pdb=" O THR R 264 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL R 269 " --> pdb=" O GLY R 265 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU R 271 " --> pdb=" O TRP R 267 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.624A pdb=" N PHE A 142 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 37 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 39 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A 74 " --> pdb=" O PHE A 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.690A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.694A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.416A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.663A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 45 through 51 removed outlier: 3.571A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.706A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 Processing sheet with id= K, first strand: chain 'N' and resid 95 through 99 removed outlier: 5.386A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 147 through 149 removed outlier: 6.871A pdb=" N LYS N 245 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY N 226 " --> pdb=" O LEU N 246 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR N 176 " --> pdb=" O MET N 231 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU N 188 " --> pdb=" O LEU N 179 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 156 through 161 removed outlier: 3.680A pdb=" N VAL N 156 " --> pdb=" O ILE N 217 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1044 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: 2.48 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2820 1.34 - 1.46: 1434 1.46 - 1.58: 4610 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8936 Sorted by residual: bond pdb=" N VAL N 225 " pdb=" CA VAL N 225 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.12e+01 bond pdb=" N VAL A 109 " pdb=" CA VAL A 109 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.10e-02 8.26e+03 1.09e+01 bond pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N CYS B 149 " pdb=" CA CYS B 149 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N PHE N 68 " pdb=" CA PHE N 68 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.21e-02 6.83e+03 9.98e+00 ... (remaining 8931 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.18: 202 106.18 - 113.16: 4785 113.16 - 120.14: 3219 120.14 - 127.12: 3822 127.12 - 134.10: 110 Bond angle restraints: 12138 Sorted by residual: angle pdb=" CA ILE A 107 " pdb=" C ILE A 107 " pdb=" N PHE A 108 " ideal model delta sigma weight residual 115.25 122.32 -7.07 9.50e-01 1.11e+00 5.54e+01 angle pdb=" O ILE A 107 " pdb=" C ILE A 107 " pdb=" N PHE A 108 " ideal model delta sigma weight residual 121.96 115.79 6.17 8.40e-01 1.42e+00 5.40e+01 angle pdb=" C PHE B 151 " pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " ideal model delta sigma weight residual 110.19 103.47 6.72 1.62e+00 3.81e-01 1.72e+01 angle pdb=" C ARG N 192 " pdb=" N MET N 193 " pdb=" CA MET N 193 " ideal model delta sigma weight residual 121.54 129.46 -7.92 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C GLN N 82 " pdb=" N MET N 83 " pdb=" CA MET N 83 " ideal model delta sigma weight residual 121.86 115.34 6.52 1.58e+00 4.01e-01 1.70e+01 ... (remaining 12133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4626 17.81 - 35.63: 532 35.63 - 53.44: 133 53.44 - 71.26: 21 71.26 - 89.07: 3 Dihedral angle restraints: 5315 sinusoidal: 2056 harmonic: 3259 Sorted by residual: dihedral pdb=" C CYS B 233 " pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" CB CYS B 233 " ideal model delta harmonic sigma weight residual -122.60 -113.27 -9.33 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CB CYS N 160 " pdb=" SG CYS N 160 " pdb=" SG CYS N 230 " pdb=" CB CYS N 230 " ideal model delta sinusoidal sigma weight residual 93.00 61.99 31.01 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA MET N 231 " pdb=" C MET N 231 " pdb=" N GLN N 232 " pdb=" CA GLN N 232 " ideal model delta harmonic sigma weight residual 180.00 162.74 17.26 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1065 0.053 - 0.106: 225 0.106 - 0.160: 57 0.160 - 0.213: 15 0.213 - 0.266: 6 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CA LEU B 152 " pdb=" N LEU B 152 " pdb=" C LEU B 152 " pdb=" CB LEU B 152 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LEU A 36 " pdb=" N LEU A 36 " pdb=" C LEU A 36 " pdb=" CB LEU A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA LEU N 79 " pdb=" N LEU N 79 " pdb=" C LEU N 79 " pdb=" CB LEU N 79 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1365 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 HXA R 302 " 0.066 2.00e-02 2.50e+03 1.25e-01 1.57e+02 pdb=" C16 HXA R 302 " -0.165 2.00e-02 2.50e+03 pdb=" C17 HXA R 302 " 0.164 2.00e-02 2.50e+03 pdb=" C18 HXA R 302 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 HXA R 302 " 0.109 2.00e-02 2.50e+03 1.10e-01 1.21e+02 pdb=" C4 HXA R 302 " -0.106 2.00e-02 2.50e+03 pdb=" C5 HXA R 302 " -0.114 2.00e-02 2.50e+03 pdb=" C6 HXA R 302 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 HXA R 302 " -0.041 2.00e-02 2.50e+03 7.44e-02 5.54e+01 pdb=" C7 HXA R 302 " 0.097 2.00e-02 2.50e+03 pdb=" C8 HXA R 302 " -0.097 2.00e-02 2.50e+03 pdb=" C9 HXA R 302 " 0.041 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 403 2.72 - 3.26: 8881 3.26 - 3.81: 14349 3.81 - 4.35: 17607 4.35 - 4.90: 29979 Nonbonded interactions: 71219 Sorted by model distance: nonbonded pdb=" O TYR R 240 " pdb=" OG SER R 243 " model vdw 2.175 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.215 2.440 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.229 2.440 nonbonded pdb=" NH1 ARG A 93 " pdb=" OD1 ASP A 124 " model vdw 2.279 2.520 nonbonded pdb=" O THR B 47 " pdb=" OG1 THR B 47 " model vdw 2.286 2.440 ... (remaining 71214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.000 Extract box with map and model: 4.020 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.540 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 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 : 0.005 0.044 8936 Z= 0.316 Angle : 0.808 12.674 12138 Z= 0.509 Chirality : 0.053 0.266 1368 Planarity : 0.007 0.125 1555 Dihedral : 15.857 89.070 3214 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.44 % Allowed : 25.66 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1120 helix: 1.36 (0.28), residues: 350 sheet: -0.41 (0.32), residues: 263 loop : -0.03 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS R 216 PHE 0.020 0.001 PHE B 151 TYR 0.017 0.001 TYR B 59 ARG 0.007 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7495 (m-80) cc_final: 0.7010 (m-80) REVERT: B 217 MET cc_start: 0.6921 (tpt) cc_final: 0.6685 (tpt) REVERT: N 34 MET cc_start: 0.4780 (mmt) cc_final: 0.4238 (mmt) REVERT: N 76 LYS cc_start: 0.7339 (mtpp) cc_final: 0.6758 (mppt) REVERT: N 173 THR cc_start: 0.4018 (m) cc_final: 0.3806 (m) REVERT: R 8 SER cc_start: 0.7843 (m) cc_final: 0.7388 (t) REVERT: R 35 ARG cc_start: 0.5935 (mmm160) cc_final: 0.5725 (mmp-170) outliers start: 4 outliers final: 0 residues processed: 227 average time/residue: 0.1981 time to fit residues: 61.8000 Evaluate side-chains 172 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN B 266 HIS N 168 HIS N 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8936 Z= 0.269 Angle : 0.678 13.608 12138 Z= 0.339 Chirality : 0.045 0.182 1368 Planarity : 0.005 0.052 1555 Dihedral : 5.080 44.238 1312 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.13 % Allowed : 22.82 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1120 helix: 1.47 (0.28), residues: 355 sheet: -0.49 (0.32), residues: 267 loop : 0.17 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 297 HIS 0.007 0.001 HIS B 62 PHE 0.030 0.003 PHE B 199 TYR 0.020 0.002 TYR B 59 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 183 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.6059 (ptt) REVERT: A 53 MET cc_start: 0.7357 (tmm) cc_final: 0.7054 (tmm) REVERT: A 182 GLU cc_start: 0.6280 (pm20) cc_final: 0.5100 (pt0) REVERT: B 124 TYR cc_start: 0.8281 (m-80) cc_final: 0.7843 (m-80) REVERT: B 176 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: B 212 ASP cc_start: 0.7172 (t0) cc_final: 0.6911 (t0) REVERT: B 234 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7455 (m-80) REVERT: N 71 SER cc_start: 0.7798 (p) cc_final: 0.7458 (m) REVERT: N 76 LYS cc_start: 0.7239 (mtpp) cc_final: 0.7026 (mppt) REVERT: N 108 PHE cc_start: 0.7883 (m-80) cc_final: 0.7680 (m-80) REVERT: R 20 PHE cc_start: 0.7913 (t80) cc_final: 0.7694 (t80) REVERT: R 28 ARG cc_start: 0.8188 (tmt-80) cc_final: 0.7562 (mmm160) REVERT: R 35 ARG cc_start: 0.6222 (mmm160) cc_final: 0.5605 (mmp-170) outliers start: 47 outliers final: 19 residues processed: 218 average time/residue: 0.1781 time to fit residues: 56.1006 Evaluate side-chains 181 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 155 SER Chi-restraints excluded: chain N residue 168 HIS Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 30.0000 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 168 HIS N 180 GLN R 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8936 Z= 0.202 Angle : 0.590 10.148 12138 Z= 0.292 Chirality : 0.042 0.171 1368 Planarity : 0.004 0.046 1555 Dihedral : 4.785 37.286 1312 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.71 % Allowed : 23.91 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1120 helix: 1.64 (0.28), residues: 367 sheet: -0.36 (0.31), residues: 277 loop : 0.21 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.010 0.001 HIS N 168 PHE 0.017 0.002 PHE B 199 TYR 0.014 0.001 TYR B 59 ARG 0.006 0.000 ARG R 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 1.029 Fit side-chains REVERT: A 53 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6909 (tmm) REVERT: A 182 GLU cc_start: 0.6474 (pm20) cc_final: 0.5269 (pt0) REVERT: B 66 ASP cc_start: 0.7304 (t0) cc_final: 0.6947 (t0) REVERT: B 124 TYR cc_start: 0.8449 (m-80) cc_final: 0.7383 (m-80) REVERT: B 212 ASP cc_start: 0.7226 (t0) cc_final: 0.6780 (t0) REVERT: B 217 MET cc_start: 0.7540 (ptp) cc_final: 0.7214 (ptt) REVERT: N 60 TYR cc_start: 0.7150 (m-80) cc_final: 0.6689 (m-80) REVERT: N 76 LYS cc_start: 0.7545 (mtpp) cc_final: 0.7198 (mppt) REVERT: N 83 MET cc_start: 0.6122 (mmm) cc_final: 0.5846 (mmt) REVERT: R 184 PHE cc_start: 0.6934 (t80) cc_final: 0.6683 (t80) REVERT: R 253 LEU cc_start: 0.7522 (tt) cc_final: 0.7287 (mt) outliers start: 34 outliers final: 19 residues processed: 179 average time/residue: 0.1883 time to fit residues: 48.2744 Evaluate side-chains 161 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 168 HIS Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 257 TRP Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS N 168 HIS R 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.7290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8936 Z= 0.388 Angle : 0.706 12.679 12138 Z= 0.356 Chirality : 0.047 0.273 1368 Planarity : 0.005 0.037 1555 Dihedral : 5.300 44.263 1312 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.93 % Allowed : 25.22 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1120 helix: 1.46 (0.28), residues: 356 sheet: -0.51 (0.32), residues: 265 loop : -0.16 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 131 HIS 0.022 0.003 HIS N 168 PHE 0.026 0.002 PHE N 213 TYR 0.023 0.002 TYR B 59 ARG 0.015 0.001 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6826 (tmt) REVERT: A 126 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8314 (tttm) REVERT: B 170 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: B 212 ASP cc_start: 0.7401 (t0) cc_final: 0.7032 (t0) REVERT: B 260 GLU cc_start: 0.8030 (tt0) cc_final: 0.7692 (tt0) REVERT: B 266 HIS cc_start: 0.8388 (t-90) cc_final: 0.7957 (t-90) REVERT: B 322 ASP cc_start: 0.7862 (t0) cc_final: 0.7614 (t0) REVERT: N 76 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7675 (mppt) REVERT: N 83 MET cc_start: 0.7345 (mmm) cc_final: 0.7137 (mmm) REVERT: N 91 THR cc_start: 0.4275 (OUTLIER) cc_final: 0.3669 (t) REVERT: N 168 HIS cc_start: 0.8568 (t70) cc_final: 0.8365 (t-170) REVERT: N 232 GLN cc_start: 0.8206 (pp30) cc_final: 0.7552 (pp30) REVERT: R 35 ARG cc_start: 0.6614 (mmm160) cc_final: 0.5754 (mmp-170) REVERT: R 43 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8126 (m) REVERT: R 90 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7781 (mp) REVERT: R 253 LEU cc_start: 0.7745 (tt) cc_final: 0.7446 (mt) outliers start: 36 outliers final: 24 residues processed: 207 average time/residue: 0.2028 time to fit residues: 58.2178 Evaluate side-chains 189 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 276 THR Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.0570 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.7512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8936 Z= 0.179 Angle : 0.596 13.029 12138 Z= 0.292 Chirality : 0.041 0.162 1368 Planarity : 0.004 0.036 1555 Dihedral : 4.978 46.346 1312 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.73 % Allowed : 25.98 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1120 helix: 1.83 (0.28), residues: 355 sheet: -0.32 (0.32), residues: 263 loop : -0.11 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.003 0.001 HIS B 62 PHE 0.019 0.001 PHE R 16 TYR 0.016 0.001 TYR N 59 ARG 0.004 0.000 ARG R 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6702 (tmt) REVERT: A 243 TYR cc_start: 0.7817 (m-10) cc_final: 0.7609 (m-80) REVERT: B 129 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7172 (mmm160) REVERT: B 170 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: B 212 ASP cc_start: 0.7220 (t0) cc_final: 0.6906 (t0) REVERT: B 232 ILE cc_start: 0.8818 (tt) cc_final: 0.8596 (tt) REVERT: B 259 GLN cc_start: 0.7915 (pt0) cc_final: 0.7131 (pt0) REVERT: B 266 HIS cc_start: 0.8355 (t-90) cc_final: 0.7880 (t-90) REVERT: B 311 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.8179 (t-90) REVERT: N 76 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7564 (mppt) REVERT: N 82 GLN cc_start: 0.7568 (mm110) cc_final: 0.7356 (mm110) REVERT: N 83 MET cc_start: 0.7600 (mmm) cc_final: 0.7356 (mmt) REVERT: N 232 GLN cc_start: 0.8117 (pp30) cc_final: 0.7547 (pp30) REVERT: R 35 ARG cc_start: 0.6499 (mmm160) cc_final: 0.5694 (mmp-170) REVERT: R 253 LEU cc_start: 0.7681 (tt) cc_final: 0.7416 (mt) outliers start: 25 outliers final: 15 residues processed: 190 average time/residue: 0.2211 time to fit residues: 57.1179 Evaluate side-chains 170 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 257 TRP Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 223 ASN N 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.7676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8936 Z= 0.173 Angle : 0.577 13.985 12138 Z= 0.281 Chirality : 0.041 0.170 1368 Planarity : 0.003 0.034 1555 Dihedral : 4.774 50.187 1312 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.15 % Allowed : 24.45 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1120 helix: 2.00 (0.28), residues: 355 sheet: -0.32 (0.32), residues: 265 loop : 0.00 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.004 0.001 HIS R 216 PHE 0.015 0.001 PHE B 199 TYR 0.015 0.001 TYR N 59 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6673 (tmt) REVERT: B 66 ASP cc_start: 0.7684 (t0) cc_final: 0.7348 (t0) REVERT: B 129 ARG cc_start: 0.7490 (mtp85) cc_final: 0.7237 (mmm160) REVERT: B 153 ASP cc_start: 0.7272 (m-30) cc_final: 0.6906 (m-30) REVERT: B 170 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: B 212 ASP cc_start: 0.7177 (t0) cc_final: 0.6850 (t0) REVERT: B 214 ARG cc_start: 0.8587 (ptm160) cc_final: 0.8372 (ptp-170) REVERT: B 259 GLN cc_start: 0.7757 (pt0) cc_final: 0.7529 (pt0) REVERT: B 266 HIS cc_start: 0.8336 (t-90) cc_final: 0.7842 (t-90) REVERT: B 311 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.8077 (t-90) REVERT: B 322 ASP cc_start: 0.8004 (t70) cc_final: 0.7463 (t0) REVERT: N 60 TYR cc_start: 0.7464 (m-80) cc_final: 0.7097 (m-80) REVERT: N 76 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7489 (mppt) REVERT: N 82 GLN cc_start: 0.7582 (mm110) cc_final: 0.7357 (mm110) REVERT: N 87 ARG cc_start: 0.6432 (ptp90) cc_final: 0.4946 (ptp90) REVERT: N 232 GLN cc_start: 0.8024 (pp30) cc_final: 0.7530 (pp30) REVERT: R 28 ARG cc_start: 0.8190 (tmt-80) cc_final: 0.6677 (mmp-170) REVERT: R 35 ARG cc_start: 0.6505 (mmm160) cc_final: 0.5715 (mmp-170) REVERT: R 253 LEU cc_start: 0.7666 (tt) cc_final: 0.7441 (mt) outliers start: 38 outliers final: 24 residues processed: 201 average time/residue: 0.2044 time to fit residues: 56.6141 Evaluate side-chains 187 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 257 TRP Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.0570 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 0.0980 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 0.0370 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.7835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8936 Z= 0.149 Angle : 0.572 12.144 12138 Z= 0.276 Chirality : 0.041 0.167 1368 Planarity : 0.003 0.033 1555 Dihedral : 4.616 53.104 1312 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.71 % Allowed : 25.55 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1120 helix: 2.20 (0.28), residues: 353 sheet: -0.21 (0.32), residues: 266 loop : 0.12 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.004 0.001 HIS N 35 PHE 0.020 0.001 PHE R 16 TYR 0.011 0.001 TYR N 191 ARG 0.005 0.000 ARG R 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7045 (tmm) cc_final: 0.6656 (tmt) REVERT: B 66 ASP cc_start: 0.7657 (t0) cc_final: 0.7358 (t0) REVERT: B 124 TYR cc_start: 0.8266 (m-80) cc_final: 0.8045 (m-80) REVERT: B 129 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7245 (mmm160) REVERT: B 153 ASP cc_start: 0.7268 (m-30) cc_final: 0.6894 (m-30) REVERT: B 170 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: B 212 ASP cc_start: 0.7031 (t0) cc_final: 0.6749 (t0) REVERT: B 214 ARG cc_start: 0.8601 (ptm160) cc_final: 0.8387 (ptp-170) REVERT: B 311 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.8042 (t-90) REVERT: B 322 ASP cc_start: 0.7863 (t70) cc_final: 0.7387 (t0) REVERT: G 47 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7694 (mt-10) REVERT: N 39 GLN cc_start: 0.7577 (tt0) cc_final: 0.7356 (tt0) REVERT: N 60 TYR cc_start: 0.7453 (m-80) cc_final: 0.7128 (m-80) REVERT: N 76 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7527 (mppt) REVERT: N 87 ARG cc_start: 0.6389 (ptp90) cc_final: 0.4902 (ptp90) REVERT: R 28 ARG cc_start: 0.8166 (tmt-80) cc_final: 0.6636 (mmt180) REVERT: R 35 ARG cc_start: 0.6673 (mmm160) cc_final: 0.5825 (mmp-170) REVERT: R 119 ARG cc_start: 0.7000 (mtm-85) cc_final: 0.6665 (mtm110) REVERT: R 250 TYR cc_start: 0.6422 (OUTLIER) cc_final: 0.5222 (m-80) REVERT: R 253 LEU cc_start: 0.7663 (tt) cc_final: 0.7459 (mt) outliers start: 34 outliers final: 24 residues processed: 189 average time/residue: 0.2182 time to fit residues: 56.2347 Evaluate side-chains 181 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 250 TYR Chi-restraints excluded: chain R residue 257 TRP Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 30.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.8157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8936 Z= 0.243 Angle : 0.614 13.593 12138 Z= 0.301 Chirality : 0.043 0.174 1368 Planarity : 0.003 0.031 1555 Dihedral : 4.848 58.815 1312 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.82 % Allowed : 26.31 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1120 helix: 2.02 (0.28), residues: 355 sheet: -0.30 (0.31), residues: 267 loop : 0.05 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.003 0.001 HIS R 216 PHE 0.014 0.002 PHE B 199 TYR 0.029 0.001 TYR A 212 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 53 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6713 (tmt) REVERT: A 126 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8271 (tttm) REVERT: A 244 ASN cc_start: 0.8411 (m110) cc_final: 0.8100 (t0) REVERT: B 129 ARG cc_start: 0.7582 (mtp85) cc_final: 0.7348 (mmm160) REVERT: B 153 ASP cc_start: 0.7331 (m-30) cc_final: 0.6963 (m-30) REVERT: B 170 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7699 (m-30) REVERT: B 212 ASP cc_start: 0.7147 (t0) cc_final: 0.6897 (t0) REVERT: B 214 ARG cc_start: 0.8592 (ptm160) cc_final: 0.8367 (ptp-170) REVERT: B 219 ARG cc_start: 0.7577 (tpp80) cc_final: 0.7274 (ttm-80) REVERT: B 311 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.8005 (t-90) REVERT: B 322 ASP cc_start: 0.8124 (t70) cc_final: 0.7569 (t0) REVERT: N 60 TYR cc_start: 0.7543 (m-80) cc_final: 0.7165 (m-80) REVERT: N 76 LYS cc_start: 0.8022 (mtpp) cc_final: 0.7676 (mppt) REVERT: R 28 ARG cc_start: 0.8178 (tmt-80) cc_final: 0.6638 (mmt180) REVERT: R 35 ARG cc_start: 0.6785 (mmm160) cc_final: 0.6241 (ptp-170) REVERT: R 119 ARG cc_start: 0.7095 (mtm-85) cc_final: 0.6885 (mtm110) REVERT: R 250 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.5340 (m-80) REVERT: R 253 LEU cc_start: 0.7733 (tt) cc_final: 0.7514 (mt) outliers start: 35 outliers final: 26 residues processed: 194 average time/residue: 0.2270 time to fit residues: 59.5711 Evaluate side-chains 194 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 250 TYR Chi-restraints excluded: chain R residue 257 TRP Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.0270 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 168 HIS R 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.8382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8936 Z= 0.210 Angle : 0.595 12.942 12138 Z= 0.290 Chirality : 0.042 0.168 1368 Planarity : 0.003 0.030 1555 Dihedral : 4.774 49.631 1312 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.71 % Allowed : 26.86 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1120 helix: 2.02 (0.28), residues: 355 sheet: -0.23 (0.32), residues: 265 loop : 0.08 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 131 HIS 0.003 0.001 HIS N 35 PHE 0.015 0.001 PHE B 199 TYR 0.013 0.001 TYR N 191 ARG 0.004 0.000 ARG R 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7602 (tm-30) REVERT: A 53 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6664 (tmt) REVERT: A 126 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8264 (tttm) REVERT: A 244 ASN cc_start: 0.8292 (m110) cc_final: 0.8008 (t0) REVERT: B 129 ARG cc_start: 0.7578 (mtp85) cc_final: 0.7337 (mmm160) REVERT: B 153 ASP cc_start: 0.7323 (m-30) cc_final: 0.6937 (m-30) REVERT: B 170 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: B 212 ASP cc_start: 0.7095 (t0) cc_final: 0.6885 (t0) REVERT: B 219 ARG cc_start: 0.7581 (tpp80) cc_final: 0.7262 (ttm-80) REVERT: B 311 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7927 (t-90) REVERT: B 322 ASP cc_start: 0.7923 (t70) cc_final: 0.7599 (t70) REVERT: N 76 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7653 (mppt) REVERT: R 28 ARG cc_start: 0.8132 (tmt-80) cc_final: 0.6564 (mmt180) REVERT: R 35 ARG cc_start: 0.6803 (mmm160) cc_final: 0.6227 (ptp-170) REVERT: R 119 ARG cc_start: 0.7020 (mtm-85) cc_final: 0.6806 (mtm110) REVERT: R 250 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.5423 (m-80) REVERT: R 253 LEU cc_start: 0.7753 (tt) cc_final: 0.7525 (mt) outliers start: 34 outliers final: 27 residues processed: 185 average time/residue: 0.2272 time to fit residues: 56.5401 Evaluate side-chains 187 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 250 TYR Chi-restraints excluded: chain R residue 257 TRP Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.0770 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 chunk 69 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 168 HIS R 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.8516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8936 Z= 0.161 Angle : 0.577 12.810 12138 Z= 0.278 Chirality : 0.041 0.153 1368 Planarity : 0.003 0.030 1555 Dihedral : 4.570 39.689 1312 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.95 % Allowed : 27.62 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1120 helix: 2.17 (0.28), residues: 355 sheet: -0.32 (0.31), residues: 283 loop : 0.21 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 131 HIS 0.003 0.001 HIS N 35 PHE 0.021 0.001 PHE R 16 TYR 0.016 0.001 TYR A 212 ARG 0.004 0.000 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 53 MET cc_start: 0.6887 (tmm) cc_final: 0.6541 (tmt) REVERT: A 126 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8211 (tttm) REVERT: B 124 TYR cc_start: 0.8294 (m-80) cc_final: 0.8087 (m-80) REVERT: B 129 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7328 (mmm160) REVERT: B 153 ASP cc_start: 0.7297 (m-30) cc_final: 0.6930 (m-30) REVERT: B 170 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: B 219 ARG cc_start: 0.7602 (tpp80) cc_final: 0.7345 (ttm-80) REVERT: B 311 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7865 (t-90) REVERT: B 322 ASP cc_start: 0.8066 (t70) cc_final: 0.7534 (t0) REVERT: N 5 VAL cc_start: 0.7895 (t) cc_final: 0.7663 (p) REVERT: N 60 TYR cc_start: 0.7505 (m-80) cc_final: 0.7279 (m-80) REVERT: N 76 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7607 (mppt) REVERT: R 28 ARG cc_start: 0.8070 (tmt-80) cc_final: 0.6500 (mmt180) REVERT: R 35 ARG cc_start: 0.6857 (mmm160) cc_final: 0.6221 (ptp-170) REVERT: R 250 TYR cc_start: 0.6543 (OUTLIER) cc_final: 0.5445 (m-80) REVERT: R 253 LEU cc_start: 0.7732 (tt) cc_final: 0.7498 (mt) outliers start: 27 outliers final: 21 residues processed: 184 average time/residue: 0.2152 time to fit residues: 53.6750 Evaluate side-chains 183 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 250 TYR Chi-restraints excluded: chain R residue 257 TRP Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN N 168 HIS R 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.182111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126640 restraints weight = 10531.047| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.94 r_work: 0.3446 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.8672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8936 Z= 0.230 Angle : 0.614 12.543 12138 Z= 0.303 Chirality : 0.043 0.175 1368 Planarity : 0.003 0.030 1555 Dihedral : 4.659 39.652 1312 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.60 % Allowed : 27.07 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1120 helix: 1.94 (0.28), residues: 361 sheet: -0.35 (0.31), residues: 281 loop : 0.20 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.004 0.001 HIS A 214 PHE 0.014 0.001 PHE B 199 TYR 0.027 0.001 TYR A 212 ARG 0.004 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.35 seconds wall clock time: 40 minutes 32.08 seconds (2432.08 seconds total)