Starting phenix.real_space_refine on Tue Feb 13 21:21:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31088/02_2024/7efo_31088_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31088/02_2024/7efo_31088.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31088/02_2024/7efo_31088_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31088/02_2024/7efo_31088_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31088/02_2024/7efo_31088_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31088/02_2024/7efo_31088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31088/02_2024/7efo_31088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31088/02_2024/7efo_31088_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31088/02_2024/7efo_31088_updated.pdb" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.128 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 38 5.16 5 C 4725 2.51 5 N 1220 2.21 5 O 1319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7306 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1833 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "B" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1840 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 228} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1699 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "G" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1734 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 200 Unusual residues: {'JSG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.43, per 1000 atoms: 0.61 Number of scatterers: 7306 At special positions: 0 Unit cell: (68.64, 100.88, 101.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 4 15.00 O 1319 8.00 N 1220 7.00 C 4725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.4 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 6 sheets defined 55.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 95 through 105 removed outlier: 4.179A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.770A pdb=" N ASP A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 140 through 154 removed outlier: 3.605A pdb=" N ARG A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.665A pdb=" N GLU A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 72 through 78 Don't know bonding for helix class unknown. No H-bonds generated for 'chain 'B' and resid 72 through 78' Processing helix chain 'B' and resid 95 through 103 removed outlier: 4.398A pdb=" N MET B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.657A pdb=" N ALA B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 140 through 152 removed outlier: 3.673A pdb=" N ARG B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.886A pdb=" N ILE B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.628A pdb=" N VAL B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 40 removed outlier: 3.739A pdb=" N ALA F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.159A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 95 through 118 removed outlier: 4.738A pdb=" N PHE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.862A pdb=" N GLU F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 283 removed outlier: 4.447A pdb=" N VAL F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 274 " --> pdb=" O PHE F 270 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 316 Proline residue: F 301 - end of helix Processing helix chain 'F' and resid 331 through 346 removed outlier: 3.573A pdb=" N LEU F 345 " --> pdb=" O LEU F 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 40 removed outlier: 3.705A pdb=" N ASP G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 64 removed outlier: 4.384A pdb=" N TYR G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) Proline residue: G 61 - end of helix removed outlier: 4.243A pdb=" N ILE G 64 " --> pdb=" O VAL G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 85 removed outlier: 3.739A pdb=" N LEU G 74 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 78 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY G 81 " --> pdb=" O LEU G 77 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 94 Processing helix chain 'G' and resid 99 through 118 removed outlier: 3.655A pdb=" N ALA G 103 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 3.594A pdb=" N LEU G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 133 Processing helix chain 'G' and resid 271 through 279 Processing helix chain 'G' and resid 281 through 297 Processing helix chain 'G' and resid 305 through 324 removed outlier: 3.568A pdb=" N TYR G 320 " --> pdb=" O GLY G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 333 removed outlier: 4.746A pdb=" N LEU G 331 " --> pdb=" O GLY G 327 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL G 332 " --> pdb=" O PRO G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 353 Proline residue: G 344 - end of helix removed outlier: 3.634A pdb=" N PHE G 348 " --> pdb=" O SER G 345 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 353 " --> pdb=" O LEU G 350 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 Processing sheet with id= B, first strand: chain 'A' and resid 32 through 36 removed outlier: 7.389A pdb=" N ARG A 206 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LEU A 35 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR A 208 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER A 211 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 80 through 83 removed outlier: 6.705A pdb=" N PHE A 158 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A 83 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A 160 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLY A 189 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 161 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU A 191 " --> pdb=" O LEU A 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 24 through 27 Processing sheet with id= E, first strand: chain 'B' and resid 214 through 217 removed outlier: 6.445A pdb=" N ILE B 209 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 190 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU B 34 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 192 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 159 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY B 81 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.349A pdb=" N TYR B 13 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 933 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: 2.07 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1157 1.30 - 1.43: 1738 1.43 - 1.56: 4462 1.56 - 1.69: 7 1.69 - 1.82: 71 Bond restraints: 7435 Sorted by residual: bond pdb=" C7 JSG F 401 " pdb=" N2 JSG F 401 " ideal model delta sigma weight residual 1.621 1.344 0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" CDO JSG F 401 " pdb=" NAO JSG F 401 " ideal model delta sigma weight residual 1.505 1.342 0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" C LEU G 23 " pdb=" O LEU G 23 " ideal model delta sigma weight residual 1.236 1.169 0.068 1.15e-02 7.56e+03 3.50e+01 bond pdb=" CEE JSG F 401 " pdb=" OAQ JSG F 401 " ideal model delta sigma weight residual 1.469 1.356 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" CAN JSG F 401 " pdb=" NAO JSG F 401 " ideal model delta sigma weight residual 1.577 1.471 0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 7430 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.43: 188 105.43 - 112.66: 4049 112.66 - 119.88: 2715 119.88 - 127.11: 3050 127.11 - 134.34: 67 Bond angle restraints: 10069 Sorted by residual: angle pdb=" N ARG B 131 " pdb=" CA ARG B 131 " pdb=" C ARG B 131 " ideal model delta sigma weight residual 110.97 123.88 -12.91 1.09e+00 8.42e-01 1.40e+02 angle pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" C ASP B 132 " ideal model delta sigma weight residual 112.94 98.20 14.74 1.41e+00 5.03e-01 1.09e+02 angle pdb=" N GLN G 65 " pdb=" CA GLN G 65 " pdb=" C GLN G 65 " ideal model delta sigma weight residual 112.90 101.10 11.80 1.31e+00 5.83e-01 8.11e+01 angle pdb=" N ASP G 63 " pdb=" CA ASP G 63 " pdb=" C ASP G 63 " ideal model delta sigma weight residual 111.14 120.26 -9.12 1.08e+00 8.57e-01 7.14e+01 angle pdb=" N TRP F 332 " pdb=" CA TRP F 332 " pdb=" C TRP F 332 " ideal model delta sigma weight residual 113.23 104.83 8.40 1.24e+00 6.50e-01 4.59e+01 ... (remaining 10064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 4029 23.14 - 46.28: 382 46.28 - 69.42: 67 69.42 - 92.56: 12 92.56 - 115.71: 6 Dihedral angle restraints: 4496 sinusoidal: 1873 harmonic: 2623 Sorted by residual: dihedral pdb=" C ASP A 194 " pdb=" N ASP A 194 " pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " ideal model delta harmonic sigma weight residual -122.60 -110.40 -12.20 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" N ASP A 194 " pdb=" C ASP A 194 " pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " ideal model delta harmonic sigma weight residual 122.80 112.89 9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" CCB JSG F 401 " pdb=" CCF JSG F 401 " pdb=" OCL JSG F 401 " pdb=" CCE JSG F 401 " ideal model delta sinusoidal sigma weight residual -52.94 62.77 -115.71 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 4493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.930: 1209 0.930 - 1.860: 0 1.860 - 2.790: 0 2.790 - 3.721: 0 3.721 - 4.651: 1 Chirality restraints: 1210 Sorted by residual: chirality pdb=" CCB JSG F 401 " pdb=" CCC JSG F 401 " pdb=" OBF JSG F 401 " pdb=" OCL JSG F 401 " both_signs ideal model delta sigma weight residual False 2.42 -2.24 4.65 2.00e-01 2.50e+01 5.41e+02 chirality pdb=" CA ILE G 313 " pdb=" N ILE G 313 " pdb=" C ILE G 313 " pdb=" CB ILE G 313 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CBP JSG F 401 " pdb=" CBM JSG F 401 " pdb=" CBQ JSG F 401 " pdb=" OBW JSG F 401 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 1207 not shown) Planarity restraints: 1238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 325 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C ILE G 325 " 0.074 2.00e-02 2.50e+03 pdb=" O ILE G 325 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE G 326 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 86 " 0.020 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C GLU B 86 " -0.072 2.00e-02 2.50e+03 pdb=" O GLU B 86 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA B 87 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 36 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C GLY A 36 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY A 36 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO A 37 " -0.023 2.00e-02 2.50e+03 ... (remaining 1235 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 201 2.64 - 3.20: 7488 3.20 - 3.77: 11761 3.77 - 4.33: 16694 4.33 - 4.90: 25341 Nonbonded interactions: 61485 Sorted by model distance: nonbonded pdb=" O ASP G 63 " pdb=" N PHE G 68 " model vdw 2.071 2.520 nonbonded pdb=" O ILE F 329 " pdb=" CE3 TRP F 330 " model vdw 2.130 3.340 nonbonded pdb=" O ILE F 63 " pdb=" N SER F 67 " model vdw 2.202 2.520 nonbonded pdb=" O LEU F 54 " pdb=" NE2 GLN F 128 " model vdw 2.210 2.520 nonbonded pdb=" OG SER A 94 " pdb=" O ARG A 131 " model vdw 2.218 2.440 ... (remaining 61480 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 'A' and (resid 2 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 141 or (resid 142 and (name N or \ name CA or name C or name O or name CB )) or resid 143 through 236)) selection = (chain 'B' and resid 2 through 236) } 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: 0.730 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: 1.990 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.900 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 0.010 0.277 7435 Z= 0.689 Angle : 1.203 14.739 10069 Z= 0.743 Chirality : 0.147 4.651 1210 Planarity : 0.008 0.110 1238 Dihedral : 18.366 115.706 2806 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 58.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.08 % Favored : 92.81 % Rotamer: Outliers : 6.18 % Allowed : 24.34 % Favored : 69.47 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.27), residues: 904 helix: -0.97 (0.23), residues: 489 sheet: -1.15 (0.73), residues: 47 loop : -2.10 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 276 HIS 0.002 0.000 HIS F 89 PHE 0.010 0.001 PHE A 90 TYR 0.012 0.001 TYR A 234 ARG 0.003 0.000 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 253 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8542 (mtm110) cc_final: 0.8330 (ttt180) REVERT: B 122 MET cc_start: 0.8373 (ttp) cc_final: 0.7832 (ttt) REVERT: B 143 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8185 (ttp-170) REVERT: G 29 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7923 (mt) REVERT: G 30 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.7940 (t) REVERT: G 47 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6119 (p90) REVERT: G 82 MET cc_start: 0.7679 (tpt) cc_final: 0.7323 (tpp) REVERT: G 357 MET cc_start: 0.7676 (ppp) cc_final: 0.7415 (ppp) outliers start: 47 outliers final: 17 residues processed: 275 average time/residue: 0.1803 time to fit residues: 66.9145 Evaluate side-chains 258 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 325 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 218 HIS B 104 GLN B 136 GLN F 116 ASN F 128 GLN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN G 272 GLN ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7435 Z= 0.248 Angle : 0.810 9.492 10069 Z= 0.384 Chirality : 0.045 0.262 1210 Planarity : 0.006 0.065 1238 Dihedral : 14.260 102.618 1169 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 6.58 % Allowed : 25.92 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.27), residues: 904 helix: -0.62 (0.22), residues: 503 sheet: -1.35 (0.61), residues: 63 loop : -1.90 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 330 HIS 0.004 0.001 HIS B 195 PHE 0.022 0.002 PHE F 27 TYR 0.022 0.002 TYR F 338 ARG 0.007 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 270 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.6766 (t0) cc_final: 0.6341 (t0) REVERT: A 100 MET cc_start: 0.7972 (tpt) cc_final: 0.7385 (tpt) REVERT: A 115 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8067 (tp30) REVERT: A 169 ASP cc_start: 0.8422 (p0) cc_final: 0.8123 (p0) REVERT: B 163 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8493 (mt-10) REVERT: F 10 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6760 (tm-30) REVERT: F 31 LEU cc_start: 0.9142 (tt) cc_final: 0.8882 (tt) REVERT: F 59 MET cc_start: 0.8573 (mtm) cc_final: 0.7803 (mtm) REVERT: F 267 HIS cc_start: 0.6408 (m90) cc_final: 0.5911 (m90) REVERT: F 299 MET cc_start: 0.7851 (mtt) cc_final: 0.7646 (mtm) REVERT: F 337 LEU cc_start: 0.9091 (tp) cc_final: 0.8859 (tp) REVERT: G 47 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.5757 (p90) REVERT: G 82 MET cc_start: 0.7664 (tpt) cc_final: 0.6811 (tpp) REVERT: G 131 MET cc_start: 0.8020 (mtt) cc_final: 0.7578 (mtm) REVERT: G 283 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8285 (tm) REVERT: G 319 PHE cc_start: 0.8703 (t80) cc_final: 0.8420 (t80) outliers start: 50 outliers final: 26 residues processed: 297 average time/residue: 0.1838 time to fit residues: 73.9911 Evaluate side-chains 260 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain F residue 33 ARG Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 87 optimal weight: 0.0050 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 218 HIS F 128 GLN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 GLN G 274 ASN ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7435 Z= 0.292 Angle : 0.777 8.777 10069 Z= 0.370 Chirality : 0.045 0.212 1210 Planarity : 0.005 0.068 1238 Dihedral : 13.410 98.903 1142 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 8.03 % Allowed : 27.11 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.27), residues: 904 helix: -0.58 (0.22), residues: 509 sheet: -0.85 (0.67), residues: 57 loop : -1.76 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 123 HIS 0.011 0.001 HIS A 218 PHE 0.024 0.002 PHE G 326 TYR 0.017 0.002 TYR G 320 ARG 0.005 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 242 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8013 (tpt) cc_final: 0.7466 (tpt) REVERT: A 115 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8076 (tp30) REVERT: A 134 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7701 (tt) REVERT: A 169 ASP cc_start: 0.8402 (p0) cc_final: 0.8144 (p0) REVERT: A 199 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7899 (tp30) REVERT: F 26 PHE cc_start: 0.8713 (m-80) cc_final: 0.8463 (m-80) REVERT: F 59 MET cc_start: 0.8749 (mtm) cc_final: 0.8260 (mtm) REVERT: F 267 HIS cc_start: 0.6359 (m90) cc_final: 0.6022 (m170) REVERT: F 305 LEU cc_start: 0.8471 (tp) cc_final: 0.8270 (tt) REVERT: F 337 LEU cc_start: 0.9100 (tp) cc_final: 0.8823 (tp) REVERT: G 26 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7925 (tp) REVERT: G 47 TYR cc_start: 0.6586 (OUTLIER) cc_final: 0.5681 (p90) REVERT: G 67 PHE cc_start: 0.8524 (m-80) cc_final: 0.8212 (t80) REVERT: G 86 ARG cc_start: 0.9015 (mtm180) cc_final: 0.8801 (mtm180) REVERT: G 131 MET cc_start: 0.8131 (mtt) cc_final: 0.7682 (mtm) REVERT: G 283 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8454 (tm) REVERT: G 288 MET cc_start: 0.8355 (mmp) cc_final: 0.8080 (tpp) REVERT: G 319 PHE cc_start: 0.8726 (t80) cc_final: 0.8467 (t80) REVERT: G 354 TRP cc_start: 0.5947 (t-100) cc_final: 0.5139 (t-100) outliers start: 61 outliers final: 43 residues processed: 274 average time/residue: 0.1905 time to fit residues: 69.8678 Evaluate side-chains 275 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 228 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 33 ARG Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 218 HIS F 313 GLN ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7435 Z= 0.260 Angle : 0.754 12.471 10069 Z= 0.353 Chirality : 0.044 0.242 1210 Planarity : 0.005 0.059 1238 Dihedral : 12.877 95.452 1139 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 7.63 % Allowed : 28.16 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.28), residues: 904 helix: -0.44 (0.23), residues: 508 sheet: -1.08 (0.66), residues: 67 loop : -1.83 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 123 HIS 0.003 0.001 HIS B 195 PHE 0.017 0.002 PHE G 326 TYR 0.020 0.002 TYR G 320 ARG 0.007 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 236 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8297 (tptp) cc_final: 0.8054 (tptp) REVERT: A 100 MET cc_start: 0.8024 (tpt) cc_final: 0.7355 (tpt) REVERT: A 106 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7371 (mtm-85) REVERT: A 115 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8017 (tp30) REVERT: A 122 MET cc_start: 0.6552 (mtp) cc_final: 0.6178 (mtp) REVERT: A 134 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7736 (tt) REVERT: A 155 ASN cc_start: 0.7479 (t0) cc_final: 0.6600 (t0) REVERT: A 169 ASP cc_start: 0.8457 (p0) cc_final: 0.8189 (p0) REVERT: A 199 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7968 (tp30) REVERT: B 100 MET cc_start: 0.6992 (mmt) cc_final: 0.6742 (mmm) REVERT: F 26 PHE cc_start: 0.8693 (m-80) cc_final: 0.8093 (m-80) REVERT: F 59 MET cc_start: 0.8823 (mtm) cc_final: 0.8017 (mtm) REVERT: F 267 HIS cc_start: 0.6257 (m90) cc_final: 0.6011 (m170) REVERT: F 337 LEU cc_start: 0.9094 (tp) cc_final: 0.8845 (tp) REVERT: G 26 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7751 (tp) REVERT: G 47 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.5503 (p90) REVERT: G 67 PHE cc_start: 0.8536 (m-80) cc_final: 0.8244 (t80) REVERT: G 95 SER cc_start: 0.8978 (m) cc_final: 0.8578 (t) REVERT: G 131 MET cc_start: 0.8125 (mtt) cc_final: 0.7707 (mtm) REVERT: G 283 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8549 (tm) REVERT: G 354 TRP cc_start: 0.5872 (t-100) cc_final: 0.5173 (t-100) outliers start: 58 outliers final: 41 residues processed: 267 average time/residue: 0.1815 time to fit residues: 66.3101 Evaluate side-chains 269 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7435 Z= 0.257 Angle : 0.733 12.028 10069 Z= 0.347 Chirality : 0.043 0.212 1210 Planarity : 0.005 0.064 1238 Dihedral : 12.726 91.544 1137 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 8.82 % Allowed : 28.16 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.28), residues: 904 helix: -0.37 (0.23), residues: 508 sheet: -1.03 (0.67), residues: 67 loop : -1.90 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 119 HIS 0.005 0.001 HIS B 195 PHE 0.021 0.002 PHE G 319 TYR 0.013 0.002 TYR G 320 ARG 0.005 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 242 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8343 (tptp) cc_final: 0.8029 (tptp) REVERT: A 100 MET cc_start: 0.8018 (tpt) cc_final: 0.7337 (tpt) REVERT: A 106 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7288 (mtp85) REVERT: A 134 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7845 (tt) REVERT: A 155 ASN cc_start: 0.7528 (t0) cc_final: 0.7314 (t0) REVERT: A 169 ASP cc_start: 0.8472 (p0) cc_final: 0.8228 (p0) REVERT: A 199 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7920 (tp30) REVERT: A 201 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7671 (mm) REVERT: B 96 TYR cc_start: 0.7357 (t80) cc_final: 0.6968 (t80) REVERT: B 181 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7800 (mm-30) REVERT: F 4 ILE cc_start: 0.9515 (mp) cc_final: 0.9130 (pt) REVERT: F 59 MET cc_start: 0.8793 (mtm) cc_final: 0.8211 (mtm) REVERT: F 267 HIS cc_start: 0.6259 (m90) cc_final: 0.6015 (m170) REVERT: F 337 LEU cc_start: 0.9080 (tp) cc_final: 0.8856 (tp) REVERT: G 47 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.5446 (p90) REVERT: G 95 SER cc_start: 0.8970 (m) cc_final: 0.8616 (t) REVERT: G 131 MET cc_start: 0.8121 (mtt) cc_final: 0.7710 (mtm) REVERT: G 283 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8624 (tm) REVERT: G 290 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8612 (tm) REVERT: G 354 TRP cc_start: 0.5892 (t-100) cc_final: 0.5154 (t-100) outliers start: 67 outliers final: 45 residues processed: 280 average time/residue: 0.1804 time to fit residues: 68.7992 Evaluate side-chains 276 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 33 ARG Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 39 optimal weight: 0.0040 chunk 7 optimal weight: 0.0070 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 0.4980 chunk 83 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7435 Z= 0.193 Angle : 0.731 14.285 10069 Z= 0.340 Chirality : 0.043 0.215 1210 Planarity : 0.005 0.065 1238 Dihedral : 12.642 90.026 1137 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 6.84 % Allowed : 30.53 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.28), residues: 904 helix: -0.23 (0.23), residues: 509 sheet: -0.88 (0.68), residues: 67 loop : -1.88 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 332 HIS 0.005 0.001 HIS B 195 PHE 0.017 0.001 PHE G 315 TYR 0.013 0.001 TYR F 338 ARG 0.005 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 246 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8187 (tptp) cc_final: 0.7844 (tptp) REVERT: A 122 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.6150 (mtp) REVERT: A 155 ASN cc_start: 0.7455 (t0) cc_final: 0.7194 (t0) REVERT: A 199 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7977 (tp30) REVERT: A 201 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7651 (mm) REVERT: A 218 HIS cc_start: 0.7853 (p-80) cc_final: 0.7572 (p-80) REVERT: F 4 ILE cc_start: 0.9487 (mp) cc_final: 0.9206 (pt) REVERT: F 267 HIS cc_start: 0.6174 (m90) cc_final: 0.5964 (m170) REVERT: F 337 LEU cc_start: 0.9034 (tp) cc_final: 0.8829 (tp) REVERT: G 47 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5484 (p90) REVERT: G 131 MET cc_start: 0.7978 (mtt) cc_final: 0.7600 (mtm) REVERT: G 283 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8694 (tm) REVERT: G 290 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8758 (tm) REVERT: G 354 TRP cc_start: 0.5776 (t-100) cc_final: 0.5138 (t-100) outliers start: 52 outliers final: 37 residues processed: 278 average time/residue: 0.1719 time to fit residues: 65.8850 Evaluate side-chains 271 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 229 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 33 ARG Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 72 optimal weight: 0.0470 chunk 85 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 GLN ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7435 Z= 0.206 Angle : 0.735 11.420 10069 Z= 0.344 Chirality : 0.043 0.220 1210 Planarity : 0.005 0.070 1238 Dihedral : 12.520 89.981 1137 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 7.63 % Allowed : 30.53 % Favored : 61.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.28), residues: 904 helix: -0.18 (0.23), residues: 508 sheet: -0.96 (0.66), residues: 67 loop : -1.85 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 332 HIS 0.005 0.001 HIS B 195 PHE 0.022 0.002 PHE G 16 TYR 0.014 0.001 TYR G 10 ARG 0.008 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 240 time to evaluate : 0.794 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: A 7 LYS cc_start: 0.8210 (tptp) cc_final: 0.7887 (tptp) REVERT: A 100 MET cc_start: 0.7971 (tpt) cc_final: 0.7596 (tpt) REVERT: A 122 MET cc_start: 0.6437 (mtp) cc_final: 0.6067 (mtp) REVERT: A 134 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7780 (tt) REVERT: A 155 ASN cc_start: 0.7511 (t0) cc_final: 0.7255 (t0) REVERT: A 199 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7945 (tp30) REVERT: A 201 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7627 (mm) REVERT: B 16 ARG cc_start: 0.8529 (ttp-170) cc_final: 0.8059 (ptt-90) REVERT: B 86 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7838 (mm-30) REVERT: B 143 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7987 (ttp-170) REVERT: B 174 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8593 (mp) REVERT: B 228 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: F 4 ILE cc_start: 0.9488 (mp) cc_final: 0.9164 (pt) REVERT: F 57 PRO cc_start: 0.9355 (Cg_exo) cc_final: 0.9145 (Cg_endo) REVERT: F 267 HIS cc_start: 0.6137 (m90) cc_final: 0.5927 (m170) REVERT: F 337 LEU cc_start: 0.9029 (tp) cc_final: 0.8812 (tp) REVERT: G 47 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.5433 (p90) REVERT: G 107 MET cc_start: 0.8015 (mmt) cc_final: 0.7750 (mmt) REVERT: G 131 MET cc_start: 0.7966 (mtt) cc_final: 0.7577 (mtm) REVERT: G 283 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8749 (tm) REVERT: G 288 MET cc_start: 0.8388 (tpp) cc_final: 0.8095 (tpp) REVERT: G 290 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8750 (tm) REVERT: G 320 TYR cc_start: 0.7825 (t80) cc_final: 0.7622 (t80) outliers start: 58 outliers final: 43 residues processed: 276 average time/residue: 0.1765 time to fit residues: 66.6092 Evaluate side-chains 277 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 226 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 33 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 GLN ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7435 Z= 0.224 Angle : 0.749 10.983 10069 Z= 0.352 Chirality : 0.043 0.223 1210 Planarity : 0.005 0.069 1238 Dihedral : 12.447 89.733 1137 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 7.37 % Allowed : 31.18 % Favored : 61.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.28), residues: 904 helix: -0.12 (0.23), residues: 507 sheet: -0.93 (0.67), residues: 67 loop : -1.83 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 123 HIS 0.008 0.001 HIS A 73 PHE 0.018 0.002 PHE A 158 TYR 0.014 0.001 TYR G 10 ARG 0.007 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 235 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7902 (tpt) cc_final: 0.7516 (tpt) REVERT: A 122 MET cc_start: 0.6459 (mtp) cc_final: 0.6060 (mtp) REVERT: A 134 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7802 (tt) REVERT: A 155 ASN cc_start: 0.7487 (t0) cc_final: 0.7265 (t0) REVERT: A 199 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7997 (tp30) REVERT: A 201 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7576 (mm) REVERT: B 16 ARG cc_start: 0.8563 (ttp-170) cc_final: 0.8102 (ptt-90) REVERT: B 100 MET cc_start: 0.6715 (mmm) cc_final: 0.6232 (mmm) REVERT: B 174 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8659 (mp) REVERT: B 228 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: F 4 ILE cc_start: 0.9502 (mp) cc_final: 0.9177 (pt) REVERT: F 57 PRO cc_start: 0.9344 (Cg_exo) cc_final: 0.9122 (Cg_endo) REVERT: F 337 LEU cc_start: 0.9023 (tp) cc_final: 0.8799 (tp) REVERT: G 47 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.5415 (p90) REVERT: G 67 PHE cc_start: 0.8268 (m-80) cc_final: 0.7962 (m-80) REVERT: G 131 MET cc_start: 0.8036 (mtt) cc_final: 0.7653 (mtm) REVERT: G 290 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8747 (tm) REVERT: G 354 TRP cc_start: 0.5867 (t-100) cc_final: 0.5290 (t-100) outliers start: 56 outliers final: 45 residues processed: 269 average time/residue: 0.1778 time to fit residues: 65.7242 Evaluate side-chains 282 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 231 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 33 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 0.0470 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7435 Z= 0.198 Angle : 0.753 12.401 10069 Z= 0.353 Chirality : 0.043 0.237 1210 Planarity : 0.005 0.069 1238 Dihedral : 12.215 89.559 1135 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 6.97 % Allowed : 31.71 % Favored : 61.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.28), residues: 904 helix: -0.05 (0.23), residues: 502 sheet: -0.93 (0.66), residues: 67 loop : -1.78 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 276 HIS 0.006 0.001 HIS B 129 PHE 0.032 0.002 PHE G 319 TYR 0.015 0.001 TYR G 10 ARG 0.006 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.8168 (m) cc_final: 0.7946 (t) REVERT: A 100 MET cc_start: 0.7931 (tpt) cc_final: 0.7557 (tpt) REVERT: A 122 MET cc_start: 0.6417 (mtp) cc_final: 0.5980 (mtp) REVERT: A 134 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7769 (tt) REVERT: A 155 ASN cc_start: 0.7492 (t0) cc_final: 0.7284 (t0) REVERT: A 199 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7994 (tp30) REVERT: A 201 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7584 (mm) REVERT: B 16 ARG cc_start: 0.8561 (ttp-170) cc_final: 0.8127 (ptt-90) REVERT: B 100 MET cc_start: 0.6729 (mmm) cc_final: 0.6328 (mmm) REVERT: B 174 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8651 (mp) REVERT: B 228 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: F 4 ILE cc_start: 0.9464 (mp) cc_final: 0.9160 (pt) REVERT: F 57 PRO cc_start: 0.9402 (Cg_exo) cc_final: 0.9162 (Cg_endo) REVERT: F 337 LEU cc_start: 0.8986 (tp) cc_final: 0.8758 (tp) REVERT: G 24 PHE cc_start: 0.7149 (m-10) cc_final: 0.6513 (t80) REVERT: G 47 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.4983 (p90) REVERT: G 290 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8801 (tm) REVERT: G 354 TRP cc_start: 0.5838 (t-100) cc_final: 0.5287 (t-100) outliers start: 53 outliers final: 40 residues processed: 287 average time/residue: 0.1715 time to fit residues: 67.0901 Evaluate side-chains 285 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 239 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain F residue 33 ARG Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7435 Z= 0.239 Angle : 0.769 11.267 10069 Z= 0.361 Chirality : 0.044 0.203 1210 Planarity : 0.005 0.071 1238 Dihedral : 12.196 89.288 1135 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.92 % Allowed : 32.50 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.28), residues: 904 helix: -0.04 (0.23), residues: 507 sheet: -0.87 (0.67), residues: 67 loop : -1.78 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 276 HIS 0.011 0.001 HIS B 73 PHE 0.015 0.002 PHE G 319 TYR 0.016 0.001 TYR G 10 ARG 0.007 0.000 ARG A 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 240 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8182 (tptp) cc_final: 0.7819 (tptp) REVERT: A 25 THR cc_start: 0.8194 (m) cc_final: 0.7973 (t) REVERT: A 100 MET cc_start: 0.7899 (tpt) cc_final: 0.7534 (tpt) REVERT: A 122 MET cc_start: 0.6470 (mtp) cc_final: 0.6038 (mtp) REVERT: A 134 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7818 (tt) REVERT: A 199 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7935 (tp30) REVERT: A 201 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7504 (mm) REVERT: B 16 ARG cc_start: 0.8610 (ttp-170) cc_final: 0.8162 (ptt-90) REVERT: B 174 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8574 (mp) REVERT: B 228 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: F 4 ILE cc_start: 0.9497 (mp) cc_final: 0.9168 (pt) REVERT: F 30 LYS cc_start: 0.7142 (mptt) cc_final: 0.6936 (mptt) REVERT: F 57 PRO cc_start: 0.9424 (Cg_exo) cc_final: 0.9187 (Cg_endo) REVERT: F 337 LEU cc_start: 0.9014 (tp) cc_final: 0.8788 (tp) REVERT: G 16 PHE cc_start: 0.8342 (t80) cc_final: 0.8067 (t80) REVERT: G 20 MET cc_start: 0.8350 (tpt) cc_final: 0.8034 (tpt) REVERT: G 24 PHE cc_start: 0.7206 (m-10) cc_final: 0.6513 (t80) REVERT: G 47 TYR cc_start: 0.5709 (OUTLIER) cc_final: 0.4859 (p90) REVERT: G 67 PHE cc_start: 0.8294 (m-80) cc_final: 0.8020 (m-80) REVERT: G 131 MET cc_start: 0.7882 (mtt) cc_final: 0.7456 (mtm) REVERT: G 354 TRP cc_start: 0.5850 (t-100) cc_final: 0.5334 (t-100) outliers start: 45 outliers final: 40 residues processed: 265 average time/residue: 0.1755 time to fit residues: 62.8842 Evaluate side-chains 273 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain F residue 33 ARG Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.175167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154719 restraints weight = 11847.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158912 restraints weight = 6554.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.161799 restraints weight = 4229.391| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7435 Z= 0.208 Angle : 0.769 10.977 10069 Z= 0.359 Chirality : 0.043 0.162 1210 Planarity : 0.005 0.072 1238 Dihedral : 12.054 89.245 1135 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.66 % Allowed : 33.42 % Favored : 60.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.28), residues: 904 helix: -0.00 (0.23), residues: 508 sheet: -0.49 (0.69), residues: 69 loop : -1.82 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 276 HIS 0.009 0.001 HIS B 195 PHE 0.018 0.002 PHE F 26 TYR 0.016 0.001 TYR G 10 ARG 0.007 0.000 ARG B 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.39 seconds wall clock time: 35 minutes 29.27 seconds (2129.27 seconds total)