Starting phenix.real_space_refine on Fri Nov 15 08:35:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh3_39280/11_2024/8yh3_39280.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh3_39280/11_2024/8yh3_39280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh3_39280/11_2024/8yh3_39280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh3_39280/11_2024/8yh3_39280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh3_39280/11_2024/8yh3_39280.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh3_39280/11_2024/8yh3_39280.cif" } resolution = 3.4 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= 1.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5560 2.51 5 N 1462 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8691 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2198 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1700 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 208} Chain breaks: 2 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'6MD%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 5.58, per 1000 atoms: 0.64 Number of scatterers: 8691 At special positions: 0 Unit cell: (85.47, 123.21, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1603 8.00 N 1462 7.00 C 5560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.01 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 38.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.705A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'R' and resid 10 through 40 Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 45 through 64 Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 79 through 115 removed outlier: 3.735A pdb=" N THR R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 145 through 148 Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.501A pdb=" N VAL R 170 " --> pdb=" O ARG R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 179 removed outlier: 3.553A pdb=" N MET R 176 " --> pdb=" O ARG R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 185 through 207 Processing helix chain 'R' and resid 225 through 254 Proline residue: R 244 - end of helix Processing helix chain 'R' and resid 259 through 282 removed outlier: 3.862A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 285 through 295 Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.502A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.548A pdb=" N LYS A 279 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.690A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 349 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.915A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.955A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.847A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.635A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.137A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.757A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.028A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.409A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.472A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.391A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.597A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.278A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.555A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.190A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1182 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: 2.62 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1487 1.31 - 1.44: 2371 1.44 - 1.57: 4918 1.57 - 1.69: 0 1.69 - 1.82: 98 Bond restraints: 8874 Sorted by residual: bond pdb=" C ASP A 200 " pdb=" O ASP A 200 " ideal model delta sigma weight residual 1.236 1.297 -0.061 1.22e-02 6.72e+03 2.49e+01 bond pdb=" CA SER R 100 " pdb=" CB SER R 100 " ideal model delta sigma weight residual 1.528 1.456 0.073 1.56e-02 4.11e+03 2.18e+01 bond pdb=" C PHE R 167 " pdb=" O PHE R 167 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.17e-02 7.31e+03 2.05e+01 bond pdb=" C TYR R 118 " pdb=" O TYR R 118 " ideal model delta sigma weight residual 1.236 1.287 -0.051 1.15e-02 7.56e+03 1.93e+01 bond pdb=" C ILE R 267 " pdb=" O ILE R 267 " ideal model delta sigma weight residual 1.237 1.289 -0.051 1.17e-02 7.31e+03 1.93e+01 ... (remaining 8869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 10759 2.05 - 4.10: 1146 4.10 - 6.15: 99 6.15 - 8.20: 8 8.20 - 10.25: 6 Bond angle restraints: 12018 Sorted by residual: angle pdb=" N PRO G 53 " pdb=" CA PRO G 53 " pdb=" C PRO G 53 " ideal model delta sigma weight residual 111.14 121.39 -10.25 1.56e+00 4.11e-01 4.32e+01 angle pdb=" N GLY B 162 " pdb=" CA GLY B 162 " pdb=" C GLY B 162 " ideal model delta sigma weight residual 114.67 108.01 6.66 1.10e+00 8.26e-01 3.66e+01 angle pdb=" N LEU R 84 " pdb=" CA LEU R 84 " pdb=" C LEU R 84 " ideal model delta sigma weight residual 111.82 105.46 6.36 1.16e+00 7.43e-01 3.01e+01 angle pdb=" C HIS S 35 " pdb=" CA HIS S 35 " pdb=" CB HIS S 35 " ideal model delta sigma weight residual 109.80 101.52 8.28 1.65e+00 3.67e-01 2.52e+01 angle pdb=" N VAL R 121 " pdb=" CA VAL R 121 " pdb=" C VAL R 121 " ideal model delta sigma weight residual 113.42 107.70 5.72 1.17e+00 7.31e-01 2.39e+01 ... (remaining 12013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 4648 15.91 - 31.82: 490 31.82 - 47.73: 105 47.73 - 63.63: 23 63.63 - 79.54: 5 Dihedral angle restraints: 5271 sinusoidal: 2069 harmonic: 3202 Sorted by residual: dihedral pdb=" CD ARG S 67 " pdb=" NE ARG S 67 " pdb=" CZ ARG S 67 " pdb=" NH1 ARG S 67 " ideal model delta sinusoidal sigma weight residual 0.00 75.41 -75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CD ARG R 172 " pdb=" NE ARG R 172 " pdb=" CZ ARG R 172 " pdb=" NH1 ARG R 172 " ideal model delta sinusoidal sigma weight residual 0.00 -52.92 52.92 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" C1' 6MD R 801 " pdb=" C2' 6MD R 801 " pdb=" C3' 6MD R 801 " pdb=" C4' 6MD R 801 " ideal model delta sinusoidal sigma weight residual -35.00 2.40 -37.40 1 8.00e+00 1.56e-02 3.08e+01 ... (remaining 5268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1070 0.098 - 0.196: 275 0.196 - 0.294: 27 0.294 - 0.392: 2 0.392 - 0.489: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" C PRO G 53 " pdb=" CB PRO G 53 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CB VAL R 112 " pdb=" CA VAL R 112 " pdb=" CG1 VAL R 112 " pdb=" CG2 VAL R 112 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 1373 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 6MD R 801 " -0.174 2.00e-02 2.50e+03 7.31e-02 1.47e+02 pdb=" C2 6MD R 801 " 0.008 2.00e-02 2.50e+03 pdb=" C4 6MD R 801 " 0.060 2.00e-02 2.50e+03 pdb=" C5 6MD R 801 " 0.044 2.00e-02 2.50e+03 pdb=" C6 6MD R 801 " -0.002 2.00e-02 2.50e+03 pdb=" C8 6MD R 801 " 0.048 2.00e-02 2.50e+03 pdb=" N1 6MD R 801 " -0.016 2.00e-02 2.50e+03 pdb=" N3 6MD R 801 " 0.049 2.00e-02 2.50e+03 pdb=" N6 6MD R 801 " -0.115 2.00e-02 2.50e+03 pdb=" N7 6MD R 801 " 0.039 2.00e-02 2.50e+03 pdb=" N9 6MD R 801 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 67 " -1.060 9.50e-02 1.11e+02 4.75e-01 1.36e+02 pdb=" NE ARG S 67 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG S 67 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG S 67 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG S 67 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 172 " 0.861 9.50e-02 1.11e+02 3.86e-01 9.04e+01 pdb=" NE ARG R 172 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG R 172 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG R 172 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 172 " 0.023 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 232 2.68 - 3.23: 8682 3.23 - 3.79: 13582 3.79 - 4.34: 19393 4.34 - 4.90: 31082 Nonbonded interactions: 72971 Sorted by model distance: nonbonded pdb=" OE1 GLN S 130 " pdb=" OG1 THR S 231 " model vdw 2.121 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.135 3.040 nonbonded pdb=" OG SER S 99 " pdb=" O PRO S 107 " model vdw 2.191 3.040 nonbonded pdb=" O LEU A 249 " pdb=" OG SER A 252 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR A 287 " pdb=" OE1 GLN A 306 " model vdw 2.211 3.040 ... (remaining 72966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.130 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 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 0.073 8874 Z= 0.654 Angle : 1.218 10.252 12018 Z= 0.865 Chirality : 0.081 0.489 1376 Planarity : 0.022 0.475 1498 Dihedral : 13.857 79.543 3196 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.52 % Favored : 95.30 % Rotamer: Outliers : 1.15 % Allowed : 3.36 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1085 helix: 0.37 (0.26), residues: 362 sheet: -0.95 (0.30), residues: 269 loop : -0.72 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 211 HIS 0.019 0.004 HIS A 322 PHE 0.041 0.005 PHE A 334 TYR 0.029 0.004 TYR R 292 ARG 0.013 0.001 ARG R 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 323 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 MET cc_start: 0.6520 (mmp) cc_final: 0.6261 (mmp) REVERT: A 337 ASP cc_start: 0.5559 (m-30) cc_final: 0.5110 (m-30) REVERT: A 354 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5566 (m-80) outliers start: 11 outliers final: 0 residues processed: 331 average time/residue: 0.2680 time to fit residues: 115.7092 Evaluate side-chains 184 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 HIS R 249 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 213 HIS A 244 HIS A 255 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8874 Z= 0.236 Angle : 0.691 10.863 12018 Z= 0.365 Chirality : 0.045 0.225 1376 Planarity : 0.005 0.049 1498 Dihedral : 5.072 57.493 1216 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 2.41 % Allowed : 14.48 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1085 helix: 1.04 (0.27), residues: 365 sheet: -0.85 (0.29), residues: 287 loop : -0.63 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.021 0.002 PHE S 108 TYR 0.022 0.002 TYR S 178 ARG 0.007 0.001 ARG R 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 258 ASP cc_start: 0.3939 (m-30) cc_final: 0.3182 (t0) REVERT: A 354 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.5069 (m-80) REVERT: S 183 LEU cc_start: 0.7707 (tp) cc_final: 0.7505 (mt) outliers start: 23 outliers final: 12 residues processed: 240 average time/residue: 0.2461 time to fit residues: 79.0804 Evaluate side-chains 182 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 91 HIS ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 295 ASN R 95 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8874 Z= 0.342 Angle : 0.750 11.470 12018 Z= 0.401 Chirality : 0.047 0.189 1376 Planarity : 0.005 0.048 1498 Dihedral : 5.145 57.746 1216 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 2.83 % Allowed : 17.63 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1085 helix: 1.08 (0.28), residues: 363 sheet: -0.87 (0.30), residues: 277 loop : -0.62 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 184 HIS 0.007 0.002 HIS R 95 PHE 0.022 0.002 PHE R 200 TYR 0.019 0.002 TYR S 223 ARG 0.009 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: A 354 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.5823 (m-80) REVERT: S 34 MET cc_start: 0.6604 (mmp) cc_final: 0.6128 (mmp) REVERT: S 82 GLN cc_start: 0.5196 (tp-100) cc_final: 0.4681 (tp-100) outliers start: 27 outliers final: 14 residues processed: 213 average time/residue: 0.2562 time to fit residues: 71.9202 Evaluate side-chains 176 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 17 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.2980 chunk 105 optimal weight: 0.1980 chunk 94 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN R 249 ASN A 244 HIS A 256 ASN A 304 GLN S 130 GLN S 182 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.6531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8874 Z= 0.195 Angle : 0.683 9.798 12018 Z= 0.354 Chirality : 0.044 0.158 1376 Planarity : 0.004 0.041 1498 Dihedral : 4.757 57.494 1216 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 3.36 % Allowed : 19.83 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1085 helix: 1.48 (0.28), residues: 370 sheet: -0.72 (0.30), residues: 268 loop : -0.55 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 184 HIS 0.004 0.001 HIS B 225 PHE 0.036 0.002 PHE R 50 TYR 0.013 0.001 TYR S 60 ARG 0.009 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.5438 (tp) REVERT: A 267 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: A 354 PHE cc_start: 0.6344 (OUTLIER) cc_final: 0.5719 (m-80) outliers start: 32 outliers final: 14 residues processed: 214 average time/residue: 0.2413 time to fit residues: 68.6689 Evaluate side-chains 174 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 78 optimal weight: 0.0050 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 53 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN A 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8874 Z= 0.272 Angle : 0.698 9.960 12018 Z= 0.365 Chirality : 0.045 0.188 1376 Planarity : 0.004 0.041 1498 Dihedral : 4.799 58.570 1216 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 4.41 % Allowed : 22.04 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 1085 helix: 1.42 (0.28), residues: 369 sheet: -0.79 (0.30), residues: 264 loop : -0.59 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 184 HIS 0.006 0.001 HIS A 322 PHE 0.021 0.002 PHE B 253 TYR 0.024 0.002 TYR S 178 ARG 0.007 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.057 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: R 30 ASN cc_start: 0.6754 (m-40) cc_final: 0.6303 (m-40) REVERT: R 58 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6562 (t70) REVERT: R 284 LYS cc_start: 0.7291 (mmmm) cc_final: 0.7039 (mmmm) REVERT: A 267 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: A 354 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.6013 (m-80) REVERT: S 82 GLN cc_start: 0.4728 (tp-100) cc_final: 0.4465 (tp-100) REVERT: S 183 LEU cc_start: 0.8184 (tp) cc_final: 0.7838 (mt) outliers start: 42 outliers final: 20 residues processed: 199 average time/residue: 0.2389 time to fit residues: 63.3093 Evaluate side-chains 178 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 30.0000 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8874 Z= 0.249 Angle : 0.736 11.740 12018 Z= 0.376 Chirality : 0.045 0.180 1376 Planarity : 0.004 0.039 1498 Dihedral : 4.879 59.126 1216 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 2.73 % Allowed : 25.50 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1085 helix: 1.44 (0.28), residues: 369 sheet: -0.69 (0.31), residues: 259 loop : -0.55 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP R 184 HIS 0.004 0.001 HIS A 322 PHE 0.033 0.002 PHE R 50 TYR 0.022 0.002 TYR S 178 ARG 0.008 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 284 LYS cc_start: 0.7220 (mmmm) cc_final: 0.6967 (mmmt) REVERT: A 354 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: S 183 LEU cc_start: 0.8112 (tp) cc_final: 0.7793 (mt) outliers start: 26 outliers final: 18 residues processed: 191 average time/residue: 0.2324 time to fit residues: 59.6156 Evaluate side-chains 176 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 40.0000 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.0470 chunk 41 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN S 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.7753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8874 Z= 0.201 Angle : 0.735 13.090 12018 Z= 0.375 Chirality : 0.045 0.203 1376 Planarity : 0.004 0.038 1498 Dihedral : 4.822 58.614 1216 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 2.83 % Allowed : 25.18 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1085 helix: 1.44 (0.27), residues: 376 sheet: -0.57 (0.32), residues: 259 loop : -0.57 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP R 184 HIS 0.003 0.001 HIS A 322 PHE 0.019 0.002 PHE B 253 TYR 0.021 0.001 TYR S 178 ARG 0.009 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 252 LEU cc_start: 0.6450 (tt) cc_final: 0.6149 (tp) REVERT: R 284 LYS cc_start: 0.7240 (mmmm) cc_final: 0.7002 (mmmt) REVERT: A 354 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: S 183 LEU cc_start: 0.8103 (tp) cc_final: 0.7826 (mt) outliers start: 27 outliers final: 18 residues processed: 186 average time/residue: 0.2226 time to fit residues: 56.1100 Evaluate side-chains 171 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.8123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8874 Z= 0.299 Angle : 0.786 16.092 12018 Z= 0.397 Chirality : 0.045 0.192 1376 Planarity : 0.004 0.038 1498 Dihedral : 5.040 59.350 1216 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 3.25 % Allowed : 25.60 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1085 helix: 1.35 (0.27), residues: 377 sheet: -0.62 (0.30), residues: 278 loop : -0.61 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 184 HIS 0.006 0.001 HIS A 322 PHE 0.028 0.002 PHE R 50 TYR 0.022 0.002 TYR S 223 ARG 0.008 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: A 354 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: S 183 LEU cc_start: 0.8070 (tp) cc_final: 0.7821 (mt) outliers start: 31 outliers final: 21 residues processed: 180 average time/residue: 0.2443 time to fit residues: 58.8362 Evaluate side-chains 174 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 159 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.8281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8874 Z= 0.230 Angle : 0.793 17.298 12018 Z= 0.395 Chirality : 0.045 0.201 1376 Planarity : 0.004 0.038 1498 Dihedral : 5.003 58.588 1216 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 2.52 % Allowed : 26.76 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1085 helix: 1.36 (0.27), residues: 379 sheet: -0.72 (0.30), residues: 281 loop : -0.56 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 211 HIS 0.009 0.001 HIS B 225 PHE 0.031 0.002 PHE R 50 TYR 0.024 0.002 TYR R 15 ARG 0.006 0.001 ARG R 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: S 183 LEU cc_start: 0.8038 (tp) cc_final: 0.7781 (mt) outliers start: 24 outliers final: 21 residues processed: 178 average time/residue: 0.2365 time to fit residues: 56.5865 Evaluate side-chains 177 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 159 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.8455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8874 Z= 0.229 Angle : 0.815 17.821 12018 Z= 0.404 Chirality : 0.045 0.196 1376 Planarity : 0.004 0.037 1498 Dihedral : 4.980 58.353 1216 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.73 % Allowed : 26.86 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1085 helix: 1.38 (0.27), residues: 380 sheet: -0.59 (0.30), residues: 279 loop : -0.58 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 211 HIS 0.006 0.001 HIS B 225 PHE 0.020 0.002 PHE B 180 TYR 0.022 0.002 TYR R 15 ARG 0.009 0.001 ARG S 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.103 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 251 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6299 (t70) REVERT: S 183 LEU cc_start: 0.7928 (tp) cc_final: 0.7688 (mt) outliers start: 26 outliers final: 20 residues processed: 177 average time/residue: 0.2287 time to fit residues: 54.5505 Evaluate side-chains 173 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 159 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.125482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.100565 restraints weight = 21918.195| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 4.41 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.8612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8874 Z= 0.216 Angle : 0.796 17.704 12018 Z= 0.397 Chirality : 0.045 0.283 1376 Planarity : 0.004 0.036 1498 Dihedral : 4.639 25.083 1214 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.31 % Allowed : 27.28 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1085 helix: 1.39 (0.27), residues: 380 sheet: -0.60 (0.31), residues: 269 loop : -0.58 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 211 HIS 0.006 0.001 HIS B 225 PHE 0.030 0.002 PHE R 50 TYR 0.023 0.002 TYR R 109 ARG 0.006 0.001 ARG R 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2264.81 seconds wall clock time: 42 minutes 13.89 seconds (2533.89 seconds total)